› 6az3

Electron Microscopy
2.5Å resolution

Cryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin

Released:
DOI: 10.2210/pdb6az3/pdb
PDB entry 6az3 coloured by chain, front view.
PDB entry 6az3 coloured by chain, side view.
PDB entry 6az3 coloured by chain, top view.
Source organism: Leishmania donovani
Primary publication:
Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.
Shalev-Benami M, Zhang Y, Rozenberg H, Nobe Y, Taoka M, Matzov D, Zimmerman E, Bashan A, Isobe T, Jaffe CL, Yonath A, Skiniotis G
Nat Commun 8 1589 (2017)
PMID: 29150609
Related structures: EMD-7025

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 50-mer (preferred)
PDBe Complex ID:
PDB-CPX-236782 (preferred)
Entry contents:
42 distinct polypeptide molecules
8 distinct RNA molecules
Macromolecules (50 distinct):
ribosomal protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 254 amino acids
Theoretical weight: 27.52 KDa
Source organism: Leishmania donovani
ribosomal protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 402 amino acids
Theoretical weight: 45.74 KDa
Source organism: Leishmania donovani
Large ribosomal subunit protein uL4 C-terminal domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 366 amino acids
Theoretical weight: 40.52 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3S5H7L0 (Residues: 4-369; Coverage: 98%)
Gene names: CGC20_25535, CGC20_25540, CGC20_25545, CGC21_28090, CGC21_28095, CGC21_28100, CGC21_28105, LDBPK_291160, LDHU3_29.1610, LDHU3_29.1620, LDHU3_29.1630, LdCL_290016700, LdCL_290016800, LdCL_290016900
Sequence domains:
60S ribosomal protein L11 (L5, L16) Chain: D
Molecule details ›
Chain: D
Length: 168 amino acids
Theoretical weight: 19.25 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3S5H5A8 (Residues: 8-175; Coverage: 89%)
Gene names: CGC20_15690, CGC20_16800, CGC21_2680, CGC21_32945, LDBPK_220004, LDHU3_04.0620, LDHU3_22.0070, LdCL_040010100, LdCL_220005300
Sequence domains:
Large ribosomal subunit protein uL6 alpha-beta domain-containing protein Chain: E
Molecule details ›
Chain: E
Length: 186 amino acids
Theoretical weight: 21.12 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3S7X3V0 (Residues: 2-187; Coverage: 98%)
Gene names: CGC20_6165, CGC21_36380, LDHU3_30.4490, LdCL_300039500
Sequence domains: Ribosomal protein L6
ribosomal protein eL6 Chain: F
Molecule details ›
Chain: F
Length: 195 amino acids
Theoretical weight: 21.21 KDa
Source organism: Leishmania donovani
60S ribosomal protein L7a Chain: G
Molecule details ›
Chain: G
Length: 348 amino acids
Theoretical weight: 39.18 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: E9B949 (Residues: 1-348; Coverage: 100%)
Gene name: LDBPK_070550
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
ribosomal protein uL13 Chain: H
Molecule details ›
Chain: H
Length: 221 amino acids
Theoretical weight: 25.35 KDa
Source organism: Leishmania donovani
ribosomal protein eL13 Chain: I
Molecule details ›
Chain: I
Length: 212 amino acids
Theoretical weight: 23.9 KDa
Source organism: Leishmania donovani
60S ribosomal protein L23, putative Chain: J
Molecule details ›
Chain: J
Length: 134 amino acids
Theoretical weight: 14.42 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8IIA7 (Residues: 6-139; Coverage: 96%)
Gene names: CGC20_14830, CGC20_14835, CGC21_7365, CGC21_7370, LDBPK_353840, LDHU3_35.5000, LDHU3_35.5010, LdCL_350043400, LdCL_350043500
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL14 Chain: K
Molecule details ›
Chain: K
Length: 149 amino acids
Theoretical weight: 17.04 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: Q25278 (Residues: 3-151; Coverage: 85%)
Gene names: LPD23, RPL14
Sequence domains:
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 144 amino acids
Theoretical weight: 16.03 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8IGI9 (Residues: 2-145; Coverage: 99%)
