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5tky

Crystal structure of the co-translational Hsp70 chaperone Ssb in the ATP-bound, open conformation

Method: X-RAY DIFFRACTION Dmax: 134.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Putative uncharacterized protein

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

UniProt G0SCU5

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 4–624 Chain B； UniProt 4–624 Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M ammonium phosphate Resolution 2.60 Å R-free 0.264

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 5TKY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7OLC Thermophilic eukaryotic 80S ribosome at idle POST state Deposited 2021-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain C 1–614（614 aa）
Not recorded MG MAGNESIUM ION × 571 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8OO0 Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome Deposited 2023-04-04 Different construct 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 × 81 PDB declaration: 85-meric
Chain C 1–614（614 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G0SCU5_CHATD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 11–620； UniProt 4–624 Author chain B； PDBConstruct 11–620； UniProt 4–624

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 5tky

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5tky
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5tky
Deposition date deposition_date2016-10-10
Structure title titleCrystal structure of the co-translational Hsp70 chaperone Ssb in the ATP-bound, open conformation
Keywords keywordsHsp70, chaperone, ribosome, translation; CHAPERONE
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_guinier34.53 Å
Radius of gyration Rg (electron density) rg_electron34.29 Å
Forward intensity I(0) i0266570000.00
Molecular weight molecular_weight130490.0 kDa
Excluded volume excluded_volume163360 ų
Envelope volume envelope_volume214810 ų
Hydration-shell volume shell_volume52246 ų
Envelope diameter envelope_diameter147.1 Å
Shell Rg shell_rg40.54 Å
Envelope Rg envelope_rg34.77 Å
Shape Rg shape_rg34.26 Å
Total Rg total_rg34.83 Å
Total atoms total_atoms9161
Residues n_residues1188
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 dmax134.3 Å
Rg (real space) rg_real34.57 Å
Rg uncertainty (real space) rg_real_error1.47 Å
I(0) (real space) i0_real2.6660e+08
I(0) uncertainty (real space) i0_real_error4.9590e+06
Rg (reciprocal space) rg_reciprocal34.54 Å
I(0) (reciprocal space) i0_reciprocal266600000.0000
Solution quality estimate total_estimate0.8021
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.9 Å
Skewness Skewness skewness0.484
Kurtosis Kurtosis kurtosis0.150
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha68610000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.503; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.963
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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

CATH v4.4 (10 domains)

Domain ID domain_id5tkyA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5tkyA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5tkyA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
Domain ID domain_id5tkyA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Domain ID domain_id5tkyA05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5tkyB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5tkyB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5tkyB03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
Domain ID domain_id5tkyB04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology34 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Substrate Binding Domain Of DNAk; Chain A, domain 1
Domain ID domain_id5tkyB05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)