8EEC | pdb_00008eec

Crystal structure of HPK1 citron-homology domain

• PDB DOI: https://doi.org/10.2210/pdb8EEC/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-09-06 Released: 2024-03-27 
• Deposition Author(s): Wu, P., Lehoux, I., Wang, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

HPK1 citron homology domain regulates phosphorylation of SLP76 and modulates kinase domain interaction dynamics

Chitre, A.S., Wu, P., Walters, B.T., Wang, X., Bouyssou, A., Du, X., Lehoux, I., Fong, R., Arata, A., Chan, J., Wang, D., Franke, Y., Grogan, J.L., Mellman, I., Comps-Agrar, L., Wang, W.

(2024) Nat Commun 15: 3725

• DOI: https://doi.org/10.1038/s41467-024-48014-9

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.97 kDa 
• Atom Count: 2,553 
• Modeled Residue Count: 317 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Mitogen-activated protein kinase kinase kinase kinase 1	A	343	Homo sapiens	Mutation(s): 0  Gene Names: MAP4K1, HPK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92918 (Homo sapiens) Explore Q92918  Go to UniProtKB:  Q92918
PHAROS:  Q92918 GTEx:  ENSG00000104814

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.667	α = 90
b = 81.667	β = 90
c = 140.535	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Wu, P., Lehoux, I., Wang, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Database references, Structure summary