› 7aih

Electron Microscopy
3.6Å resolution

The Large subunit of the Kinetoplastid mitochondrial ribosome

Released:
DOI: 10.2210/pdb7aih/pdb
PDB entry 7aih coloured by chain, front view.
PDB entry 7aih coloured by chain, side view.
PDB entry 7aih coloured by chain, top view.
Source organism: Leishmania major
Primary publication:
Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.
Soufari H, Waltz F, Parrot C, Durrieu-Gaillard S, Bochler A, Kuhn L, Sissler M, Hashem Y
Proc Natl Acad Sci U S A 117 29851-29861 (2020)
PMID: 33168716
Related structures: EMD-11796

Function and Biology Details

Reaction catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 71-mer (preferred)
PDBe Complex ID:
PDB-CPX-105274 (preferred)
Entry contents:
70 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (71 distinct):
Ribosomal protein L3-like protein Chain: A
Molecule details ›
Chain: A
Length: 467 amino acids
Theoretical weight: 54.03 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: E9ADK5 (Residues: 1-467; Coverage: 100%)
Gene name: LMJF_29_0030
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4m Chain: B
Molecule details ›
Chain: B
Length: 436 amino acids
Theoretical weight: 50 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QGU6 (Residues: 1-436; Coverage: 100%)
Gene name: LMJF_11_1360
Sequence domains: Ribosomal protein L4/L1 family
Ribosomal protein L9 domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 262 amino acids
Theoretical weight: 30.51 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QIE5 (Residues: 1-262; Coverage: 100%)
Gene name: LMJF_08_0240
Sequence domains: Ribosomal protein L9, N-terminal domain
uL10m Chain: D
Molecule details ›
Chain: D
Length: 204 amino acids
Theoretical weight: 22.17 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QI77 (Residues: 1-204; Coverage: 100%)
Gene name: LMJF_08_0920
Large ribosomal subunit protein uL11m Chain: E
Molecule details ›
Chain: E
Length: 346 amino acids
Theoretical weight: 40.27 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: E9ACT9 (Residues: 1-346; Coverage: 100%)
Gene name: LMJF_27_2220
Sequence domains:
50S ribosomal protein L13-like protein Chain: F
Molecule details ›
Chain: F
Length: 171 amino acids
Theoretical weight: 20.5 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q2H6 (Residues: 1-171; Coverage: 100%)
Gene name: LMJF_34_3680
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 374 amino acids
Theoretical weight: 43.57 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QF19 (Residues: 1-374; Coverage: 100%)
Gene name: LMJF_16_0010
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Ribosomal_L16 domain-containing protein Chain: H
Molecule details ›
Chain: H
Length: 168 amino acids
Theoretical weight: 19.13 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QFP0 (Residues: 1-168; Coverage: 100%)
Gene name: LMJF_14_0950
Sequence domains: Ribosomal protein L16p/L10e
Putative 50S ribosomal protein L17 Chain: I
Molecule details ›
Chain: I
Length: 305 amino acids
Theoretical weight: 35.83 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QF04 (Residues: 1-305; Coverage: 100%)
Gene name: LMJF_16_0160
Sequence domains: Ribosomal protein L17
bL19m Chain: J
Molecule details ›
Chain: J
Length: 144 amino acids
Theoretical weight: 16.7 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QCY7 (Residues: 1-144; Coverage: 100%)
Gene name: LMJF_20_0530
Large ribosomal subunit protein bL20c Chain: K
Molecule details ›
Chain: K
Length: 194 amino acids
Theoretical weight: 22.44 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q192 (Residues: 1-194; Coverage: 100%)
Gene name: LMJF_36_3260
Large ribosomal subunit protein bL21m Chain: L
Molecule details ›
Chain: L
Length: 186 amino acids
Theoretical weight: 21.04 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QFQ5 (Residues: 1-186; Coverage: 100%)
Gene name: LMJF_14_0780
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22c Chain: M
Molecule details ›
Chain: M
Length: 279 amino acids
Theoretical weight: 32.28 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QBR0 (Residues: 1-279; Coverage: 100%)
Gene name: LMJF_22_0870
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23m Chain: N
Molecule details ›
Chain: N
Length: 252 amino acids
Theoretical weight: 28.84 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QA05 (Residues: 1-252; Coverage: 100%)
Gene name: LMJF_25_0890
KOW domain-containing protein Chain: O
