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4a0v

model refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP

Method: ELECTRON MICROSCOPY Dmax: 193.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

T-COMPLEX PROTEIN 1 SUBUNIT BETA

OrganismNot specified

UniProt Q3ZBH0

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 × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain A； UniProt 14–526 Chain B； UniProt 14–526 Chain C； UniProt 14–526 Chain D； UniProt 14–526 Chain E； UniProt 14–526 Chain F； UniProt 14–526 Chain G； UniProt 14–526 Chain H； UniProt 14–526 Chain I； UniProt 14–526 Chain J； UniProt 14–526 Chain K； UniProt 14–526 Chain L； UniProt 14–526 Chain M； UniProt 14–526 Chain N； UniProt 14–526 Chain O； UniProt 14–526 Chain P； UniProt 14–526 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE Resolution 10.70 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 4A0V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3IYG Ca model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map Deposited 2009-11-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 14–526（513 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions two-side blotting for 1 second before plunging；101 K；Cryogen ETHANE；vitrification using ethane as cryogen
Resolution 4.00 Å
3KTT Atomic model of bovine TRiC CCT2(beta) subunit derived from a 4.0 Angstrom cryo-EM map Deposited 2009-11-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 14–526（513 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；vitrification using ethane as cryogen
Resolution 4.00 Å
4A0O Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state Deposited 2011-09-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric
Chain A 14–526（513 aa） Fragment：RESIDUES 14-526
Chain B 14–526（513 aa） Fragment：RESIDUES 14-526
Chain C 14–526（513 aa） Fragment：RESIDUES 14-526
Chain D 14–526（513 aa） Fragment：RESIDUES 14-526
Chain E 14–526（513 aa） Fragment：RESIDUES 14-526
Chain F 14–526（513 aa） Fragment：RESIDUES 14-526
Chain G 14–526（513 aa） Fragment：RESIDUES 14-526
Chain H 14–526（513 aa） Fragment：RESIDUES 14-526
Chain I 14–526（513 aa） Fragment：RESIDUES 14-526
Chain J 14–526（513 aa） Fragment：RESIDUES 14-526
Chain K 14–526（513 aa） Fragment：RESIDUES 14-526
Chain L 14–526（513 aa） Fragment：RESIDUES 14-526
Chain M 14–526（513 aa） Fragment：RESIDUES 14-526
Chain N 14–526（513 aa） Fragment：RESIDUES 14-526
Chain O 14–526（513 aa） Fragment：RESIDUES 14-526
Chain P 14–526（513 aa） Fragment：RESIDUES 14-526
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHEN
Resolution 10.50 Å
4A0W model built against symmetry-free cryo-EM map of TRiC-ADP-AlFx Deposited 2011-09-13 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric
Chain A 14–526（513 aa）
Chain B 14–526（513 aa）
Chain C 14–526（513 aa）
Chain D 14–526（513 aa）
Chain E 14–526（513 aa）
Chain F 14–526（513 aa）
Chain G 14–526（513 aa）
Chain H 14–526（513 aa）
Chain I 14–526（513 aa）
Chain J 14–526（513 aa）
Chain K 14–526（513 aa）
Chain L 14–526（513 aa）
Chain M 14–526（513 aa）
Chain N 14–526（513 aa）
Chain O 14–526（513 aa）
Chain P 14–526（513 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 13.90 Å
4A13 model refined against symmetry-free cryo-EM map of TRiC-ADP Deposited 2011-09-13 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric
Chain A 14–526（513 aa）
Chain B 14–526（513 aa）
Chain C 14–526（513 aa）
Chain D 14–526（513 aa）
Chain E 14–526（513 aa）
Chain F 14–526（513 aa）
Chain G 14–526（513 aa）
Chain H 14–526（513 aa）
Chain I 14–526（513 aa）
Chain J 14–526（513 aa）
Chain K 14–526（513 aa）
Chain L 14–526（513 aa）
Chain M 14–526（513 aa）
Chain N 14–526（513 aa）
Chain O 14–526（513 aa）
Chain P 14–526（513 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.30 Å
4B2T The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning Deposited 2012-07-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain B 1–535（535 aa）
Chain b 1–535（535 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 5.50 Å R-free 0.399
9FQR 96-nm repeat of axonemal doublet microtubules from bovine sperm Deposited 2024-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 1574 PDB declaration: 1574-meric
Chain Im 1–535（535 aa）
Chain In 1–535（535 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 342 MG MAGNESIUM ION × 345 GDP GUANOSINE-5'-DIPHOSPHATE × 345 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.00 Å
9KCF Bovine Flagellar TRiC Deposited 2024-11-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain B 1–535（535 aa）
Chain J 1–535（535 aa）
Not recorded MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

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

View Construct and Data Evidence
UniProt name TCPB_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–513； UniProt 14–526 Author chain B； PDBConstruct 1–513； UniProt 14–526 Author chain C； PDBConstruct 1–513； UniProt 14–526 Author chain D； PDBConstruct 1–513； UniProt 14–526 Author chain E； PDBConstruct 1–513； UniProt 14–526 Author chain F； PDBConstruct 1–513； UniProt 14–526 Author chain G； PDBConstruct 1–513； UniProt 14–526 Author chain H； PDBConstruct 1–513； UniProt 14–526 Author chain I； PDBConstruct 1–513； UniProt 14–526 Author chain J； PDBConstruct 1–513； UniProt 14–526 Author chain K； PDBConstruct 1–513； UniProt 14–526 Author chain L； PDBConstruct 1–513； UniProt 14–526 Author chain M； PDBConstruct 1–513； UniProt 14–526 Author chain N； PDBConstruct 1–513； UniProt 14–526 Author chain O； PDBConstruct 1–513； UniProt 14–526 Author chain P； PDBConstruct 1–513； UniProt 14–526

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 4a0v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4a0v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4a0v
Deposition date deposition_date2011-09-13
Structure title titlemodel refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP
Keywords keywordsCHAPERONE, CHAPERONIN, PROTEIN FOLDING; CHAPERONE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier72.38 Å
Radius of gyration Rg (electron density) rg_electron71.82 Å
Forward intensity I(0) i010118700000.00
Molecular weight molecular_weight852310.0 kDa
Excluded volume excluded_volume1068900 ų
Envelope volume envelope_volume2038300 ų
Hydration-shell volume shell_volume226970 ų
Envelope diameter envelope_diameter206.6 Å
Shell Rg shell_rg84.13 Å
Envelope Rg envelope_rg66.30 Å
Shape Rg shape_rg71.83 Å
Total Rg total_rg71.95 Å
Total atoms total_atoms59707
Residues n_residues7959
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 dmax193.9 Å
Rg (real space) rg_real71.89 Å
Rg uncertainty (real space) rg_real_error0.60 Å
I(0) (real space) i0_real1.0120e+10
I(0) uncertainty (real space) i0_real_error1.6510e+08
Rg (reciprocal space) rg_reciprocal73.99 Å
I(0) (reciprocal space) i0_reciprocal10160000000.0000
Solution quality estimate total_estimate0.5978
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary114.6 Å
Skewness Skewness skewness-0.213
Kurtosis Kurtosis kurtosis-0.600
Angular range angular_range— – 0.1100 Å−1
Current regularization parameter α current_alpha0.0004
Highest regularization parameter α highest_alpha2510000000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 0.006; Positv: 1.000; Valcen: 0.946; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)