PDBe 6gxm

Electron Microscopy
3.8Å resolution

Cryo-EM structure of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State II)


Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
Entry contents:
53 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (58 distinct):
50S ribosomal protein L2 Chain: C
Molecule details ›
Chain: C
Length: 271 amino acids
Theoretical weight: 29.66 KDa
Source organism: Escherichia coli
  • Canonical: P60422 (Residues: 2-272; Coverage: 99%)
Gene names: JW3279, b3317, rplB
Sequence domains:
50S ribosomal protein L3 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 22.28 KDa
  • Canonical: P60438 (Residues: 1-209; Coverage: null%)
Gene names: JW3282, b3320, rplC
50S ribosomal protein L4 Chain: E
Molecule details ›
Chain: E
Length: 201 amino acids
Theoretical weight: 22.12 KDa
  • Canonical: P60723 (Residues: 1-201; Coverage: null%)
Gene names: JW3281, b3319, eryA, rplD
50S ribosomal protein L5 Chain: F
Molecule details ›
Chain: F
Length: 177 amino acids
Theoretical weight: 20.07 KDa
  • Canonical: P62399 (Residues: 2-178; Coverage: null%)
Gene names: JW3270, b3308, rplE
50S ribosomal protein L6 Chain: G
Molecule details ›
Chain: G
Length: 176 amino acids
Theoretical weight: 18.8 KDa
  • Canonical: P0AG55 (Residues: 2-177; Coverage: null%)
Gene names: JW3267, b3305, rplF
50S ribosomal protein L9 Chain: H
Molecule details ›
Chain: H
Length: 149 amino acids
Theoretical weight: 15.79 KDa
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: null%)
Gene names: JW4161, b4203, rplI
50S ribosomal protein L11 Chain: I
Molecule details ›
Chain: I
Length: 141 amino acids
Theoretical weight: 14.76 KDa
  • Canonical: P0A7J7 (Residues: 2-142; Coverage: null%)
Gene names: JW3946, b3983, relC, rplK
50S ribosomal protein L13 Chain: J
Molecule details ›
Chain: J
Length: 142 amino acids
Theoretical weight: 16.05 KDa
  • Canonical: P0AA10 (Residues: 1-142; Coverage: null%)
Gene names: JW3200, b3231, rplM
50S ribosomal protein L14 Chain: K
Molecule details ›
Chain: K
Length: 122 amino acids
Theoretical weight: 13.45 KDa
  • Canonical: P0ADY3 (Residues: 1-122; Coverage: null%)
Gene names: JW3272, b3310, rplN
50S ribosomal protein L15 Chain: L
Molecule details ›
Chain: L
Length: 143 amino acids
Theoretical weight: 14.88 KDa
  • Canonical: P02413 (Residues: 2-144; Coverage: null%)
Gene names: JW3263, b3301, rplO
50S ribosomal protein L16 Chain: M
Molecule details ›
Chain: M
Length: 136 amino acids
Theoretical weight: 15.31 KDa
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: null%)
Gene names: JW3275, b3313, rplP
50S ribosomal protein L17 Chain: N
Molecule details ›
Chain: N
Length: 120 amino acids
Theoretical weight: 13.72 KDa
  • Canonical: P0AG44 (Residues: 1-120; Coverage: null%)
Gene names: JW3256, b3294, rplQ
50S ribosomal protein L18 Chain: O
Molecule details ›
Chain: O
Length: 116 amino acids
Theoretical weight: 12.66 KDa
  • Canonical: P0C018 (Residues: 2-117; Coverage: null%)
Gene names: JW3266, b3304, rplR
50S ribosomal protein L19 Chain: P
Molecule details ›
Chain: P
Length: 114 amino acids
Theoretical weight: 13.03 KDa
  • Canonical: P0A7K6 (Residues: 2-115; Coverage: null%)
Gene names: JW2587, b2606, rplS
50S ribosomal protein L20 Chain: Q
Molecule details ›
Chain: Q
Length: 117 amino acids
Theoretical weight: 13.4 KDa
  • Canonical: P0A7L3 (Residues: 2-118; Coverage: null%)
Gene names: JW1706, b1716, pdzA, rplT
50S ribosomal protein L21 Chain: R
Molecule details ›
Chain: R
Length: 103 amino acids
Theoretical weight: 11.59 KDa
  • Canonical: P0AG48 (Residues: 1-103; Coverage: null%)
Gene names: JW3153, b3186, rplU
50S ribosomal protein L22 Chain: S
Molecule details ›
Chain: S
Length: 110 amino acids
Theoretical weight: 12.25 KDa
  • Canonical: P61175 (Residues: 1-110; Coverage: null%)
Gene names: JW3277, b3315, eryB, rplV
50S ribosomal protein L23 Chain: T
Molecule details ›
Chain: T
Length: 93 amino acids
Theoretical weight: 10.55 KDa
