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

Validation slider image for 8YUK

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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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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

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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.