9IUS | pdb_00009ius

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

• PDB DOI: https://doi.org/10.2210/pdb9IUS/pdb
• EM Map EMD-60913: EMDB EMDataResource

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


• Deposited: 2024-07-22 Released: 2025-04-23 
• Deposition Author(s): Fang, B.H., Zhang, L.J.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 9.80 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Literature

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

Fang, B.H., Zhang, L.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 30-mer - A30 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,944.82 kDa 
• Atom Count: 12,812 
• Modeled Residue Count: 2,183 
• Deposited Residue Count: 23,400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
axialfibril	A [auth X], AA [auth T], B [auth A], BA [auth U], C [auth B], CA [auth V], D [auth C], DA [auth W], 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], P [auth O], Q [auth P], R [auth Q], S [auth Y], T [auth Z], U [auth 1], V [auth 2], W [auth 3], X [auth 4], Y [auth R], Z [auth S]	780	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 9.80 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Fang, B.H., Zhang, L.J.

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

Revision History  

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