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9vm8

Structure of DOCK6 octamer

Method: ELECTRON MICROSCOPY Dmax: 338.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dedicator of cytokinesis protein 6

Homo sapiens

UniProt Q96HP0

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–2047 Chain B； UniProt 1–2047 Chain C； UniProt 1–2047 Chain D； UniProt 1–2047 Chain E； UniProt 1–2047 Chain F； UniProt 1–2047 Chain G； UniProt 1–2047 Chain H； UniProt 1–2047 Not recorded No other associated polymer ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 7.53 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 9VM8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9VM2 Structure of DOCK6-Cdc42 complex protomer Deposited 2025-06-27 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–2047（2047 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.94 Å
9VM3 Structure of DOCK6-Cdc42 complex Deposited 2025-06-27 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2047（2047 aa）
Chain C 1–2047（2047 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.52 Å
9VM4 Structure of DOCK6-Rac1 complex protomer Deposited 2025-06-27 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–2047（2047 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.20 Å
9VM5 Structure of DOCK6-Rac1 complex Deposited 2025-06-27 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2047（2047 aa）
Chain C 1–2047（2047 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 5.32 Å
9VM6 Structure of DOCK6 tetramer Deposited 2025-06-27 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–2047（2047 aa）
Chain B 1–2047（2047 aa）
Chain C 1–2047（2047 aa）
Chain D 1–2047（2047 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.27 Å
9VM7 Structure of DOCK6 tetramer complexed with Rac1 Deposited 2025-06-27 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–2047（2047 aa）
Chain C 1–2047（2047 aa）
Chain E 1–2047（2047 aa）
Chain G 1–2047（2047 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 6.85 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DOCK6_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–2053； UniProt 1–2047 Author chain B； PDBConstruct 7–2053； UniProt 1–2047 Author chain C； PDBConstruct 7–2053； UniProt 1–2047 Author chain D； PDBConstruct 7–2053； UniProt 1–2047 Author chain E； PDBConstruct 7–2053； UniProt 1–2047 Author chain F； PDBConstruct 7–2053； UniProt 1–2047 Author chain G； PDBConstruct 7–2053； UniProt 1–2047 Author chain H； PDBConstruct 7–2053； UniProt 1–2047

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 9vm8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9vm8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9vm8
Deposition date deposition_date2025-06-27
Structure title titleStructure of DOCK6 octamer
Keywords keywordsDOCK, GEF, Rho, small GTPase, Rac, Cdc42, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier— Å
Radius of gyration Rg (electron density) rg_electron113.80 Å
Forward intensity I(0) i030820100000.00
Molecular weight molecular_weight1526300.0 kDa
Excluded volume excluded_volume1921200 ų
Envelope volume envelope_volume3604100 ų
Hydration-shell volume shell_volume286350 ų
Envelope diameter envelope_diameter397.2 Å
Shell Rg shell_rg89.35 Å
Envelope Rg envelope_rg110.60 Å
Shape Rg shape_rg113.80 Å
Total Rg total_rg113.70 Å
Total atoms total_atoms107608
Residues n_residues13488
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 dmax338.4 Å
Rg (real space) rg_real109.10 Å
Rg uncertainty (real space) rg_real_error1.90 Å
I(0) (real space) i0_real2.9980e+10
I(0) uncertainty (real space) i0_real_error6.8560e+08
Rg (reciprocal space) rg_reciprocal100.20 Å
I(0) (reciprocal space) i0_reciprocal29630000000.0000
Solution quality estimate total_estimate0.8591
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary96.7 Å
Skewness Skewness skewness0.569
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.0700 Å−1
Current regularization parameter α current_alpha0.7444
Highest regularization parameter α highest_alpha14050000000.0000
Real-space data points n_real_points15
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.001; Oscil: 0.752; Stabil: 0.958; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.046
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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)