9GFR | pdb_00009gfr

Crystal structure of anti-collagen type II antibody Fab (PC12) complexed with collagen triple helical peptide (THP59)

• PDB DOI: https://doi.org/10.2210/pdb9GFR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-12 Released: 2026-03-04 
• Deposition Author(s): Ge, C., Dobritzsch, D., Holmdahl, R.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.247 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of anti-collagen type II antibody Fab (PC12) complexed with collagen triple helical peptide (THP59)

Ge, C., Dobritzsch, D., Holmdahl, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.95 kDa 
• Atom Count: 5,347 
• Modeled Residue Count: 686 
• Deposited Residue Count: 687 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
the light chain of anti-collagen type II antibody Fab (PC12)	A [auth L]	213	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
the heavy chain of anti-collagen type II antibody Fab (PC12)	B [auth H]	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombinant collagen triple helical peptide (THP59) covalently linked to foldon trimerization domain	C [auth E], D [auth F], E [auth G]	85	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.247 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.555	α = 90
b = 69.845	β = 90
c = 240.356	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data scaling
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-04 
Deposition Author(s): Ge, C., Dobritzsch, D., Holmdahl, R.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2026-03-04
  Type: Initial release