7YGY | pdb_00007ygy

Crystal structure of the Zn2+-bound EFhd2/Swiprosin-1

• PDB DOI: https://doi.org/10.2210/pdb7YGY/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-12 Released: 2023-03-15 
• Deposition Author(s): Mun, S.A., Park, J., Kang, J.Y., Park, T., Jin, M., Yang, J., Eom, S.H.
• Funding Organization(s): National Research Foundation (NRF, Korea), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.260 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Structural and biochemical insights into Zn 2+ -bound EF-hand proteins, EFhd1 and EFhd2.

Mun, S.A., Park, J., Kang, J.Y., Park, T., Jin, M., Yang, J., Eom, S.H.

(2023) IUCrJ 10: 233-245

• PubMed: 36862489 
• DOI: https://doi.org/10.1107/S2052252523001501
• Primary Citation Related Structures: 
  7YGV, 7YGW, 7YGY


• PubMed Abstract: 
  

  EF-hand proteins, which contain a Ca ²⁺ -binding EF-hand motif, are involved in regulating diverse cellular functions. Ca ²⁺ binding induces conformational changes that modulate the activities of EF-hand proteins. Moreover, these proteins occasionally modify their activities by coordinating metals other than Ca ²⁺ , including Mg ²⁺ , Pb ²⁺ and Zn ²⁺ , within their EF-hands. EFhd1 and EFhd2 are homologous EF-hand proteins with similar structures. Although separately localized within cells, both are actin-binding proteins that modulate F-actin rearrangement through Ca ²⁺ -independent actin-binding and Ca ²⁺ -dependent actin-bundling activity. Although Ca ²⁺ is known to affect the activities of EFhd1 and EFhd2, it is not known whether their actin-related activities are affected by other metals. Here, the crystal structures of the EFhd1 and EFhd2 core domains coordinating Zn ²⁺ ions within their EF-hands are reported. The presence of Zn ²⁺ within EFhd1 and EFhd2 was confirmed by analyzing anomalous signals and the difference between anomalous signals using data collected at the peak positions as well as low-energy remote positions at the Zn K-edge. EFhd1 and EFhd2 were also found to exhibit Zn ²⁺ -independent actin-binding and Zn ²⁺ -dependent actin-bundling activity. This suggests the actin-related activities of EFhd1 and EFhd2 could be regulated by Zn ²⁺ as well as Ca ²⁺ .

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Organizational Affiliation: 
• School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea.
Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.91 kDa 
• Atom Count: 783 
• Modeled Residue Count: 99 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EF-hand domain-containing protein D2	A	120	Homo sapiens	Mutation(s): 0  Gene Names: EFHD2, SWS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96C19 (Homo sapiens) Explore Q96C19  Go to UniProtKB:  Q96C19
PHAROS:  Q96C19 GTEx:  ENSG00000142634

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.260 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.9	α = 90
b = 92.9	β = 90
c = 92.9	γ = 90

Software Package:

Software Name	Purpose
DIALS	data reduction
Aimless	data scaling
PHENIX	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Mun, S.A., Park, J., Kang, J.Y., Park, T., Jin, M., Yang, J., Eom, S.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1A2C1006267
Other private	Korea, Republic Of	GIST Research Institute (GRI) IIBR

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection