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1zn0

Coordinates of RRF and EF-G fitted into Cryo-EM map of the 50S subunit bound with both EF-G (GDPNP) and RRF

Method: ELECTRON MICROSCOPY Dmax: 136.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribosome recycling factor

OrganismNot specified

UniProt P0A805

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–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 1–185 Not recorded 16S RIBOSOMAL RNA × 1 ELONGATION FACTOR G × 1 ELECTRON MICROSCOPY cryo-EM buffer：Polymix buffer；pH 7.5；Polymix buffer cryo-EM vitrification conditions：Cryogen ETHANE；Rapid-freezing in liquid ethane Resolution 15.50 Å

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 1ZN0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EK8 CRYSTAL STRUCTURE OF THE RIBOSOME RECYCLING FACTOR (RRF) FROM ESCHERICHIA COLI Deposited 2000-03-07 Different oligomeric state 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 1–185（185 aa）
Not recorded HG MERCURY (II) ION × 3 DEM DECYLOXY-METHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；0.1 M MES-NaOH, 10 % PEG 350 MME, 12 % PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution 2.30 Å R-free 0.297
1ISE Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly Deposited 2001-11-30 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–185（185 aa）
Mutation：R132G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；50mM MES-NaOH, PEG 1500, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.297
1Y69 RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2004-12-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain 8 1–30（30 aa） Fragment：UNP residues 1-30 and 106-185
Chain 8 106–185（80 aa） Fragment：UNP residues 1-30 and 106-185
Mutation：RRF domain II deletion and GGG insertion Mutation：RRF domain II deletion and GGG insertion No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 3.33 Å R-free 0.338
1ZN1 Coordinates of RRF fitted into Cryo-EM map of the 70S post-termination complex Deposited 2005-05-11 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–185（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer Polymix buffer；pH 7.5；Polymix buffer
cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane
Resolution 14.10 Å
2RDO 50S subunit with EF-G(GDPNP) and RRF bound Deposited 2007-09-24 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain 8 1–185（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer PolyMix；pH 7.5；PolyMix
cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane by Vitrobot
Resolution 9.10 Å
4V9C Allosteric control of the ribosome by small-molecule antibiotics Deposited 2012-07-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric
Chain CY 1–185（185 aa）
Not recorded MG MAGNESIUM ION × 266 NMY NEOMYCIN × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；PEG800, MPD, pH 6.5, microbatch, temperature 291K
Resolution 3.30 Å R-free 0.255
4V9D Structures of the bacterial ribosome in classical and hybrid states of tRNA binding Deposited 2012-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric
Chain AY 2–183（182 aa）
Not recorded MG MAGNESIUM ION × 271 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K
Resolution 3.00 Å R-free 0.260
4WOI 4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2 Deposited 2014-10-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric
Chain AV 1–185（185 aa）
Not recorded MG MAGNESIUM ION × 269 PAR PAROMOMYCIN × 6 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KCl, KSCN
Resolution 3.00 Å R-free 0.253

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RRF_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–185； UniProt 1–185

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 1zn0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1zn0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1zn0
Deposition date deposition_date2005-05-11
Structure title titleCoordinates of RRF and EF-G fitted into Cryo-EM map of the 50S subunit bound with both EF-G (GDPNP) and RRF
Keywords keywordsribosome recycling factor, elongation factor G, 50S subunit, TRANSLATION-BIOSYNTHETIC PROTEIN-RNA COMPLEX; TRANSLATION/BIOSYNTHETIC PROTEIN/RNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.97 Å
Radius of gyration Rg (electron density) rg_electron39.51 Å
Forward intensity I(0) i0141079000.00
Molecular weight molecular_weight94710.0 kDa
Excluded volume excluded_volume115200 ų
Envelope volume envelope_volume114660 ų
Hydration-shell volume shell_volume27149 ų
Envelope diameter envelope_diameter133.6 Å
Shell Rg shell_rg39.98 Å
Envelope Rg envelope_rg37.65 Å
Shape Rg shape_rg39.80 Å
Total Rg total_rg39.53 Å
Total atoms total_atoms40
Residues n_residues40
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 dmax136.1 Å
Rg (real space) rg_real40.25 Å
Rg uncertainty (real space) rg_real_error1.11 Å
I(0) (real space) i0_real1.4110e+08
I(0) uncertainty (real space) i0_real_error2.3400e+06
Rg (reciprocal space) rg_reciprocal40.08 Å
I(0) (reciprocal space) i0_reciprocal141100000.0000
Solution quality estimate total_estimate0.8773
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.8 Å
Skewness Skewness skewness0.367
Kurtosis Kurtosis kurtosis-0.571
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha7226000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.835; Smooth: 0.893
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1zn0a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.67 — RRF/tRNA synthetase additional domain-like
Superfamily Superfamily superfamilyd.67.3 — Ribosome recycling factor, RRF
Family Family familyd.67.3.1 — Ribosome recycling factor, RRF
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8. Citations (3)

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9. Files and Curves (10)