Gene names: CGC20_14840, CGC20_14850, CGC21_7350, CGC21_7360, LDBPK_353810, LDHU3_35.4970, LDHU3_35.4990, LdCL_350043100, LdCL_350043300
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Ribosomal protein L15 Chain: M
Molecule details ›
Chain: M
Length: 203 amino acids
Theoretical weight: 24.37 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: E9BMB4 (Residues: 2-204; Coverage: 100%)
Gene names: CGC20_0090, CGC20_6005, CGC21_36545, CGC21_6465, LDBPK_303710, LDBPK_351890, LDHU3_30.4940, LdCL_300042500, LdCL_350024100
Sequence domains: Ribosomal L15
60S ribosomal protein L10, putative Chain: N
Molecule details ›
Chain: N
Length: 213 amino acids
Theoretical weight: 24.61 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3S5H5C4 (Residues: 1-213; Coverage: 100%)
Gene names: CGC20_9400, CGC20_9495, CGC21_2805, CGC21_2905, LDBPK_040750, LDHU3_04.0970, LDHU3_04.1190, LdCL_040013100, LdCL_040015100
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein Chain: O
Molecule details ›
Chain: O
Length: 305 amino acids
Theoretical weight: 34.1 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8IJC5 (Residues: 1-305; Coverage: 100%)
Gene names: CGC20_0095, CGC20_0100, CGC20_0105, CGC20_0110, CGC21_6440, CGC21_6445, CGC21_6450, CGC21_6455, CGC21_6460, LDBPK_351870, LDHU3_35.2440, LDHU3_35.2450, LDHU3_35.2460, LDHU3_35.2470, LDHU3_35.2480, LdCL_350023600, LdCL_350023700, LdCL_350023800, LdCL_350023900, LdCL_350024000
Sequence domains:
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: P
Molecule details ›
Chain: P
Length: 197 amino acids
Theoretical weight: 21.94 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3S7XBN1 (Residues: 2-198; Coverage: 100%)
Gene names: CGC20_27670, CGC21_14640, CGC21_33175, LDBPK_364730, LDHU3_13.0620, LDHU3_36.6360, LdCL_130009900, LdCL_360054400
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19 domain-containing protein Chain: Q
Molecule details ›
Chain: Q
Length: 189 amino acids
Theoretical weight: 22.9 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A504XXD2 (Residues: 2-190; Coverage: 79%)
Gene name: CGC20_20145
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L18a Chain: R
Molecule details ›
Chain: R
Length: 178 amino acids
Theoretical weight: 20.7 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8IT55 (Residues: 2-179; Coverage: 99%)
Gene names: CGC20_0675, CGC20_33790, CGC21_20030, LDHU3_32.1220, LDHU3_35.0740, LdCL_320014900
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
60S_ribosomal_protein_L21_putative/GeneDB:LmjF.16.0460/GeneDB:LmjF.34.3650 Chain: S
Molecule details ›
Chain: S
Length: 154 amino acids
Theoretical weight: 17.44 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8ICH0 (Residues: 2-155; Coverage: 97%)
Gene names: CGC20_20775, CGC20_36460, CGC21_25130, CGC21_27025, LDBPK_343440, LDHU3_16.0550, LDHU3_34.5670, LdCL_160009600, LdCL_340043800
Sequence domains: Ribosomal protein L21e
Ribosomal protein L22 Chain: T
Molecule details ›
Chain: T
Length: 154 amino acids
Theoretical weight: 17.83 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3S7WY02 (Residues: 2-155; Coverage: 93%)
Gene names: CGC20_11495, CGC21_15705, LDBPK_240040, LDHU3_24.0060, LdCL_240005300
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL22 Chain: U
Molecule details ›
Chain: U
Length: 121 amino acids
Theoretical weight: 14.04 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8IJA8 (Residues: 2-122; Coverage: 94%)
Gene names: CGC20_28260, CGC21_14000, LDBPK_363430, LDHU3_36.4690, LdCL_360041100
Sequence domains: Ribosomal L22e protein family
60S ribosomal protein L23a Chain: V
Molecule details ›
Chain: V
Length: 118 amino acids
Theoretical weight: 13.46 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: E9B8R9 (Residues: 28-144; Coverage: 81%)
Gene names: CGC20_20065, CGC20_20070, CGC21_24275, CGC21_24280, LDBPK_060590, LDBPK_060600, LDHU3_06.0690, LDHU3_06.0700, LdCL_060011000, LdCL_060011100
Sequence domains: Ribosomal protein L23