Molecule details ›
Chain: O
Length: 476 amino acids
Theoretical weight: 53.62 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q9S7 (Residues: 1-476; Coverage: 100%)
Gene name: LMJF_25_1640
bL27m Chain: P
Molecule details ›
Chain: P
Length: 185 amino acids
Theoretical weight: 21.61 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QG34 (Residues: 1-185; Coverage: 100%)
Gene name: LMJF_13_1200
39S ribosomal protein L28, mitochondrial Chain: Q
Molecule details ›
Chain: Q
Length: 234 amino acids
Theoretical weight: 27.22 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q719 (Residues: 1-234; Coverage: 100%)
Gene name: LMJF_30_2750
Large ribosomal subunit protein uL29m Chain: R
Molecule details ›
Chain: R
Length: 480 amino acids
Theoretical weight: 54.24 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q9XZY7 (Residues: 1-480; Coverage: 100%)
Gene name: LMJF_04_0270
Sequence domains: Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
Ribosomal protein L30 ferredoxin-like fold domain-containing protein Chain: S
Molecule details ›
Chain: S
Length: 409 amino acids
Theoretical weight: 45.56 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q9U0Z7 (Residues: 1-409; Coverage: 100%)
Gene name: LMJF_04_0860
bL32m Chain: T
Molecule details ›
Chain: T
Length: 83 amino acids
Theoretical weight: 9.87 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q2W9 (Residues: 1-83; Coverage: 100%)
Gene name: LMJF_34_2310
bL33m Chain: U
Molecule details ›
Chain: U
Length: 118 amino acids
Theoretical weight: 13.47 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q2Q8 (Residues: 1-118; Coverage: 100%)
Gene name: LMJF_34_2860
bL35m Chain: V
Molecule details ›
Chain: V
Length: 151 amino acids
Theoretical weight: 18.39 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QCK6 (Residues: 1-151; Coverage: 100%)
Gene name: LMJF_21_0100
39S ribosomal protein L36, mitochondrial Chain: W
Molecule details ›
Chain: W
Length: 186 amino acids
Theoretical weight: 21.85 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q6A3 (Residues: 1-186; Coverage: 100%)
Gene name: LMJF_31_1590
Phosphatidylethanolamine-binding protein Chain: X
Molecule details ›
Chain: X
Length: 513 amino acids
Theoretical weight: 58.12 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q5A3 (Residues: 1-513; Coverage: 100%)
Gene name: LMJF_32_1770
mL40 Chain: Y
Molecule details ›
Chain: Y
Length: 292 amino acids
Theoretical weight: 33.21 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q448 (Residues: 1-292; Coverage: 100%)
Gene name: LMJF_33_1390
mL41 Chain: Z
Molecule details ›
Chain: Z
Length: 197 amino acids
Theoretical weight: 22.67 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q152 (Residues: 1-197; Coverage: 100%)
Gene name: LMJF_36_3653
Rhodanese domain-containing protein Chain: BA
Molecule details ›
Chain: BA
Length: 167 amino acids
Theoretical weight: 17.89 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: E9ACP5 (Residues: 1-167; Coverage: 100%)
Gene name: LMJF_04_0045
UA Chain: UA
Molecule details ›
Chain: UA
Length: 203 amino acids
Theoretical weight: 17.29 KDa
Source organism: Leishmania major
mL95 Chain: BB
Molecule details ›
Chain: BB
Length: 156 amino acids
Theoretical weight: 18.69 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q4D6 (Residues: 1-156; Coverage: 100%)
Gene name: LMJF_33_0690
mL89 Chain: Aw
Molecule details ›
Chain: Aw
Length: 187 amino acids
Theoretical weight: 21.56 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: E9AD00 (Residues: 1-187; Coverage: 100%)
Gene name: LMJF_27_0230
bL31m Chain: Bj
Molecule details ›
Chain: Bj
Length: 185 amino acids
Theoretical weight: 21.26 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q0E1 (Residues: 1-185; Coverage: 100%)
Gene name: LMJF_36_6190
mL76 Chain: An
Molecule details ›
Chain: An
Length: 331 amino acids
Theoretical weight: 38.66 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q0F5 (Residues: 1-331; Coverage: 100%)
Gene name: LMJF_36_6050
mL74 Chain: Al
Molecule details ›
Chain: Al
Length: 346 amino acids
Theoretical weight: 39.39 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q1C8 (Residues: 1-346; Coverage: 100%)
Gene name: LMJF_36_2910
Peptidyl-prolyl cis-trans isomerase Chain: BI
Molecule details ›
Chain: BI
Length: 266 amino acids
Theoretical weight: 28.92 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q1A6 (Residues: 1-266; Coverage: 100%)
Gene names: CYP10, LMJF_36_3130
