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3dry

X-ray crystal structure of human KCTD5 protein crystallized in low-salt buffer

Method: X-RAY DIFFRACTION Dmax: 117.9 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 34–234 Chain B； UniProt 34–234 Chain C； UniProt 34–234 Chain D； UniProt 34–234 Chain E； UniProt 34–234 Fragment：UNP residues 34-234 No other associated polymer 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

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 3DRY 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 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
3DRZ X-ray crystal structure of the N-terminal BTB domain of human KCTD5 protein 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 40–145（106 aa） Fragment：N-terminal domain, UNP residues 40-145
Chain B 40–145（106 aa） Fragment：N-terminal domain, UNP residues 40-145
Chain C 40–145（106 aa） Fragment：N-terminal domain, UNP residues 40-145
Chain D 40–145（106 aa） Fragment：N-terminal domain, UNP residues 40-145
Chain E 40–145（106 aa） Fragment：N-terminal domain, UNP residues 40-145
Not recorded No recorded non-water small molecule 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
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 2–202； UniProt 34–234 Author chain B； PDBConstruct 2–202； UniProt 34–234 Author chain C； PDBConstruct 2–202； UniProt 34–234 Author chain D； PDBConstruct 2–202； UniProt 34–234 Author chain E； PDBConstruct 2–202； UniProt 34–234

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 3dry

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3dry
Deposition date deposition_date2008-07-11
Structure title titleX-ray crystal structure of human KCTD5 protein crystallized in low-salt buffer
Keywords keywordsKCTD5, BTB/POZ, Golgi, GRASP55, potassium channel DOMAIN T1, PENTAMERIC ASSEMBLY, Host-virus interaction, Nucleus, 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_guinier36.29 Å
Radius of gyration Rg (electron density) rg_electron35.50 Å
Forward intensity I(0) i0146895000.00
Molecular weight molecular_weight96794.0 kDa
Excluded volume excluded_volume121160 ų
Envelope volume envelope_volume170450 ų
Hydration-shell volume shell_volume41854 ų
Envelope diameter envelope_diameter127.9 Å
Shell Rg shell_rg40.02 Å
Envelope Rg envelope_rg35.11 Å
Shape Rg shape_rg35.48 Å
Total Rg total_rg35.92 Å
Total atoms total_atoms6810
Residues n_residues844
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 dmax117.9 Å
Rg (real space) rg_real36.45 Å
Rg uncertainty (real space) rg_real_error0.93 Å
I(0) (real space) i0_real1.4690e+08
I(0) uncertainty (real space) i0_real_error2.3590e+06
Rg (reciprocal space) rg_reciprocal36.35 Å
I(0) (reciprocal space) i0_reciprocal146900000.0000
Solution quality estimate total_estimate0.8660
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.9 Å
Skewness Skewness skewness0.409
Kurtosis Kurtosis kurtosis-0.573
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30870000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.819
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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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7. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id3dryA01
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_id3dryA02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily750 —
Domain ID domain_id3dryA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2000 —
Domain ID domain_id3dryB01
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_id3dryB02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily750 —
Domain ID domain_id3dryB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2000 —
Domain ID domain_id3dryC01
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_id3dryC02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily750 —
Domain ID domain_id3dryC03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2000 —
Domain ID domain_id3dryD01
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_id3dryD02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily750 —
Domain ID domain_id3dryD03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2000 —
Domain ID domain_id3dryE01
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_id3dryE02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily750 —
Domain ID domain_id3dryE03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2000 —
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8. Citations (1)

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9. Files and Curves (10)