› 4v48

Electron Microscopy
11.5Å resolution

Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the initiation-like state of E. coli 70S ribosome

Released:
DOI: 10.2210/pdb4v48/pdb
PDB entry 4v48 coloured by chain, front view.
PDB entry 4v48 coloured by chain, side view.
PDB entry 4v48 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J
Cell 113 789-801 (2003)
PMID: 12809609

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 48-mer (preferred)
PDBe Complex ID:
PDB-CPX-135673 (preferred)
Entry contents:
44 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (48 distinct):
Large ribosomal subunit protein uL2 Chain: AA
Molecule details ›
Chain: AA
Length: 272 amino acids
Theoretical weight: 29.79 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60422 (Residues: 2-273; Coverage: 100%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: AB
Molecule details ›
Chain: AB
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: AC
Molecule details ›
Chain: AC
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: AD
Molecule details ›
Chain: AD
Length: 178 amino acids
Theoretical weight: 20.2 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P62399 (Residues: 2-179; Coverage: 99%)
Gene names: JW3270, b3308, rplE
Sequence domains:
50S ribosomal protein L6 Chain: AE
Molecule details ›
Chain: AE
Length: 176 amino acids
Theoretical weight: 18.8 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL9 Chain: AF
Molecule details ›
Chain: AF
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 uL11 Chain: AG
Molecule details ›
Chain: AG
Length: 141 amino acids
Theoretical weight: 14.76 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7J7 (Residues: 2-142; Coverage: 99%)
Gene names: JW3946, b3983, relC, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chain: AH
Molecule details ›
Chain: AH
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
50S ribosomal protein L14 Chain: AI
Molecule details ›
Chain: AI
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL15 Chain: AJ
Molecule details ›
Chain: AJ
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
50S ribosomal protein L16 Chain: AK
Molecule details ›
Chain: AK
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli
50S ribosomal protein L17 Chain: AL
Molecule details ›
Chain: AL
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL18 Chain: AM
Molecule details ›
Chain: AM
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 bL19 Chain: AN
Molecule details ›
Chain: AN
Length: 114 amino acids
Theoretical weight: 13.03 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7K6 (Residues: 2-115; Coverage: 99%)
Gene names: JW2587, b2606, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: AO
Molecule details ›
Chain: AO
Length: 117 amino acids
Theoretical weight: 13.4 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L3 (Residues: 2-118; Coverage: 99%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein uL22 Chain: AQ
Molecule details ›
Chain: AQ
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
50S ribosomal protein L23 Chain: AR
Molecule details ›
Chain: AR
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL24 Chain: AS
Molecule details ›
Chain: AS
Length: 103 amino acids
Theoretical weight: 11.21 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60624 (Residues: 2-104; Coverage: 99%)
Gene names: JW3271, b3309, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: AT
Molecule details ›
Chain: AT
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
Large ribosomal subunit protein bL27 Chain: AU
Molecule details ›
Chain: AU
Length: 84 amino acids
Theoretical weight: 9.02 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L8 (Residues: 2-85; Coverage: 99%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein uL29 Chain: AW
Molecule details ›
Chain: AW
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
50S ribosomal protein L30 Chain: AX
Molecule details ›
Chain: AX
Length: 58 amino acids
Theoretical weight: 6.42 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL32 Chain: AZ
Molecule details ›
Chain: AZ
Length: 56 amino acids
Theoretical weight: 6.33 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N4 (Residues: 2-57; Coverage: 98%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: A1
Molecule details ›
Chain: A1
Length: 54 amino acids
Theoretical weight: 6.26 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N9 (Residues: 2-55; Coverage: 98%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL36A Chain: A4
Molecule details ›
Chain: A4
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
30S RIBOSOMAL PROTEIN S2 Chain: BB
Molecule details ›
Chain: BB
Length: 240 amino acids
Theoretical weight: 26.65 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S3 Chain: BC
Molecule details ›
Chain: BC
Length: 232 amino acids
Theoretical weight: 25.9 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S4 Chain: BD
Molecule details ›
Chain: BD
Length: 205 amino acids
Theoretical weight: 23.38 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S5 Chain: BE
Molecule details ›
Chain: BE
Length: 166 amino acids
Theoretical weight: 17.5 KDa
Source organism: Escherichia coli
Small ribosomal subunit protein bS6 Chain: BF
Molecule details ›
Chain: BF
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 Chain: BG
Molecule details ›
Chain: BG
Length: 178 amino acids
Theoretical weight: 19.92 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02359 (Residues: 2-179; Coverage: 99%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S RIBOSOMAL PROTEIN S8 Chain: BH
Molecule details ›
Chain: BH
Length: 129 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S9 Chain: BI
Molecule details ›
Chain: BI
Length: 129 amino acids
Theoretical weight: 14.76 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S10 Chain: BJ
Molecule details ›
Chain: BJ
Length: 103 amino acids
Theoretical weight: 11.76 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S11 Chain: BK
Molecule details ›
Chain: BK
Length: 128 amino acids
Theoretical weight: 13.74 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S12 Chain: BL
Molecule details ›
Chain: BL
Length: 123 amino acids
Theoretical weight: 13.64 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S13 Chain: BM
Molecule details ›
Chain: BM
Length: 117 amino acids
Theoretical weight: 13 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S14 Chain: BN
Molecule details ›
Chain: BN
Length: 100 amino acids
Theoretical weight: 11.48 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S15 Chain: BO
Molecule details ›
Chain: BO
Length: 88 amino acids
Theoretical weight: 10.16 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S16 Chain: BP
Molecule details ›
Chain: BP
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S17 Chain: BQ
Molecule details ›
Chain: BQ
Length: 83 amino acids
Theoretical weight: 9.59 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S18 Chain: BR
Molecule details ›
Chain: BR
Length: 74 amino acids
Theoretical weight: 8.87 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S19 Chain: BS
Molecule details ›
Chain: BS
Length: 91 amino acids
Theoretical weight: 10.32 KDa
Source organism: Escherichia coli
30S RIBOSOMAL PROTEIN S20 Chain: BT
Molecule details ›
Chain: BT
Length: 86 amino acids
Theoretical weight: 9.58 KDa
Source organism: Escherichia coli
23S ribosomal RNA Chain: A0
Molecule details ›
Chain: A0
Length: 2904 nucleotides
Theoretical weight: 941.61 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: A9
Molecule details ›
Chain: A9
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Sequence domains: 5S ribosomal RNA
tRNA-PHE Chain: A6
Molecule details ›
Chain: A6
Length: 76 nucleotides
Theoretical weight: 24.52 KDa
Sequence domains: tRNA
16S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 1543 nucleotides
Theoretical weight: 500 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 11.5Å

Quick links

Citations

35 review citations

What recent ribosome structures have revealed about the mechanism of translation.
Schmeing et al. (2009)
34 more

2 mentions without citation

Prediction of Synergistic Antibiotic Combinations by Graph Learning.
Lv et al. (2022)
1 more