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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：C3SR52 New Search
31PDB entries
31Biological assembly
31chain/assembly records
Main Difference Dimensions in This Set
Different construct Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
4V85 Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome. Deposited 2011-06-13 Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric（59） Consistent with all polymers
Chain AM 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 493 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；Tris Ac PH.7.0, 25-35 mM KCL, 6.1% PEG 20000, 1% glycerol, 50mM sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 3.20 Å R-free 0.250
6YSR Structure of the P+9 stalled ribosome complex Deposited 2020-04-23 Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric（57） Consistent with all polymers
Chain m 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 332 ZN ZINC ION × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES, 30 mM KCl, 7 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.10 Å
6YSS Structure of the P+9 ArfB-ribosome complex in the post-hydrolysis state Deposited 2020-04-23 Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric（58） Consistent with all polymers
Chain m 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 387 ZN ZINC ION × 2 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES, 30 mM KCl, 7 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 2.60 Å
6YST Structure of the P+9 ArfB-ribosome complex with P/E hybrid tRNA in the post-hydrolysis state Deposited 2020-04-23 Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric（58） Consistent with all polymers
Chain m 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 253 ZN ZINC ION × 2 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES, 30 mM KCl, 7 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.20 Å
6YSU Structure of the P+0 ArfB-ribosome complex in the post-hydrolysis state Deposited 2020-04-23 Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric（57） Consistent with all polymers
Chain m 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 356 ZN ZINC ION × 1 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES, 30 mM KCl, 7 mM MgCl2, 0.1 % w/v DDM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ZTJ E. coli 70S-RNAP expressome complex in NusG-coupled state (38 nt intervening mRNA) Deposited 2020-07-20 Assembly 1 Other combination Heteromer；Protein × 58 PDB declaration: 66-meric（66） Consistent with all polymers
Chain AM 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 479 PHE PHENYLALANINE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6ZTM E. coli 70S-RNAP expressome complex in collided state without NusG Deposited 2020-07-20 Assembly 1 Other combination Heteromer；Protein × 52 PDB declaration: 60-meric（60） Consistent with all polymers
Chain AM 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 421 PHE PHENYLALANINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6ZTN E. coli 70S-RNAP expressome complex in NusG-coupled state (42 nt intervening mRNA) Deposited 2020-07-20 Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 63-meric（63） Consistent with all polymers
Chain AM 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 487 PHE PHENYLALANINE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6ZTO E. coli 70S-RNAP expressome complex in uncoupled state 1 Deposited 2020-07-20 Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 62-meric（62） Consistent with all polymers
Chain AM 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 487 PHE PHENYLALANINE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZTP E. coli 70S-RNAP expressome complex in uncoupled state 6 Deposited 2020-07-20 Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 62-meric（62） Consistent with all polymers
Chain AM 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 487 PHE PHENYLALANINE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZU1 E. coli 70S-RNAP expressome complex in uncoupled state 2 Deposited 2020-07-21 Assembly 1 Other combination Heteromer；Protein × 54 PDB declaration: 62-meric（62） Consistent with all polymers
Chain AM 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 487 PHE PHENYLALANINE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7AF3 Bacterial 30S ribosomal subunit assembly complex state M (head domain) Deposited 2020-09-19 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 51 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å
7AF5 Bacterial 30S ribosomal subunit assembly complex state I (head domain) Deposited 2020-09-19 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 52 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
7AF8 Bacterial 30S ribosomal subunit assembly complex state E (head domain) Deposited 2020-09-19 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 51 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
7AFA Bacterial 30S ribosomal subunit assembly complex state F (head domain) Deposited 2020-09-19 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 25 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
7AFD Bacterial 30S ribosomal subunit assembly complex state A (head domain) Deposited 2020-09-19 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 22 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
7AFH Bacterial 30S ribosomal subunit assembly complex state C (head domain) Deposited 2020-09-19 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 11 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
7AFK Bacterial 30S ribosomal subunit assembly complex state D (head domain) Deposited 2020-09-19 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 12 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
7AFN Bacterial 30S ribosomal subunit assembly complex state B (head domain) Deposited 2020-09-19 Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: nonameric（9） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 11 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
7NAX Complete Bacterial 30S ribosomal subunit assembly complex state I (Consensus Refinement) Deposited 2021-01-25 Assembly 1 Protein–RNA Heteromer；Protein × 19 PDB declaration: eicosameric（20） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 181 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
7NWT Initiated 70S ribosome in complex with 2A protein from encephalomyocarditis virus (EMCV) Deposited 2021-03-17 Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 59-meric（59） Consistent with all polymers
Chain r 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 437 FME N-FORMYLMETHIONINE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Initiated 70S ribosomes in 50 mM Tris-HCl pH 7.5, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2 were diluted tenfold into 20 mM HEPES pH 7.5, 100 mM potassium acetate, 1.5 mM MgCl2, 2.0 mM DTT. 2A protein was dialysed (3K MWCO, 277K, 16 h) into the same buffer. Crosslinking reactions of 50 microliters comprising 75 nM ribosomes, 3.0 micromolar 2A and 2.0 mM bis(sulfosuccinimidyl)suberate (BS3) were performed on ice (30 min) immediately prior to grid preparation.
