8RBH | pdb_00008rbh

Crystal structure of the kelch domain of human KLHL12 in complex with PEF1 peptide

• PDB DOI: https://doi.org/10.2210/pdb8RBH/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-04 Released: 2024-12-11 
• Deposition Author(s): Ramdass, A.E., Chen, Z., Dalietou, E.V., Manning, C.E., Bullock, A.N.
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structural basis for co-adaptor and antagonist binding to the KLHL12 E3 ligase

Ramdass, A.E., Dalietou, E.V., Chen, Z., Platt, M., Aitmakhanova, K., Fedorov, O., Bullock, A.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: fluorescence resonance energy transfer

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: fluorescence resonance energy transfer

Macromolecule Content 

• Total Structure Weight: 67.97 kDa 
• Atom Count: 4,797 
• Modeled Residue Count: 591 
• Deposited Residue Count: 624 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like protein 12	A, B	301	Homo sapiens	Mutation(s): 0  Gene Names: KLHL12, C3IP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q53G59 (Homo sapiens) Explore Q53G59  Go to UniProtKB:  Q53G59
PHAROS:  Q53G59 GTEx:  ENSG00000117153

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peflin	C, D	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBV8 (Homo sapiens) Explore Q9UBV8  Go to UniProtKB:  Q9UBV8
PHAROS:  Q9UBV8 GTEx:  ENSG00000162517

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	F [auth A], G [auth B], H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.001	α = 90
b = 78.39	β = 99.24
c = 73.784	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Ramdass, A.E., Chen, Z., Dalietou, E.V., Manning, C.E., Bullock, A.N.

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative		875510

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release