› 5gag

Electron Microscopy
3.8Å resolution

RNC in complex with SRP-SR in the closed state

Released:
DOI: 10.2210/pdb5gag/pdb
PDB entry 5gag coloured by chain, front view.
PDB entry 5gag coloured by chain, side view.
PDB entry 5gag coloured by chain, top view.
Source organisms:
Primary publication:
Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon.
Jomaa A, Boehringer D, Leibundgut M, Ban N
Nat Commun 7 10471 (2016)
PMID: 26804923
Related structures: EMD-8003

Function and Biology Details

Reactions catalysed: 
GTP + H(2)O = GDP + phosphate
A phosphate monoester + H(2)O = an alcohol + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
PDBe Complex ID:
PDB-CPX-132766 (preferred)
Entry contents:
32 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (36 distinct):
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 273 amino acids
Theoretical weight: 29.92 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60422 (Residues: 1-273; Coverage: 100%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 179 amino acids
Theoretical weight: 20.33 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P62399 (Residues: 1-179; Coverage: 100%)
Gene names: JW3270, b3308, rplE
Sequence domains:
Structure domains: 50s Ribosomal Protein L5; Chain: A,
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 177 amino acids
Theoretical weight: 18.93 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG55 (Residues: 1-177; Coverage: 100%)
Gene names: JW3267, b3305, rplF
Sequence domains: Ribosomal protein L6
Structure domains: Ribosomal protein L6, alpha-beta domain
Large ribosomal subunit protein bL9 Chain: H
Molecule details ›
Chain: H
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Sequence domains:
Large ribosomal subunit protein uL10 Chain: I
Molecule details ›
Chain: I
Length: 165 amino acids
Theoretical weight: 17.72 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7J3 (Residues: 1-165; Coverage: 100%)
Gene names: JW3948, b3985, rplJ
Sequence domains: Ribosomal protein L10
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL11 Chain: J
Molecule details ›
Chain: J
Length: 142 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7J7 (Residues: 1-142; Coverage: 100%)
Gene names: JW3946, b3983, relC, rplK
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL13 Chain: K
Molecule details ›
Chain: K
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: L
Molecule details ›
Chain: L
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY3 (Residues: 1-123; Coverage: 100%)
Gene names: JW3272, b3310, rplN
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
Large ribosomal subunit protein uL15 Chain: M
Molecule details ›
Chain: M
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02413 (Residues: 1-144; Coverage: 100%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: N
Molecule details ›
Chain: N
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
Large ribosomal subunit protein bL17 Chain: O
Molecule details ›
Chain: O
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG44 (Residues: 1-127; Coverage: 100%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
Structure domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: P
Molecule details ›
Chain: P
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0C018 (Residues: 1-117; Coverage: 100%)
Gene names: JW3266, b3304, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Structure domains: Nucleotidyltransferase; domain 5
Large ribosomal subunit protein bL19 Chain: Q
Molecule details ›
Chain: Q
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7K6 (Residues: 1-115; Coverage: 100%)
Gene names: JW2587, b2606, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: R
Molecule details ›
Chain: R
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L3 (Residues: 1-118; Coverage: 100%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: S
Molecule details ›
Chain: S
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: T
Molecule details ›
Chain: T
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P61175 (Residues: 1-110; Coverage: 100%)
Gene names: JW3277, b3315, eryB, rplV
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
Large ribosomal subunit protein uL23 Chain: U
Molecule details ›
Chain: U
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-100; Coverage: 100%)
Gene names: JW3280, b3318, rplW
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24 Chain: V
Molecule details ›
Chain: V
Length: 104 amino acids
Theoretical weight: 11.34 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60624 (Residues: 1-104; Coverage: 100%)
Gene names: JW3271, b3309, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: W
Molecule details ›
Chain: W
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
Structure domains: Ribosomal Protein L25; Chain P
Large ribosomal subunit protein bL27 Chain: X
Molecule details ›
Chain: X
Length: 85 amino acids
Theoretical weight: 9.15 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L8 (Residues: 1-85; Coverage: 100%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: Y
Molecule details ›
Chain: Y
Length: 78 amino acids
Theoretical weight: 9.03 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7M2 (Residues: 1-78; Coverage: 100%)
Gene names: JW3612, b3637, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: Z
Molecule details ›
Chain: Z
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: a
Molecule details ›
Chain: a
Length: 59 amino acids
Theoretical weight: 6.55 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG51 (Residues: 1-59; Coverage: 100%)
Gene names: JW3264, b3302, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Structure domains: Ribosomal protein L30, ferredoxin-like fold domain
Large ribosomal subunit protein bL32 Chain: b
Molecule details ›
Chain: b
Length: 57 amino acids
Theoretical weight: 6.46 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N4 (Residues: 1-57; Coverage: 100%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: c
Molecule details ›
Chain: c
Length: 55 amino acids
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N9 (Residues: 1-55; Coverage: 100%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Structure domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: d
Molecule details ›
Chain: d
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Sequence domains: Ribosomal protein L34
Structure domains: Helix Hairpins
Large ribosomal subunit protein bL35 Chain: e
Molecule details ›
Chain: e
Length: 65 amino acids
Theoretical weight: 7.31 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7Q1 (Residues: 1-65; Coverage: 100%)
Gene names: JW1707, b1717, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36A Chain: f
Molecule details ›
Chain: f
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Sequence domains: Ribosomal protein L36
Signal recognition particle protein Chain: i
Molecule details ›
Chain: i
Length: 450 amino acids
Theoretical weight: 47.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AGD7 (Residues: 4-434; Coverage: 95%)
Gene names: JW5414, b2610, ffh
Sequence domains:
Structure domains: Signal recognition particle, SRP54 subunit, M-domain
Alkaline phosphatase Chain: k
Molecule details ›
Chain: k
Length: 18 amino acids
Theoretical weight: 1.98 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P00634 (Residues: 1-18; Coverage: 0%)
Gene names: JW0374, b0383, phoA
SRP 4.5S RNA Chain: 1
Molecule details ›
Chain: 1
Length: 113 nucleotides
Theoretical weight: 36.5 KDa
Sequence domains: Bacterial small signal recognition particle RNA
tRNA CCAend Chain: 2
Molecule details ›
Chain: 2
Length: 3 nucleotides
Theoretical weight: 895 Da
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2903 nucleotides
Theoretical weight: 941.31 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 431 x MG
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-8003
Expression system: Escherichia coli

Quick links

Citations

18 review citations

Protein export through the bacterial Sec pathway.
Tsirigotaki et al. (2017)
17 more

9 mentions without citation

Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon.
Jomaa et al. (2016)
8 more