  • Canonical: P0ADZ0 (Residues: 1-93; Coverage: null%)
Gene names: JW3280, b3318, rplW
50S ribosomal protein L24 Chain: U
Molecule details ›
Chain: U
Length: 102 amino acids
Theoretical weight: 11.08 KDa
  • Canonical: P60624 (Residues: 2-103; Coverage: null%)
Gene names: JW3271, b3309, rplX
50S ribosomal protein L25 Chain: V
Molecule details ›
Chain: V
Length: 94 amino acids
Theoretical weight: 10.71 KDa
  • Canonical: P68919 (Residues: 1-94; Coverage: null%)
Gene names: JW2173, b2185, rplY
50S ribosomal protein L27 Chain: W
Molecule details ›
Chain: W
Length: 75 amino acids
Theoretical weight: 8.17 KDa
  • Canonical: P0A7L8 (Residues: 11-85; Coverage: null%)
Gene names: JW3152, b3185, rpmA
50S ribosomal protein L28 Chain: X
Molecule details ›
Chain: X
Length: 77 amino acids
Theoretical weight: 8.9 KDa
  • Canonical: P0A7M2 (Residues: 2-78; Coverage: null%)
Gene names: JW3612, b3637, rpmB
50S ribosomal protein L29 Chain: Y
Molecule details ›
Chain: Y
Length: 63 amino acids
Theoretical weight: 7.29 KDa
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: null%)
Gene names: JW3274, b3312, rpmC
50S ribosomal protein L30 Chain: Z
Molecule details ›
Chain: Z
Length: 58 amino acids
Theoretical weight: 6.42 KDa
  • Canonical: P0AG51 (Residues: 2-59; Coverage: null%)
Gene names: JW3264, b3302, rpmD
50S ribosomal protein L32 Chain: 0
Molecule details ›
Chain: 0
Length: 56 amino acids
Theoretical weight: 6.33 KDa
Source organism: Escherichia coli
  • Canonical: P0A7N4 (Residues: 2-57; Coverage: 98%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chain: 1
Molecule details ›
Chain: 1
Length: 50 amino acids
Theoretical weight: 5.81 KDa
Source organism: Escherichia coli
  • Canonical: P0A7N9 (Residues: 4-53; Coverage: 91%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chain: 2
Molecule details ›
Chain: 2
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Sequence domains: Ribosomal protein L34
50S ribosomal protein L35 Chain: 3
Molecule details ›
Chain: 3
Length: 64 amino acids
Theoretical weight: 7.18 KDa
Source organism: Escherichia coli
  • Canonical: P0A7Q1 (Residues: 2-65; Coverage: 99%)
Gene names: JW1707, b1717, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chain: 4
Molecule details ›
Chain: 4
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Sequence domains: Ribosomal protein L36
50S ribosomal protein L10 Chain: 5
Molecule details ›
Chain: 5
Length: 131 amino acids
Theoretical weight: 14.11 KDa
Source organism: Escherichia coli
  • Canonical: P0A7J3 (Residues: 1-131; Coverage: 79%)
Gene names: JW3948, b3985, rplJ
Sequence domains: Ribosomal protein L10
30S ribosomal protein S2 Chain: b
Molecule details ›
Chain: b
Length: 218 amino acids
Theoretical weight: 24.25 KDa
  • Canonical: P0A7V0 (Residues: 9-226; Coverage: null%)
Gene names: JW0164, b0169, rpsB
30S ribosomal protein S3 Chain: c
Molecule details ›
Chain: c
Length: 206 amino acids
Theoretical weight: 23.08 KDa
  • Canonical: P0A7V3 (Residues: 2-207; Coverage: null%)
Gene names: JW3276, b3314, rpsC
30S ribosomal protein S4 Chain: d
Molecule details ›
Chain: d
Length: 205 amino acids
Theoretical weight: 23.38 KDa
  • Canonical: P0A7V8 (Residues: 2-206; Coverage: null%)
Gene names: JW3258, b3296, ramA, rpsD
30S ribosomal protein S5 Chain: e
Molecule details ›
Chain: e
Length: 157 amino acids
Theoretical weight: 16.53 KDa
  • Canonical: P0A7W1 (Residues: 10-166; Coverage: null%)
Gene names: JW3265, b3303, rpsE, spc
30S ribosomal protein S6 Chain: f
Molecule details ›
Chain: f
Length: 100 amino acids
Theoretical weight: 11.67 KDa
  • Canonical: P02358 (Residues: 1-100; Coverage: null%)
Gene names: JW4158, b4200, rpsF
30S ribosomal protein S7 Chain: g
Molecule details ›
Chain: g
Length: 151 amino acids
Theoretical weight: 16.86 KDa
  • Canonical: P02359 (Residues: 2-152; Coverage: null%)
Gene names: JW3303, b3341, rpsG
30S ribosomal protein S8 Chain: h
Molecule details ›
Chain: h
Length: 129 amino acids
