5HA6 | pdb_00005ha6

Crystal structure of human syncytin-1 fusion subunit

• PDB DOI: https://doi.org/10.2210/pdb5HA6/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-12-30 Released: 2017-08-02 
• Deposition Author(s): Aydin, H., Lee, J.E.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structural and functional characterization of the human Syncytin 1 fusion protein

Aydin, H., Thavalingam, A., Bikopoulos, G., Sultana, A., Lee, J.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.71 kDa 
• Atom Count: 1,400 
• Modeled Residue Count: 172 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syncytin-1	A, B	117	Homo sapiens	Mutation(s): 1  Gene Names: ERVW-1, ERVWE1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQF0 (Homo sapiens) Explore Q9UQF0  Go to UniProtKB:  Q9UQF0
PHAROS:  Q9UQF0 GTEx:  ENSG00000242950

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.118	α = 90
b = 48.118	β = 90
c = 378.911	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Aydin, H., Lee, J.E.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	CIHR MOP-115066

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Author supporting evidence
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary