› 8r3v

Electron Microscopy
3.28Å resolution

Escherichia coli paused disome complex (non-rotated disome interface)

Released:
DOI: 10.2210/pdb8r3v/pdb
PDB entry 8r3v coloured by chain, front view.
PDB entry 8r3v coloured by chain, side view.
PDB entry 8r3v coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM.
Flügel T, Schacherl M, Unbehaun A, Schroeer B, Dabrowski M, Bürger J, Mielke T, Sprink T, Diebolder CA, Guillén Schlippe YV, Spahn CMT
OpenAccess logo Nat Commun 15 1756 (2024)
PMID: 38409277
Related structures: EMD-18875

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 65-mer (preferred)
PDBe Complex ID:
PDB-CPX-240785 (preferred)
Entry contents:
36 distinct polypeptide molecules
9 distinct RNA molecules
Macromolecules (45 distinct):
Large ribosomal subunit protein bL28 Chain: 12
Molecule details ›
Chain: 12
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 uL30 Chain: 32
Molecule details ›
Chain: 32
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
Large ribosomal subunit protein bL31 Chain: 4
Molecule details ›
Chain: 4
Length: 70 amino acids
Theoretical weight: 7.89 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7M9 (Residues: 1-70; Coverage: 100%)
Gene names: JW3907, b3936, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL35 Chain: 62
Molecule details ›
Chain: 62
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
Small ribosomal subunit protein uS2 Chains: B, B2
Molecule details ›
Chains: B, B2
Length: 241 amino acids
Theoretical weight: 26.78 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V0 (Residues: 1-241; Coverage: 100%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: C1, C2
Molecule details ›
Chains: C1, C2
Length: 233 amino acids
Theoretical weight: 26.03 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V3 (Residues: 1-233; Coverage: 100%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: D1, D2
Molecule details ›
Chains: D1, D2
Length: 206 amino acids
Theoretical weight: 23.51 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V8 (Residues: 1-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: E1, E2
Molecule details ›
Chains: E1, E2
Length: 167 amino acids
Theoretical weight: 17.63 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W1 (Residues: 1-167; Coverage: 100%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6 Chains: F1, F2
Molecule details ›
Chains: F1, F2
Length: 135 amino acids
Theoretical weight: 15.73 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02358 (Residues: 1-135; Coverage: 100%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chains: G1, G2
Molecule details ›
Chains: G1, G2
Length: 179 amino acids
Theoretical weight: 20.06 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02359 (Residues: 1-179; Coverage: 100%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chains: H1, H2
Molecule details ›
Chains: H1, H2
Length: 130 amino acids
Theoretical weight: 14.15 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W7 (Residues: 1-130; Coverage: 100%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chains: I1, I2
Molecule details ›
Chains: I1, I2
Length: 130 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7X3 (Residues: 1-130; Coverage: 100%)
Gene names: JW3199, b3230, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chains: J1, J2
Molecule details ›
Chains: J1, J2
Length: 103 amino acids
Theoretical weight: 11.76 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R5 (Residues: 1-103; Coverage: 100%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: K1, K2
Molecule details ›
Chains: K1, K2
Length: 129 amino acids
Theoretical weight: 13.87 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R9 (Residues: 1-129; Coverage: 100%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: L1, L2
Molecule details ›
Chains: L1, L2
Length: 124 amino acids
Theoretical weight: 13.77 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S3 (Residues: 1-124; Coverage: 100%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: M1, M2
Molecule details ›
Chains: M1, M2
Length: 118 amino acids
Theoretical weight: 13.13 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S9 (Residues: 1-118; Coverage: 100%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chains: N1, N2
Molecule details ›
Chains: N1, N2
Length: 101 amino acids
Theoretical weight: 11.61 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG59 (Residues: 1-101; Coverage: 100%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chains: O1, O2
Molecule details ›
Chains: O1, O2
Length: 89 amino acids
Theoretical weight: 10.29 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADZ4 (Residues: 1-89; Coverage: 100%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: P1
Molecule details ›
Chain: P1
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chains: Q1, Q2
Molecule details ›
Chains: Q1, Q2
Length: 84 amino acids
Theoretical weight: 9.72 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG63 (Residues: 1-84; Coverage: 100%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chains: R1, R2
Molecule details ›
Chains: R1, R2
Length: 75 amino acids
Theoretical weight: 9.01 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T7 (Residues: 1-75; Coverage: 100%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: S1, S2
Molecule details ›
Chains: S1, S2
Length: 92 amino acids
Theoretical weight: 10.46 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U3 (Residues: 1-92; Coverage: 100%)
Gene names: JW3278, b3316, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: T1
Molecule details ›
Chain: T1
Length: 87 amino acids
Theoretical weight: 9.71 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U7 (Residues: 1-87; Coverage: 100%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chains: U1, U2
Molecule details ›
Chains: U1, U2
Length: 71 amino acids
Theoretical weight: 8.52 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P68679 (Residues: 1-71; Coverage: 100%)
Gene names: JW3037, b3065, rpsU
Sequence domains: Ribosomal protein S21
Small ribosomal subunit protein bS1 Chain: Z1
Molecule details ›
Chain: Z1
Length: 557 amino acids
Theoretical weight: 61.24 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG67 (Residues: 1-557; Coverage: 100%)
Gene names: JW0894, b0911, rpsA, ssyF
Sequence domains: S1 RNA binding domain
Large ribosomal subunit protein uL1 Chain: a2
Molecule details ›
Chain: a2
Length: 234 amino acids
Theoretical weight: 24.77 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L0 (Residues: 1-234; Coverage: 100%)
Gene names: JW3947, b3984, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chain: b2
Molecule details ›
Chain: b2
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:
Large ribosomal subunit protein uL5 Chain: e2
Molecule details ›
Chain: e2
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:
Large ribosomal subunit protein bL33 Chain: g2
Molecule details ›
Chain: g2
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
Large ribosomal subunit protein uL16 Chain: h2
Molecule details ›
Chain: h2
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
Large ribosomal subunit protein bL9 Chain: i2
Molecule details ›
Chain: i2
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 bL34 Chain: l2
Molecule details ›
Chain: l2
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
Large ribosomal subunit protein uL15 Chain: o2
Molecule details ›
Chain: o2
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
Nascent chain Chain: p
Molecule details ›
Chain: p
Length: 10 amino acids
Theoretical weight: 1.09 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL18 Chain: r2
Molecule details ›
Chain: r2
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
Large ribosomal subunit protein bL27 Chain: z2
Molecule details ›
Chain: z2
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
23S ribosomal RNA Chains: 71, 72
Molecule details ›
Chains: 71, 72
Length: 2904 nucleotides
Theoretical weight: 941.81 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: 82
Molecule details ›
Chain: 82
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chains: A1, A2
Molecule details ›
Chains: A1, A2
Length: 1542 nucleotides
Theoretical weight: 499.87 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
Messenger RNA Chain: V2
Molecule details ›
Chain: V2
Length: 64 nucleotides
Theoretical weight: 20.79 KDa
tRNA-Trp (P-site) Chain: W
Molecule details ›
Chain: W
Length: 76 nucleotides
Theoretical weight: 24.63 KDa
Sequence domains: tRNA
tRNA-Phe (P-site) Chain: W1
Molecule details ›
Chain: W1
Length: 76 nucleotides
Theoretical weight: 24.65 KDa
Sequence domains: tRNA
tRNA-Arg (E-site) Chain: X2
Molecule details ›
Chain: X2
Length: 77 nucleotides
Theoretical weight: 24.98 KDa
Sequence domains: tRNA
tRNA-Val (A-site) Chain: Y1
Molecule details ›
Chain: Y1
Length: 76 nucleotides
Theoretical weight: 24.62 KDa
Sequence domains: tRNA
tRNA-Ala (A-site) Chain: Y2
Molecule details ›
Chain: Y2
Length: 76 nucleotides
Theoretical weight: 24.56 KDa
Sequence domains: tRNA

Ligands and Environments

5 bound ligands:
Ligand ZN 2 x ZN
Ligand PUT 2 x PUT
Ligand SPD 1 x SPD
Ligand MG 297 x MG
Ligand ALA 1 x ALA
21 modified residues:
Ligand 1MG 2 x 1MG
Ligand PSU 22 x PSU
Ligand 5MU 9 x 5MU
Ligand 6MZ 5 x 6MZ
Ligand 2MG 10 x 2MG
Ligand 3TD 2 x 3TD
Ligand 5MC 6 x 5MC
Ligand G7M 8 x G7M
Ligand OMG 2 x OMG
Ligand H2U 11 x H2U
Ligand OMC 2 x OMC
Ligand 2MA 3 x 2MA
Ligand OMU 2 x OMU
Ligand 4OC 2 x 4OC
Ligand UR3 2 x UR3
Ligand MA6 4 x MA6
Ligand 4SU 4 x 4SU
Ligand MIA 2 x MIA
Ligand RSP 1 x RSP
Ligand 3AU 1 x 3AU
Ligand 7MG 1 x 7MG

Experiments and Validation Details

Entry percentile scores
Resolution: 3.28Å
Relevant EMDB volumes: EMD-18875

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