8ZXL | pdb_00008zxl

Structure of a hierarchical intermediate region (spindlefirbil) of human collagen type

PDB DOI: https://doi.org/10.2210/pdb8ZXL/pdb
EM Map EMD-60543: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-14 Released: 2025-04-23
Deposition Author(s): Fang, B.H., Zhang, L.J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 8.60 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZXL

This is version 1.1 of the entry. See complete history.

Literature

Visualizing the hierarchical self-assembly process for the intricate architecture of collagen

Fang, B.H., Zhang, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 972.41 kDa
Atom Count: 6,178
Modeled Residue Count: 1,052
Deposited Residue Count: 11,700
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
spindlefibril	A [auth X] B [auth A] C [auth B] D [auth C] E [auth D] A [auth X], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N]	780	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 8.60 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA0905200

Revision History (Full details and data files)

Version 1.0: 2025-04-23
Type: Initial release
Version 1.1: 2025-07-23
Changes: Data collection

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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.