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
mL93 Chain: Az
Molecule details ›
Chain: Az
Length: 152 amino acids
Theoretical weight: 18.86 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q4D9 (Residues: 1-152; Coverage: 100%)
Gene name: LMJF_33_0660
mL86 Chain: At
Molecule details ›
Chain: At
Length: 183 amino acids
Theoretical weight: 21.07 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q4L5 (Residues: 1-183; Coverage: 100%)
Gene name: LMJF_33_0080
mL96 Chain: BC
Molecule details ›
Chain: BC
Length: 147 amino acids
Theoretical weight: 16.71 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q5D8 (Residues: 1-147; Coverage: 100%)
Gene name: LMJF_32_1440
Large ribosomal subunit protein mL43 Chain: Ab
Molecule details ›
Chain: Ab
Length: 262 amino acids
Theoretical weight: 31.23 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q6A7 (Residues: 1-262; Coverage: 100%)
Gene name: LMJF_31_1550
Sequence domains: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
AMP-dependent synthetase/ligase domain-containing protein Chain: Ai
Molecule details ›
Chain: Ai
Length: 479 amino acids
Theoretical weight: 54.18 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q7P8 (Residues: 1-479; Coverage: 100%)
Gene name: LMJF_30_0580
Sequence domains: AMP-binding enzyme
mL80 Chain: Ap
Molecule details ›
Chain: Ap
Length: 240 amino acids
Theoretical weight: 27.95 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q7V3 (Residues: 1-240; Coverage: 100%)
Gene name: LMJF_30_0060
mL87 Chain: Au
Molecule details ›
Chain: Au
Length: 186 amino acids
Theoretical weight: 22.27 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q8J6 (Residues: 1-186; Coverage: 100%)
Gene name: LMJF_28_0730
mL42 Chain: Aa
Molecule details ›
Chain: Aa
Length: 195 amino acids
Theoretical weight: 22.17 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q183 (Residues: 1-195; Coverage: 100%)
Gene name: LMJF_36_3350
mL79 Chain: Ao
Molecule details ›
Chain: Ao
Length: 284 amino acids
Theoretical weight: 33.39 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q547 (Residues: 1-284; Coverage: 100%)
Gene name: LMJF_32_2280
mL70 Chain: BM
Molecule details ›
Chain: BM
Length: 457 amino acids
Theoretical weight: 50.75 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q703 (Residues: 1-457; Coverage: 100%)
Gene name: LMJF_30_2890
mL84 Chain: Ar
Molecule details ›
Chain: Ar
Length: 205 amino acids
Theoretical weight: 24.62 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q712 (Residues: 1-205; Coverage: 100%)
Gene name: LMJF_30_2810
mL72 Chain: Aj
Molecule details ›
Chain: Aj
Length: 503 amino acids
Theoretical weight: 56.55 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q728 (Residues: 1-503; Coverage: 100%)
Gene name: LMJF_30_2660
Peptidyl-prolyl cis-trans isomerase Chain: BH
Molecule details ›
Chain: BH
Length: 229 amino acids
Theoretical weight: 25.31 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QBK2 (Residues: 1-229; Coverage: 100%)
Gene names: CYP6, LMJF_22_1450
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Mitochondrial RNA binding complex 1 subunit Chain: Am
Molecule details ›
Chain: Am
Length: 340 amino acids
Theoretical weight: 39.65 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QC22 (Residues: 1-340; Coverage: 100%)
Gene name: LMJF_21_1620
Sequence domains: PPR repeat family
mL82 Chain: Aq
Molecule details ›
Chain: Aq
Length: 341 amino acids
Theoretical weight: 37.91 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QD92 (Residues: 1-341; Coverage: 100%)
Gene name: LMJF_19_1230
mL98 Chain: BE
Molecule details ›
Chain: BE
Length: 118 amino acids
Theoretical weight: 13.26 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QE16 (Residues: 1-118; Coverage: 100%)
Gene name: LMJF_18_0260
AB hydrolase-1 domain-containing protein Chain: Ak
Molecule details ›
Chain: Ak
Length: 323 amino acids
Theoretical weight: 36.08 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QEC8 (Residues: 1-323; Coverage: 100%)
Gene name: LMJF_17_0760
mL52,mL52 Chain: BP
Molecule details ›
Chain: BP
Length: 254 amino acids
Theoretical weight: 29.2 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QGE0 (Residues: 1-186; Coverage: 100%)
Gene name: LMJF_13_0140
mL49 Chain: Ad
Molecule details ›
Chain: Ad
Length: 237 amino acids
Theoretical weight: 26.21 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QIB3 (Residues: 1-237; Coverage: 100%)
Gene name: LMJF_08_0560
mL99 Chain: BF
Molecule details ›
Chain: BF
Length: 109 amino acids
Theoretical weight: 13.05 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QIQ1 (Residues: 1-109; Coverage: 100%)
Gene name: LMJF_07_0420
mL88 Chain: Av
Molecule details ›
Chain: Av
Length: 192 amino acids
Theoretical weight: 22.34 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QIT7 (Residues: 1-192; Coverage: 100%)
Gene name: LMJF_07_0070
mL63 Chain: Af
Molecule details ›
Chain: Af
Length: 155 amino acids
Theoretical weight: 18.1 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QJB6 (Residues: 1-155; Coverage: 100%)
Gene name: LMJF_05_0860
mL85 Chain: As
Molecule details ›
Chain: As
Length: 249 amino acids
Theoretical weight: 27.53 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: E9ABZ5 (Residues: 1-249; Coverage: 100%)
Gene name: LMJF_01_0060
Ribosomal protein L9 domain-containing protein Chain: Ae
Molecule details ›
Chain: Ae
Length: 311 amino acids
Theoretical weight: 35.48 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: E9ACG2 (Residues: 1-311; Coverage: 100%)
Gene name: LMJF_03_0150
Large ribosomal subunit protein mL46 Chain: Ac
Molecule details ›
Chain: Ac
Length: 291 amino acids
Theoretical weight: 33.35 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QJ75 (Residues: 1-291; Coverage: 100%)
Gene name: LMJF_06_0040
Sequence domains: 39S mitochondrial ribosomal protein L46
mL68 Chain: Ah
Molecule details ›
Chain: Ah
Length: 570 amino acids
Theoretical weight: 65.79 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QC45 (Residues: 1-570; Coverage: 100%)
Gene name: LMJF_21_1500
mL97 Chain: BD
Molecule details ›
Chain: BD
Length: 102 amino acids
Theoretical weight: 12.08 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QE11 (Residues: 1-102; Coverage: 100%)
Gene name: LMJF_18_0310
C2H2-type domain-containing protein Chain: Ay
Molecule details ›
Chain: Ay
Length: 174 amino acids
Theoretical weight: 20.93 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: E9ADN7 (Residues: 1-174; Coverage: 100%)
Gene name: LMJF_29_0360
mL54/69 Chain: Ag
Molecule details ›
Chain: Ag
Length: 244 amino acids
Theoretical weight: 28.6 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q829 (Residues: 1-244; Coverage: 100%)
Gene name: LMJF_28_2360
LIM zinc-binding domain-containing protein Chain: Ax
Molecule details ›
Chain: Ax
Length: 216 amino acids
Theoretical weight: 25.17 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q7T1 (Residues: 1-216; Coverage: 100%)
Gene name: LMJF_30_0280
Sequence domains: LIM domain
Large ribosomal subunit protein uL2 C-terminal domain-containing protein Chain: BL
Molecule details ›
Chain: BL
Length: 380 amino acids
Theoretical weight: 43.38 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4QIE1 (Residues: 1-380; Coverage: 100%)
Gene name: LMJF_08_0280
Sequence domains: Ribosomal Proteins L2, C-terminal domain
Putative ribosomal protein L14 Chain: BO
Molecule details ›
Chain: BO
Length: 190 amino acids
Theoretical weight: 21.63 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: Q4Q2G1 (Residues: 1-190; Coverage: 100%)
Gene name: LMJF_34_3815
Sequence domains: Ribosomal protein L14p/L23e
Flagellar attachment zone protein Chain: BG
Molecule details ›
Chain: BG
Length: 1347 amino acids
Theoretical weight: 146.81 KDa
Source organism: Leishmania major
UniProt:
  • Canonical: A0A504WW14 (Residues: 1-1347; Coverage: 100%)
Gene name: CGC21_25710
UB Chain: UB
Molecule details ›
Chain: UB
Length: 67 amino acids
Theoretical weight: 5.72 KDa
Source organism: Leishmania major
UC Chain: UC
Molecule details ›
Chain: UC
Length: 144 amino acids
Theoretical weight: 12.27 KDa
Source organism: Leishmania major
UD Chain: UD
Molecule details ›
Chain: UD
Length: 95 amino acids
Theoretical weight: 8.1 KDa
Source organism: Leishmania major
Ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 9070 nucleotides
Theoretical weight: 2895.42 KDa
Sequence domains:
  • Trypanosomatid mitochondrial large subunit ribosomal RNA
  • Trypanosomatid mitochondrial small subunit ribosomal RNA

    • Ligands and Environments

    2 bound ligands:
    Ligand ZN 6 x ZN
    Ligand NAD 1 x NAD
    No modified residues

    Experiments and Validation Details

    Entry percentile scores
    Resolution: 3.6Å
    Relevant EMDB volumes: EMD-11796

    Quick links

    Citations

    5 review citations

    The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
    Gerovac et al. (2021)
    4 more