9umt

TRiC_HDAC1_close_state

Method: ELECTRON MICROSCOPY Dmax: 165.7 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

T-complex protein 1 subunit alpha

Homo sapiens

UniProt P17987

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain F; UniProt 4–535 Not recorded T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit zeta × 1 (P40227) T-complex protein 1 subunit eta × 1 (Q53HV2) T-complex protein 1 subunit theta × 1 (P50990) ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 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.

64 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain F; PDBConstruct 1–532; UniProt 4–535

T-complex protein 1 subunit beta

Homo sapiens

UniProt P78371

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 2–527 Not recorded T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit zeta × 1 (P40227) T-complex protein 1 subunit eta × 1 (Q53HV2) T-complex protein 1 subunit theta × 1 (P50990) ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 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.

64 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPB_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–526; UniProt 2–527

T-complex protein 1 subunit gamma

Homo sapiens

UniProt P49368

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain C; UniProt 5–529 Not recorded T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit zeta × 1 (P40227) T-complex protein 1 subunit eta × 1 (Q53HV2) T-complex protein 1 subunit theta × 1 (P50990) ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 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.

65 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPG_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–525; UniProt 5–529

T-complex protein 1 subunit delta

Homo sapiens

UniProt P50991

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 23–539 Not recorded T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit zeta × 1 (P40227) T-complex protein 1 subunit eta × 1 (Q53HV2) T-complex protein 1 subunit theta × 1 (P50990) ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 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.

65 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPD_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain B; PDBConstruct 1–517; UniProt 23–539

T-complex protein 1 subunit epsilon

Homo sapiens

UniProt P48643

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain G; UniProt 7–537 Not recorded T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit zeta × 1 (P40227) T-complex protein 1 subunit eta × 1 (Q53HV2) T-complex protein 1 subunit theta × 1 (P50990) ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 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.

68 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPE_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain G; PDBConstruct 1–531; UniProt 7–537

T-complex protein 1 subunit zeta

Homo sapiens

UniProt P40227

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain H; UniProt 2–526 Not recorded T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit eta × 1 (Q53HV2) T-complex protein 1 subunit theta × 1 (P50990) ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 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.

64 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPZ_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain H; PDBConstruct 1–525; UniProt 2–526

T-complex protein 1 subunit eta

Homo sapiens

UniProt Q53HV2

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain D; UniProt 3–525 Not recorded T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit zeta × 1 (P40227) T-complex protein 1 subunit theta × 1 (P50990) ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q53HV2_HUMAN
Isoform
PDB entities 7
Chains and sequence ranges Author chain D; PDBConstruct 1–523; UniProt 3–525

T-complex protein 1 subunit theta

Homo sapiens

UniProt P50990

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain E; UniProt 2–530 Not recorded T-complex protein 1 subunit alpha × 1 (P17987) T-complex protein 1 subunit beta × 1 (P78371) T-complex protein 1 subunit gamma × 1 (P49368) T-complex protein 1 subunit delta × 1 (P50991) T-complex protein 1 subunit epsilon × 1 (P48643) T-complex protein 1 subunit zeta × 1 (P40227) T-complex protein 1 subunit eta × 1 (Q53HV2) ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 AF3 ALUMINUM FLUORIDE × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 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.

64 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TCPQ_HUMAN
Isoform
PDB entities 8
Chains and sequence ranges Author chain E; PDBConstruct 1–529; UniProt 2–530

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 9umt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9umt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9umt
Deposition date deposition_date2025-04-23
Structure title titleTRiC_HDAC1_close_state
Keywords keywordsTRiC complex, CHAPERONE; CHAPERONE
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier57.44
Radius of gyration Rg (electron density) rg_electron56.69
Forward intensity I(0) i03069610000.00
Molecular weight molecular_weight463650.0 kDa
Excluded volume excluded_volume580870 ų
Envelope volume envelope_volume913620 ų
Hydration-shell volume shell_volume132080 ų
Envelope diameter envelope_diameter170.5
Shell Rg shell_rg65.01
Envelope Rg envelope_rg52.46
Shape Rg shape_rg56.71
Total Rg total_rg56.84
Total atoms total_atoms32403
Residues n_residues4208
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax165.7
Rg (real space) rg_real57.03
Rg uncertainty (real space) rg_real_error1.14
I(0) (real space) i0_real3.0700e+09
I(0) uncertainty (real space) i0_real_error5.5240e+07
Rg (reciprocal space) rg_reciprocal57.76
I(0) (reciprocal space) i0_reciprocal3073000000.0000
Solution quality estimate total_estimate0.6185
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary85.9
Skewness Skewness skewness-0.094
Kurtosis Kurtosis kurtosis-0.713
Angular range angular_range— – 0.1350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha167000000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 0.009; Positv: 1.000; Valcen: 0.965; Smooth: 0.145

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

8. Citations (1)

9. Files and Curves (10)