9HAN | pdb_00009han

Bovine collagen VI local refinement of C-terminal region

• PDB DOI: https://doi.org/10.2210/pdb9HAN/pdb
• EM Map EMD-51984: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2024-11-04 Released: 2025-08-20 
• Deposition Author(s): Godwin, A., Snee, M., Roseman, A., Baldock, C.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Collagen VI microfibril structure reveals mechanism for molecular assembly and clustering of inherited pathogenic mutations

Godwin, A., Snee, M., Becker, M., Dajani, R., Collins, R., Roseman, A., Baldock, C.

(2025) Nat Commun 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,101.13 kDa 
• Atom Count: 11,143 
• Modeled Residue Count: 1,414 
• Deposited Residue Count: 10,230 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen type VI alpha 3 chain	A [auth C], D [auth F]	3,061	Bos taurus	Mutation(s): 0
UniProt
Find proteins for A0AAA9TAB4 (Bos taurus) Explore A0AAA9TAB4  Go to UniProtKB:  A0AAA9TAB4
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen type VI alpha 1 chain	B [auth A], E [auth D]	1,027	Bos taurus	Mutation(s): 0
UniProt
Find proteins for E1BI98 (Bos taurus) Explore E1BI98  Go to UniProtKB:  E1BI98
Glycosylation
Glycosylation Sites: 1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen type VI alpha 2 chain	C [auth B], F [auth E]	1,027	Bos taurus	Mutation(s): 0
UniProt
Find proteins for A0AAA9TXG2 (Bos taurus) Explore A0AAA9TXG2  Go to UniProtKB:  A0AAA9TXG2
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, J	3		N-Glycosylation

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, I, K	2		N-Glycosylation

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	3		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth C], N [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Godwin, A., Snee, M., Roseman, A., Baldock, C.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release