cryo-EM vitrification conditions Cryogen ETHANE；Quantifoil R 2/2 400-mesh copper supports were coated with an additional ~ 60 angstrom layer of amorphous, evaporated carbon by flotation and thoroughly dried before use. Grids were made hydrophilic by glow-discharge in air for 30 s. Three microliters of crosslinking reaction was applied to grids which were then blotted for 4.5 s and vitrified by plunging into liquid ethane using a Vitrobot MK IV (FEI) at 277K, 100% relative humidity.
Resolution 2.66 Å
7PJS Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) Deposited 2021-08-24 Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric（58） Consistent with all polymers
Chain m 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 363 ZN ZINC ION × 2 NA SODIUM ION × 2 AM2 APRAMYCIN × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 2.35 Å
7PJT Structure of the 70S ribosome with tRNAs in hybrid state 1 (H1) Deposited 2021-08-24 Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric（58） Consistent with all polymers
Chain m 1–118（118 aa）
Not recorded ZN ZINC ION × 2 AM2 APRAMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 6.00 Å
7PJW Structure of the 70S-EF-G-GDP-Pi ribosome complex with tRNAs in hybrid state 2 (H2-EF-G-GDP-Pi) Deposited 2021-08-24 Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric（59） Consistent with all polymers
Chain m 1–118（118 aa）
Not recorded AM2 APRAMYCIN × 1 PO4 PHOSPHATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 4.00 Å
7PJX Structure of the 70S-EF-G-GDP ribosome complex with tRNAs in hybrid state 1 (H1-EF-G-GDP) Deposited 2021-08-24 Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric（59） Consistent with all polymers
Chain m 1–118（118 aa）
Not recorded AM2 APRAMYCIN × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 6.50 Å
7PJZ Structure of the 70S-EF-G-GDP ribosome complex with tRNAs in chimeric state 2 (CHI2-EF-G-GDP) Deposited 2021-08-24 Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 59-meric（59） Consistent with all polymers
Chain m 1–118（118 aa）
Not recorded ZN ZINC ION × 1 AM2 APRAMYCIN × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 6.00 Å
7Q4K Erythromycin-stalled Escherichia coli 70S ribosome with streptococcal MsrDL nascent chain Deposited 2021-10-31 Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric（56） Consistent with all polymers
Chain AM 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 172 ERY ERYTHROMYCIN A × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8AKN Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome Deposited 2022-07-30 Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric（57） Consistent with all polymers
Chain N 1–118（118 aa）
Not recorded ZN ZINC ION × 2 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MG MAGNESIUM ION × 305 SPM SPERMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.30 Å
8AM9 Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome Deposited 2022-08-03 Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric（56） Consistent with all polymers
Chain N 1–118（118 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 293 SPM SPERMINE × 1 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.80 Å
8GHU Methyltransferase RmtC bound to the 30S ribosomal subunit Deposited 2023-03-12 Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: pentadecameric（15） Consistent with all polymers
Chain m 2–94（93 aa）
Not recorded MG MAGNESIUM ION × 83 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9SX2 30S Doxycycline Bound E. coli Ribosome Deposited 2025-10-08 Assembly 1 Protein–RNA Heteromer；Protein × 21 PDB declaration: 22-meric（22） Consistent with all polymers
Chain M 1–118（118 aa）
Not recorded ZN ZINC ION × 1 DXT (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE × 1 MG MAGNESIUM ION × 142 K POTASSIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；BS100 ribosomal resuspension buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.08 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.