8YUK | pdb_00008yuk

Structure of a triple-helix region of human collagen type VII

PDB DOI: https://doi.org/10.2210/pdb8YUK/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2024-03-27 Released: 2025-04-02
Deposition Author(s): Zhu, Y., Yang, X., Sun, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.242 (Depositor), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.195 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of a triple-helix region of human collagen type VII

Zhu, Y., Yang, X., Sun, F.

To be published.

Macromolecule Content

Total Structure Weight: 7.81 kDa
Atom Count: 644
Modeled Residue Count: 84
Deposited Residue Count: 84
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A triple-helix region of human collagen type VII	A, B, C	28	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for W5MNE5 (Lepisosteus oculatus) Explore W5MNE5 Go to UniProtKB: W5MNE5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W5MNE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP Query on HYP	A, B, C	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.242 (Depositor), 0.240 (DCC)
R-Value Work: 0.196 (Depositor), 0.195 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 18.851	α = 90
b = 19.248	β = 91.47
c = 78.038	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
BALBES	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release

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.