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3drz

X-ray crystal structure of the N-terminal BTB domain of human KCTD5 protein

Method: X-RAY DIFFRACTION Dmax: 69.9 Å Quality: GOOD
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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 homooligomer Homooligomer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 40–145 Chain B； UniProt 40–145 Chain C； UniProt 40–145 Chain D； UniProt 40–145 Chain E； UniProt 40–145 Fragment：N-terminal domain, UNP residues 40-145 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；298 K；24% (w/v) PEG 3350, 100 mM MgCl2, 100 M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 298K Resolution 1.90 Å R-free 0.232

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 3DRZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3DRX X-ray crystal structure of human KCTD5 protein crystallized in high-salt buffer Deposited 2008-07-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 34–234（201 aa） Fragment：UNP residues 34-234
Chain B 34–234（201 aa） Fragment：UNP residues 34-234
Chain C 34–234（201 aa） Fragment：UNP residues 34-234
Chain D 34–234（201 aa） Fragment：UNP residues 34-234
Chain E 34–234（201 aa） Fragment：UNP residues 34-234
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；3.2 M NaCl, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 298K
Resolution 3.11 Å R-free 0.275
3DRY X-ray crystal structure of human KCTD5 protein crystallized in low-salt buffer Deposited 2008-07-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 34–234（201 aa） Fragment：UNP residues 34-234
Chain B 34–234（201 aa） Fragment：UNP residues 34-234
Chain C 34–234（201 aa） Fragment：UNP residues 34-234
Chain D 34–234（201 aa） Fragment：UNP residues 34-234
Chain E 34–234（201 aa） Fragment：UNP residues 34-234
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；0.2 M proline, 100 mM HEPES, 7% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION
Resolution 3.30 Å R-free 0.308
8U7Z KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(CTD)/Gbeta1gamma2 Deposited 2023-09-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain K1 1–234（234 aa）
Chain K2 1–234（234 aa）
Chain K3 1–234（234 aa）
Chain K4 1–234（234 aa）
Chain K5 1–234（234 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
8U80 KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(BTB)/Cullin3(NTD) Deposited 2023-09-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain K1 1–234（234 aa）
Chain K2 1–234（234 aa）
Chain K3 1–234（234 aa）
Chain K4 1–234（234 aa）
Chain K5 1–234（234 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8U81 KCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION Multi-body Refinement Map Deposited 2023-09-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain K1 1–233（233 aa）
Chain K2 1–233（233 aa）
Chain K3 1–233（233 aa）
Chain K4 1–233（233 aa）
Chain K5 1–233（233 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
8U82 KCTD5/Cullin3/Gbeta1gamma2 Complex: State B From Composite RELION Multi-body Refinement Map Deposited 2023-09-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain K1 1–234（234 aa）
Chain K2 1–234（234 aa）
Chain K3 1–234（234 aa）
Chain K4 1–234（234 aa）
Chain K5 1–234（234 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å
8U83 KCTD5/Cullin3/Gbeta1gamma2 Complex: State C From Composite RELION Multi-body Refinement Map Deposited 2023-09-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain K1 1–234（234 aa）
Chain K2 1–234（234 aa）
Chain K3 1–234（234 aa）
Chain K4 1–234（234 aa）
Chain K5 1–234（234 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.98 Å
8U84 KCTD5/Cullin3/Gbeta1gamma2 Complex: State D From Composite RELION Multi-body Refinement Map Deposited 2023-09-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain K1 1–234（234 aa）
Chain K2 1–234（234 aa）
Chain K3 1–234（234 aa）
Chain K4 1–234（234 aa）
Chain K5 1–234（234 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.88 Å

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 A； PDBConstruct 2–107； UniProt 40–145 Author chain B； PDBConstruct 2–107； UniProt 40–145 Author chain C； PDBConstruct 2–107； UniProt 40–145 Author chain D； PDBConstruct 2–107； UniProt 40–145 Author chain E； PDBConstruct 2–107； UniProt 40–145

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 3drz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3drz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3drz
Deposition date deposition_date2008-07-11
Structure title titleX-ray crystal structure of the N-terminal BTB domain of human KCTD5 protein
Keywords keywordsKCTD5, BTB/POZ, potassium channel domain T1, PENTAMER, UNKNOWN FUNCTION; UNKNOWN FUNCTION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.30 Å
Radius of gyration Rg (electron density) rg_electron23.04 Å
Forward intensity I(0) i051988800.00
Molecular weight molecular_weight57591.0 kDa
Excluded volume excluded_volume72785 ų
Envelope volume envelope_volume86457 ų
Hydration-shell volume shell_volume30380 ų
Envelope diameter envelope_diameter72.0 Å
Shell Rg shell_rg30.82 Å
Envelope Rg envelope_rg22.74 Å
Shape Rg shape_rg22.99 Å
Total Rg total_rg24.10 Å
Total atoms total_atoms4066
Residues n_residues494
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 dmax69.9 Å
Rg (real space) rg_real24.07 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real5.1990e+07
I(0) uncertainty (real space) i0_real_error6.3350e+05
Rg (reciprocal space) rg_reciprocal24.13 Å
I(0) (reciprocal space) i0_reciprocal51990000.0000
Solution quality estimate total_estimate0.8924
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.5 Å
Skewness Skewness skewness0.008
Kurtosis Kurtosis kurtosis-0.557
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16950000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.819
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd3drza_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.0 — automated matches
Domain ID domain_idd3drzb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.0 — automated matches
Domain ID domain_idd3drzc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.0 — automated matches
Domain ID domain_idd3drzd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.0 — automated matches
Domain ID domain_idd3drze_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.42 — POZ domain
Superfamily Superfamily superfamilyd.42.1 — POZ domain
Family Family familyd.42.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id3drzA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id3drzB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id3drzC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id3drzD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id3drzE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
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8. Citations (1)

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9. Files and Curves (10)