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2bm1

Ribosomal elongation factor G (EF-G) Fusidic acid resistant mutant G16V

Method: X-RAY DIFFRACTION Dmax: 112.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ELONGATION FACTOR G

THERMUS THERMOPHILUS

UniProt P13551

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–691 Mutation：YES GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.3；17 % PEG8000 100 MM HEPES 46 MM TRIS-HCL PH 7.3 10 MM MAGNESIUM CHLORIDE Resolution 2.60 Å R-free 0.297

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2BM1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EFG THE CRYSTAL STRUCTURE OF ELONGATION FACTOR G COMPLEXED WITH GDP, AT 2.7 ANGSTROMS RESOLUTION Deposited 1994-10-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–691（691 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；277 K；pH 7.8, temperature 277K
Resolution 2.70 Å R-free 0.396
1FNM STRUCTURE OF THERMUS THERMOPHILUS EF-G H573A Deposited 2000-08-22 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–691（691 aa）
Mutation：H573A MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；PEG 8000 (Fluka), guanosine 5'-diphophate, magnesium chloride , pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.80 Å R-free 0.295
1JQM Fitting of L11 protein and elongation factor G (EF-G) in the cryo-em map of e. coli 70S ribosome bound with EF-G, GDP and fusidic acid Deposited 2001-08-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–691（691 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
Resolution 18.00 Å
1JQS Fitting of L11 protein and elongation factor G (domain G' and V) in the cryo-em map of E. coli 70S ribosome bound with EF-G and GMPPCP, a nonhydrolysable GTP analog Deposited 2001-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 220–251（32 aa） Fragment：;part of domain G' ;
Chain C 606–673（68 aa） Fragment：domain V
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 18.00 Å
1KTV Crystal Structure of Elongation Factor G Dimer Without Nucleotide Deposited 2002-01-17 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–691（691 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；PEG 8000, HEPES, Tris, Dithiothreitol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.80 Å R-free 0.374
1KTV Crystal Structure of Elongation Factor G Dimer Without Nucleotide Deposited 2002-01-17 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–691（691 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；PEG 8000, HEPES, Tris, Dithiothreitol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.80 Å R-free 0.374
1PN6 Domain-wise fitting of the crystal structure of T.thermophilus EF-G into the low resolution map of the release complex.Puromycin.EFG.GDPNP of E.coli 70S ribosome. Deposited 2003-06-12 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–691（691 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane
Resolution 10.80 Å
2BCW Coordinates of the N-terminal domain of ribosomal protein L11,C-terminal domain of ribosomal protein L7/L12 and a portion of the G' domain of elongation factor G, as fitted into cryo-em map of an Escherichia coli 70S*EF-G*GDP*fusidic acid complex Deposited 2005-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 200–257（58 aa） Fragment：;A portion of G' domain' ;
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine；pH 7.5；20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine
cryo-EM vitrification conditions RAPID-FREEZING IN LIQUID ETHANE
Resolution 11.20 Å
2BM0 Ribosomal elongation factor G (EF-G) Fusidic acid resistant mutant T84A Deposited 2005-03-09 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–691（691 aa）
Mutation：YES GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；17% PEG 8000 100 MM HEPES 46 MM TRIS-HCL PH 7.3
Resolution 2.40 Å R-free 0.274
2BV3 Crystal structure of a mutant elongation factor G trapped with a GTP analogue Deposited 2005-06-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–691（691 aa）
Mutation：YES GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；17 % PEG8000, 10 MM MGCL2, 100 MM GDPNP, 46 MM TRIS, 100 MM HEPES, pH 7.30
Resolution 2.50 Å R-free 0.270
2EFG TRANSLATIONAL ELONGATION FACTOR G COMPLEXED WITH GDP Deposited 1998-09-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–691（691 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；18% W/V PEG8000, 20MM TRIS-HCL, 20MM AMMONIUM ACETATE, 2MM DTT, 1MM SODIUM AZIDE, 1MM GDP, pH 7.8, VAPOR DIFFUSION, HANGING DROP
Resolution 2.60 Å R-free 0.279
2J7K Crystal structure of the T84A mutant EF-G:GDPCP complex Deposited 2006-10-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–691（691 aa）
Mutation：YES GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.3；17 % PEG8000 100 MM HEPES 46 MM TRIS 10 MM MGCL2 10 MM GDPCP, pH 7.3
Resolution 2.90 Å R-free 0.288
2OM7 Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors Deposited 2007-01-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: tetradecameric
Chain L 1–691（691 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol；pH 7.8；0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.30 Å
3IZP Conformation of EF-G during translocation Deposited 2010-11-15 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–688（688 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；5 mM potassium phosphate, 5 mM magnesium acetate, 5 mM ammonium chloride, 95 mM potassium chloride, 0.5 mM calcium chloride, 8 mM putrescine, 1 mM spermidine, and 1 mM dithioerythritol
cryo-EM vitrification conditions two-face blotting for 1 second；90 K；Cryogen ETHANE
Resolution not provided
4M1K Crystal structure of elongation factor G (EFG) Deposited 2013-08-02 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–691（691 aa）
Mutation：Q500L MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；5mM Tris-HCl (pH 7.6), 10mM MgCl2, 5mM GDP, 20-23% PEG8000, 0.1M Tris-Cl PH7.5-7.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.95 Å R-free 0.292
4MYT Crystal structure of elongation factor G (EFG) Deposited 2013-09-28 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–691（691 aa）
Mutation：E579A MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；5 mM Tris-HCl (pH 7.6), 10mM MgCl2, 5mM GDP, 20-23% PEG 8000, 0.1M Tris-Cl (PH 7.5-7.6), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.50 Å R-free 0.308
4MYU Crystal structure of elongation factor G mutant(EFG) Deposited 2013-09-28 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–691（691 aa）
Mutation：H573K MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；5mM Tris-HCl (pH 7.6), 10mM MgCl2, 5mM GDP, 20-23% PEG 8000, 0.1M Tris-Cl (PH 7.5-7.6), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.00 Å R-free 0.271