ribosomal protein uL24 Chain: W
Molecule details ›
Chain: W
Length: 121 amino acids
Theoretical weight: 13.87 KDa
Source organism: Leishmania donovani
ribosomal protein eL24 Chain: X
Molecule details ›
Chain: X
Length: 65 amino acids
Theoretical weight: 7.99 KDa
Source organism: Leishmania donovani
Ribosomal L27e family protein Chain: Y
Molecule details ›
Chain: Y
Length: 132 amino acids
Theoretical weight: 15.22 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A504XEJ0 (Residues: 1144-1275; Coverage: 10%)
Gene name: CGC20_34730
Sequence domains: Ribosomal L27e protein family
Large ribosomal subunit protein eL28 Chain: Z
Molecule details ›
Chain: Z
Length: 140 amino acids
Theoretical weight: 15.53 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8I959 (Residues: 2-141; Coverage: 95%)
Gene names: CGC20_31100, CGC20_31110, CGC21_0695, CGC21_0705, LDBPK_111110, LDHU3_11.1330, LDHU3_11.1350, LDHU3_11.1370, LdCL_110017100
Sequence domains: Ribosomal L28e protein family
60S ribosomal protein L35 Chain: a
Molecule details ›
Chain: a
Length: 125 amino acids
Theoretical weight: 14.99 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: E9BIP6 (Residues: 2-126; Coverage: 98%)
Gene names: CGC20_5605, CGC20_5610, CGC21_32450, CGC21_32455, LDBPK_262350, LDBPK_262360, LDHU3_26.3070, LDHU3_26.3080
Sequence domains: Ribosomal L29 protein
60S ribosomal protein L29 Chain: b
Molecule details ›
Chain: b
Length: 68 amino acids
Theoretical weight: 7.79 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A504XJE6 (Residues: 75-142; Coverage: 48%)
Gene names: CGC20_28200, CGC21_14070
Sequence domains: Ribosomal L29e protein family
60S ribosomal protein L7 family protein Chain: c
Molecule details ›
Chain: c
Length: 227 amino acids
Theoretical weight: 26.31 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A504XVT8 (Residues: 45-271; Coverage: 84%)
Gene name: CGC20_4660
Sequence domains:
Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein Chain: d
Molecule details ›
Chain: d
Length: 92 amino acids
Theoretical weight: 10.12 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8IET6 (Residues: 9-100; Coverage: 89%)
Gene names: CGC20_0820, CGC21_5735, LDBPK_350240, LDHU3_35.0330, LdCL_350007400
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ribosomal protein L31e family protein Chain: e
Molecule details ›
Chain: e
Length: 119 amino acids
Theoretical weight: 13.5 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8IJL7 (Residues: 69-187; Coverage: 63%)
Gene names: CGC20_15065, CGC20_15070, CGC21_7135, CGC21_7140, LDHU3_35.4380, LDHU3_35.4390, LdCL_350038300, LdCL_350038400
Sequence domains: Ribosomal protein L31e
Ribosomal protein L32 family protein Chain: f
Molecule details ›
Chain: f
Length: 130 amino acids
Theoretical weight: 15.03 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A504XZK6 (Residues: 2-131; Coverage: 98%)
Gene names: CGC20_21925, LDHU3_21.2480
Sequence domains: Ribosomal protein L32
Ribosomal protein L35Ae family protein Chain: g
Molecule details ›
Chain: g
Length: 125 amino acids
Theoretical weight: 14.34 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8II82 (Residues: 20-144; Coverage: 87%)
Gene names: CGC20_21340, CGC20_35910, CGC21_23885, CGC21_26415, LDBPK_342240, LDHU3_10.0110, LDHU3_34.3730, LdCL_100005700, LdCL_340030100
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL34 Chain: h
Molecule details ›
Chain: h
Length: 125 amino acids
Theoretical weight: 14.64 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8IHK2 (Residues: 3-127; Coverage: 74%)
Gene names: LDBPK_363930, LDHU3_18.1760, LDHU3_36.5270, LdCL_180019100, LdCL_360046300
Sequence domains: Ribosomal protein L34e
60S_ribosomal_protein_L36_putative/GeneDB:LmjF.21.0730 Chain: i
Molecule details ›
Chain: i
Length: 97 amino acids
Theoretical weight: 11.05 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8IDW6 (Residues: 3-99; Coverage: 92%)
Gene names: CGC21_34065, LDBPK_210800, LDHU3_21.0900, LdCL_210012900
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37 Chain: j
Molecule details ›
Chain: j
Length: 80 amino acids
Theoretical weight: 9.53 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: P62885 (Residues: 2-81; Coverage: 96%)
Gene name: RPL37
Sequence domains: Ribosomal protein L37e
Ribosomal L38e family protein Chain: k
Molecule details ›
Chain: k
Length: 76 amino acids
Theoretical weight: 8.76 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A504WZU0 (Residues: 898-973; Coverage: 8%)
Gene name: CGC21_32395
Sequence domains: Ribosomal L38e protein family
60S ribosomal protein L39 Chain: l
Molecule details ›
Chain: l
Length: 50 amino acids
Theoretical weight: 6.37 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: E9BCX6 (Residues: 2-51; Coverage: 98%)
Gene names: LDBPK_161220, LDBPK_292480, LDHU3_16.1490, LDHU3_29.3680, LdCL_160017400, LdCL_290030800
Sequence domains: Ribosomal L39 protein
Ubiquitin-ribosomal protein eL40 fusion protein Chain: m
Molecule details ›
Chain: m
Length: 50 amino acids
Theoretical weight: 5.91 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: A0A3Q8ISR1 (Residues: 78-127; Coverage: 39%)
Gene names: CGC20_3125, CGC20_3180, CGC21_11230, CGC21_11280, CGC21_36880, LDBPK_311930, LDHU3_31.3500, LDHU3_31.3730, LdCL_090014900, LdCL_310027200, LdCL_310028700
Sequence domains: Ribosomal L40e family
ribosomal protein eL41 Chain: n
Molecule details ›
Chain: n
Length: 33 amino acids
Theoretical weight: 4.26 KDa
Source organism: Leishmania donovani
60S ribosomal protein L37a Chain: o
Molecule details ›
Chain: o
Length: 90 amino acids
Theoretical weight: 10.09 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: E9BFK4 (Residues: 2-91; Coverage: 98%)
Gene names: LDBPK_212190, LDBPK_362020, LDHU3_21.2600, LDHU3_36.2630, LdCL_210027600, LdCL_360025700
Sequence domains: Ribosomal L37ae protein family
60S ribosomal protein L44 Chain: p
Molecule details ›
Chain: p
Length: 96 amino acids
Theoretical weight: 11.14 KDa
Source organism: Leishmania donovani
UniProt:
  • Canonical: E9BBL5 (Residues: 2-97; Coverage: 91%)
Gene names: CGC20_16835, CGC20_9735, CGC21_33710, CGC21_5530, LDBPK_131410, LDBPK_333380, LDHU3_13.1930, LDHU3_33.4890, LdCL_130021400, LdCL_330041500
Sequence domains: Ribosomal protein L44
rRNA alpha Chain: 1
Molecule details ›
Chain: 1
Length: 1778 nucleotides
Theoretical weight: 575.71 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
rRNA beta Chain: 2
Molecule details ›
Chain: 2
Length: 1526 nucleotides
Theoretical weight: 492.46 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
rRNA gamma Chain: 3
Molecule details ›
Chain: 3
Length: 211 nucleotides
Theoretical weight: 67.57 KDa
rRNA delta Chain: 4
Molecule details ›
Chain: 4
Length: 183 nucleotides
Theoretical weight: 59.14 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
rRNA epsilon Chain: 5
Molecule details ›
Chain: 5
Length: 133 nucleotides
Theoretical weight: 42.87 KDa
rRNA zeta Chain: 6
Molecule details ›
Chain: 6
Length: 71 nucleotides
Theoretical weight: 22.73 KDa
5.8S ribosomal RNA Chain: 7
Molecule details ›
Chain: 7
Length: 171 nucleotides
Theoretical weight: 54.99 KDa
Sequence domains: 5.8S ribosomal RNA
5S ribosomal RNA Chain: 8
Molecule details ›
Chain: 8
Length: 118 nucleotides
Theoretical weight: 37.92 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand PAR 10 x PAR
Ligand MG 34 x MG
4 modified residues:
Ligand OMU 16 x OMU
Ligand A2M 25 x A2M
Ligand OMC 9 x OMC
Ligand OMG 18 x OMG

Experiments and Validation Details

Entry percentile scores
Resolution: 2.5Å
Relevant EMDB volumes: EMD-7025

Quick links

Citations

8 review citations

Cryo-EM in drug discovery: achievements, limitations and prospects.
Renaud et al. (2018)
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12 mentions without citation

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