8u81

KCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION Multi-body Refinement Map

Method: ELECTRON MICROSCOPY Dmax: 210.3 Å Quality: GOOD

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

BTB/POZ domain-containing protein KCTD5

Homo sapiens

UniProt Q9NXV2

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 × 20 PDB declaration: eicosameric(20) Consistent with protein copy count Chain K1; UniProt 1–233 Chain K2; UniProt 1–233 Chain K3; UniProt 1–233 Chain K4; UniProt 1–233 Chain K5; UniProt 1–233 Not recorded Cullin-3 × 5 (Q13618) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 5 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 5 (P59768) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 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.

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

View Construct and Data Evidence
UniProt name KCTD5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain K1; PDBConstruct 1–233; UniProt 1–233 Author chain K2; PDBConstruct 1–233; UniProt 1–233 Author chain K3; PDBConstruct 1–233; UniProt 1–233 Author chain K4; PDBConstruct 1–233; UniProt 1–233 Author chain K5; PDBConstruct 1–233; UniProt 1–233

Cullin-3

Homo sapiens

UniProt Q13618

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 × 20 PDB declaration: eicosameric(20) Consistent with protein copy count Chain C1; UniProt 1–381 Chain C2; UniProt 1–381 Chain C3; UniProt 1–381 Chain C4; UniProt 1–381 Chain C5; UniProt 1–381 Not recorded BTB/POZ domain-containing protein KCTD5 × 5 (Q9NXV2) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 5 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 5 (P59768) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 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.

29 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CUL3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C1; PDBConstruct 1–381; UniProt 1–381 Author chain C2; PDBConstruct 1–381; UniProt 1–381 Author chain C3; PDBConstruct 1–381; UniProt 1–381 Author chain C4; PDBConstruct 1–381; UniProt 1–381 Author chain C5; PDBConstruct 1–381; UniProt 1–381

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Homo sapiens

UniProt P62873

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 × 20 PDB declaration: eicosameric(20) Consistent with protein copy count Chain B1; UniProt 1–340 Chain B2; UniProt 1–340 Chain B3; UniProt 1–340 Chain B4; UniProt 1–340 Chain B5; UniProt 1–340 Not recorded BTB/POZ domain-containing protein KCTD5 × 5 (Q9NXV2) Cullin-3 × 5 (Q13618) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 5 (P59768) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 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.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain B1; PDBConstruct 1–340; UniProt 1–340 Author chain B2; PDBConstruct 1–340; UniProt 1–340 Author chain B3; PDBConstruct 1–340; UniProt 1–340 Author chain B4; PDBConstruct 1–340; UniProt 1–340 Author chain B5; PDBConstruct 1–340; UniProt 1–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Homo sapiens

UniProt P59768

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 × 20 PDB declaration: eicosameric(20) Consistent with protein copy count Chain G1; UniProt 1–71 Chain G2; UniProt 1–71 Chain G3; UniProt 1–71 Chain G4; UniProt 1–71 Chain G5; UniProt 1–71 Mutation:C68S BTB/POZ domain-containing protein KCTD5 × 5 (Q9NXV2) Cullin-3 × 5 (Q13618) Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 5 (P62873) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.82 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.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain G1; PDBConstruct 1–71; UniProt 1–71 Author chain G2; PDBConstruct 1–71; UniProt 1–71 Author chain G3; PDBConstruct 1–71; UniProt 1–71 Author chain G4; PDBConstruct 1–71; UniProt 1–71 Author chain G5; PDBConstruct 1–71; UniProt 1–71

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 8u81

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8u81
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8u81
Deposition date deposition_date2023-09-15
Structure title titleKCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION Multi-body Refinement Map
Keywords keywords;cullin family protein, proteasome-mediated ubiquitin-dependent protein catabolic process, complex, ubiquitin-dependent protein catabolic process, LIGASE ;; LIGASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier62.76
Radius of gyration Rg (electron density) rg_electron62.72
Forward intensity I(0) i04383770000.00
Molecular weight molecular_weight540720.0 kDa
Excluded volume excluded_volume670060 ų
Envelope volume envelope_volume1024600 ų
Hydration-shell volume shell_volume137100 ų
Envelope diameter envelope_diameter246.6
Shell Rg shell_rg63.11
Envelope Rg envelope_rg63.10
Shape Rg shape_rg62.69
Total Rg total_rg62.83
Total atoms total_atoms37890
Residues n_residues4770
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 dmax210.3
Rg (real space) rg_real62.71
Rg uncertainty (real space) rg_real_error1.61
I(0) (real space) i0_real4.3830e+09
I(0) uncertainty (real space) i0_real_error8.8920e+07
Rg (reciprocal space) rg_reciprocal62.75
I(0) (reciprocal space) i0_reciprocal4384000000.0000
Solution quality estimate total_estimate0.8451
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary75.7
Skewness Skewness skewness0.398
Kurtosis Kurtosis kurtosis-0.038
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0014
Highest regularization parameter α highest_alpha197100000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.714

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (3)

9. Files and Curves (10)