16 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EFG_THETH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–691； UniProt 1–691

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2bm1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bm1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bm1
Deposition date deposition_date2005-03-09
Structure title titleRibosomal elongation factor G (EF-G) Fusidic acid resistant mutant G16V
Keywords keywordsSWITCH II, ELONGATION FACTOR, GTP-BINDING, MUTATION GLY16VAL, PROTEIN BIOSYNTHESIS, TRANSLATION; ELONGATION FACTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.77 Å
Radius of gyration Rg (electron density) rg_electron30.53 Å
Forward intensity I(0) i085399300.00
Molecular weight molecular_weight73839.0 kDa
Excluded volume excluded_volume92947 ų
Envelope volume envelope_volume119530 ų
Hydration-shell volume shell_volume34492 ų
Envelope diameter envelope_diameter117.4 Å
Shell Rg shell_rg35.36 Å
Envelope Rg envelope_rg30.63 Å
Shape Rg shape_rg30.55 Å
Total Rg total_rg30.90 Å
Total atoms total_atoms5196
Residues n_residues660
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.0 Å
Rg (real space) rg_real30.99 Å
Rg uncertainty (real space) rg_real_error1.44 Å
I(0) (real space) i0_real8.5400e+07
I(0) uncertainty (real space) i0_real_error1.3870e+06
Rg (reciprocal space) rg_reciprocal30.90 Å
I(0) (reciprocal space) i0_reciprocal85390000.0000
Solution quality estimate total_estimate0.8200
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.1 Å
Skewness Skewness skewness0.612
Kurtosis Kurtosis kurtosis0.181
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16210000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.648; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.802; Smooth: 0.910
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd2bm1a1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.3 — Translation proteins
Family Family familyb.43.3.1 — Elongation factors
Domain ID domain_idd2bm1a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd2bm1a3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamilyd.14.1 — Ribosomal protein S5 domain 2-like
Family Family familyd.14.1.1 — Translational machinery components
Domain ID domain_idd2bm1a4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.11 — EF-G C-terminal domain-like
Family Family familyd.58.11.1 — EF-G/eEF-2 domains III and V
Domain ID domain_idd2bm1a5
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.11 — EF-G C-terminal domain-like
Family Family familyd.58.11.1 — EF-G/eEF-2 domains III and V

CATH v4.4 (5 domains)

Domain ID domain_id2bm1A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id2bm1A02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id2bm1A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily870 — Elongation Factor G (Translational Gtpase), domain 3
Domain ID domain_id2bm1A04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id2bm1A05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily240 —
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8. Citations (6)

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9. Files and Curves (10)