8CIA | pdb_00008cia

Crystal structure of the kelch domain of human KLHL20

PDB DOI: https://doi.org/10.2210/pdb8CIA/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-02-09 Released: 2023-03-22
Deposition Author(s): Sweeney, M.N., Bradshaw, W.J., Chen, Z., Bullock, A.N.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.72 Å
R-Value Free:
0.287 (Depositor), 0.286 (DCC)
R-Value Work:
0.226 (Depositor), 0.228 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the kelch domain of human KLHL20

Sweeney, M.N., Bradshaw, W.J., Chen, Z., Bullock, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 166.61 kDa
Atom Count: 10,843
Modeled Residue Count: 1,429
Deposited Residue Count: 1,535
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like protein 20	A, C, D	307	Homo sapiens	Mutation(s): 5 Gene Names: KLHL20, KLEIP, KLHLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2M5 (Homo sapiens) Explore Q9Y2M5 Go to UniProtKB: Q9Y2M5
PHAROS: Q9Y2M5 GTEx: ENSG00000076321
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2M5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch like family member 20	B	307	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2M5 (Homo sapiens) Explore Q9Y2M5 Go to UniProtKB: Q9Y2M5
PHAROS: Q9Y2M5 GTEx: ENSG00000076321
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2M5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch like family member 20	E	307	Homo sapiens	Mutation(s): 0 Gene Names: KLHL20
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2M5 (Homo sapiens) Explore Q9Y2M5 Go to UniProtKB: Q9Y2M5
PHAROS: Q9Y2M5 GTEx: ENSG00000076321
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2M5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.72 Å
R-Value Free: 0.287 (Depositor), 0.286 (DCC)
R-Value Work: 0.226 (Depositor), 0.228 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.928	α = 90
b = 152.928	β = 90
c = 195.819	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.