6m8s

Crystal structure of the KCTD12 H1 domain in complex with Gbeta1gamma2 subunits

Method: X-RAY DIFFRACTION Dmax: 121.5 Å Quality: GOOD

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

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain C; UniProt 2–340 Chain D; UniProt 2–340 Chain G; UniProt 2–340 Chain H; UniProt 2–340 Chain K; UniProt 2–340 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 5 (P59768) BTB/POZ domain-containing protein KCTD12 × 5 (Q96CX2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M sodium chloride, 0.1 M sodium cacodylate, 8% w/v PEG8000 Resolution 3.71 Å R-free 0.287

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 1
Chains and sequence ranges Author chain C; PDBConstruct 12–350; UniProt 2–340 Author chain D; PDBConstruct 12–350; UniProt 2–340 Author chain G; PDBConstruct 12–350; UniProt 2–340 Author chain H; PDBConstruct 12–350; UniProt 2–340 Author chain K; PDBConstruct 12–350; UniProt 2–340

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain E; UniProt 1–71 Chain F; UniProt 1–71 Chain I; UniProt 1–71 Chain J; UniProt 1–71 Chain L; UniProt 1–71 Not recorded Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 5 (P62873) BTB/POZ domain-containing protein KCTD12 × 5 (Q96CX2) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M sodium chloride, 0.1 M sodium cacodylate, 8% w/v PEG8000 Resolution 3.71 Å R-free 0.287

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 2
Chains and sequence ranges Author chain E; PDBConstruct 1–71; UniProt 1–71 Author chain F; PDBConstruct 1–71; UniProt 1–71 Author chain I; PDBConstruct 1–71; UniProt 1–71 Author chain J; PDBConstruct 1–71; UniProt 1–71 Author chain L; PDBConstruct 1–71; UniProt 1–71

BTB/POZ domain-containing protein KCTD12

Homo sapiens

UniProt Q96CX2

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain A; UniProt 200–325 Chain B; UniProt 200–325 Chain M; UniProt 200–325 Chain O; UniProt 200–325 Chain P; UniProt 200–325 Fragment:UNP residues 200-325 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) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M sodium chloride, 0.1 M sodium cacodylate, 8% w/v PEG8000 Resolution 3.71 Å R-free 0.287

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCD12_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 4–129; UniProt 200–325 Author chain B; PDBConstruct 4–129; UniProt 200–325 Author chain M; PDBConstruct 4–129; UniProt 200–325 Author chain O; PDBConstruct 4–129; UniProt 200–325 Author chain P; PDBConstruct 4–129; UniProt 200–325

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 6m8s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6m8s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6m8s
Deposition date deposition_date2018-08-22
Structure title titleCrystal structure of the KCTD12 H1 domain in complex with Gbeta1gamma2 subunits
Keywords keywordsbeta-propeller, homopentamer, GABAB desensitization, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.08
Radius of gyration Rg (electron density) rg_electron41.48
Forward intensity I(0) i01164960000.00
Molecular weight molecular_weight270770.0 kDa
Excluded volume excluded_volume333920 ų
Envelope volume envelope_volume449720 ų
Hydration-shell volume shell_volume84340 ų
Envelope diameter envelope_diameter123.7
Shell Rg shell_rg51.27
Envelope Rg envelope_rg40.88
Shape Rg shape_rg41.45
Total Rg total_rg41.98
Total atoms total_atoms18981
Residues n_residues2458
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 dmax121.5
Rg (real space) rg_real41.85
Rg uncertainty (real space) rg_real_error0.54
I(0) (real space) i0_real1.1650e+09
I(0) uncertainty (real space) i0_real_error1.5840e+07
Rg (reciprocal space) rg_reciprocal42.08
I(0) (reciprocal space) i0_reciprocal1165000000.0000
Solution quality estimate total_estimate0.8609
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary54.3
Skewness Skewness skewness0.082
Kurtosis Kurtosis kurtosis-0.648
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha336100000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.988; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.235

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id6m8sC00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6m8sD00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6m8sE00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily10 — Transducin (heterotrimeric G protein), gamma chain
Domain ID domain_id6m8sF00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily10 — Transducin (heterotrimeric G protein), gamma chain
Domain ID domain_id6m8sG00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6m8sH00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6m8sI00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily10 — Transducin (heterotrimeric G protein), gamma chain
Domain ID domain_id6m8sJ00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily10 — Transducin (heterotrimeric G protein), gamma chain
Domain ID domain_id6m8sK00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6m8sL00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily10 — Transducin (heterotrimeric G protein), gamma chain

8. Citations (1)

9. Files and Curves (10)