Theoretical weight: 14.02 KDa
  • Canonical: P0A7W7 (Residues: 2-130; Coverage: null%)
Gene names: JW3268, b3306, rpsH
30S ribosomal protein S9 Chain: i
Molecule details ›
Chain: i
Length: 127 amino acids
Theoretical weight: 14.55 KDa
  • Canonical: P0A7X3 (Residues: 4-130; Coverage: null%)
Gene names: JW3199, b3230, rpsI
30S ribosomal protein S10 Chain: j
Molecule details ›
Chain: j
Length: 98 amino acids
Theoretical weight: 11.2 KDa
  • Canonical: P0A7R5 (Residues: 5-102; Coverage: null%)
Gene names: JW3283, b3321, nusE, rpsJ
30S ribosomal protein S11 Chain: k
Molecule details ›
Chain: k
Length: 116 amino acids
Theoretical weight: 12.39 KDa
  • Canonical: P0A7R9 (Residues: 13-128; Coverage: null%)
Gene names: JW3259, b3297, rpsK
30S ribosomal protein S12 Chain: l
Molecule details ›
Chain: l
Length: 123 amino acids
Theoretical weight: 13.64 KDa
  • Canonical: P0A7S3 (Residues: 2-124; Coverage: null%)
Gene names: JW3304, b3342, rpsL, strA
30S ribosomal protein S13 Chain: m
Molecule details ›
Chain: m
Length: 114 amino acids
Theoretical weight: 12.63 KDa
  • Canonical: P0A7S9 (Residues: 2-115; Coverage: null%)
Gene names: JW3260, b3298, rpsM
30S ribosomal protein S14 Chain: n
Molecule details ›
Chain: n
Length: 101 amino acids
Theoretical weight: 11.55 KDa
  • Canonical: P0AG59 (Residues: 2-35, 36-101; Coverage: null%)
Gene names: JW3269, b3307, rpsN
30S ribosomal protein S15 Chain: o
Molecule details ›
Chain: o
Length: 88 amino acids
Theoretical weight: 10.16 KDa
  • Canonical: P0ADZ4 (Residues: 2-89; Coverage: null%)
Gene names: JW3134, b3165, rpsO, secC
30S ribosomal protein S16 Chain: p
Molecule details ›
Chain: p
Length: 82 amino acids
Theoretical weight: 9.21 KDa
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: null%)
Gene names: JW2590, b2609, rpsP
30S ribosomal protein S17 Chain: q
Molecule details ›
Chain: q
Length: 80 amino acids
Theoretical weight: 9.26 KDa
  • Canonical: P0AG63 (Residues: 4-83; Coverage: null%)
Gene names: JW3273, b3311, neaA, rpsQ
30S ribosomal protein S18 Chain: r
Molecule details ›
Chain: r
Length: 65 amino acids
Theoretical weight: 7.61 KDa
  • Canonical: P0A7T7 (Residues: 10-74; Coverage: null%)
Gene names: JW4160, b4202, rpsR
30S ribosomal protein S19 Chain: s
Molecule details ›
Chain: s
Length: 79 amino acids
Theoretical weight: 9.06 KDa
  • Canonical: P0A7U3 (Residues: 3-81; Coverage: null%)
Gene names: JW3278, b3316, rpsS
30S ribosomal protein S20 Chain: t
Molecule details ›
Chain: t
Length: 85 amino acids
Theoretical weight: 9.51 KDa
  • Canonical: P0A7U7 (Residues: 3-87; Coverage: null%)
Gene names: JW0022, b0023, rpsT
30S ribosomal protein S21 Chain: u
Molecule details ›
Chain: u
Length: 65 amino acids
Theoretical weight: 7.76 KDa
  • Canonical: P68679 (Residues: 4-68; Coverage: null%)
Gene names: JW3037, b3065, rpsU
Peptide chain release factor RF1 Chain: v
Molecule details ›
Chain: v
Length: 248 amino acids
Theoretical weight: 27.58 KDa
  • Canonical: P0A7I0 (Residues: 104-351; Coverage: null%)
Gene names: JW1202, b1211, prfA, sueB, uar
Peptide chain release factor RF3 Chain: w
Molecule details ›
Chain: w
Length: 529 amino acids
Theoretical weight: 59.65 KDa
  • Canonical: P0A7I4 (Residues: 1-529; Coverage: null%)
Gene names: JW5873, b4375, miaD, prfC, tos
Apidaecin Chain: z
Molecule details ›
Chain: z
Length: 14 amino acids
Theoretical weight: 1.7 KDa
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2903 nucleotides
Theoretical weight: 941.32 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 120 nucleotides
Theoretical weight: 38.81 KDa
Sequence domains: 5S ribosomal RNA
Messenger RNA Chain: 7
Molecule details ›
Chain: 7
Length: 7 nucleotides
Theoretical weight: 2.23 KDa
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1539 nucleotides
Theoretical weight: 498.73 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
fMet-tRNA Chain: x
Molecule details ›
Chain: x
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-0080