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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.233 (Depositor), 0.237 (DCC)
R-Value Work:
0.199 (Depositor), 0.213 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UQF0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233 (Depositor), 0.237 (DCC)
R-Value Work: 0.199 (Depositor), 0.213 (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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.