6SF6 | pdb_00006sf6

Crystal structure of the mAb 15A in complex with COMP-epitope P6

• PDB DOI: https://doi.org/10.2210/pdb6SF6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Rattus norvegicus
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2019-08-01 Released: 2020-06-24 
• Deposition Author(s): Dobritzsch, D., Ge, C., Holmdahl, R.
• Funding Organization(s): Knut and Alice Wallenberg Foundation, Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.203 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Models: experimental

Literature

Antibodies to cartilage oligomeric matrix protein in vivo are pathogenic and clinically relevant in rheumatoid arthritis

Ge, C., Tong, D., Loennblom, E., Bibo, L., Hagert, C., Kastbom, A., Gjertsson, I., Dobritzsch, D., Holmdahl, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 104.24 kDa 
• Atom Count: 7,616 
• Modeled Residue Count: 888 
• Deposited Residue Count: 942 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMP-reactive monoclonal antibody 15A Fab fragment, heavy chain	A [auth H], C [auth A]	233	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COMP-reactive monoclonal antibody 15A Fab fragment, light chain	B [auth L], D [auth B]	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
P6 epitope of cartilage oligomeric matrix protein (COMP)	E [auth C], F [auth D]	19	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P35444 (Rattus norvegicus) Explore P35444  Go to UniProtKB:  P35444

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth H], I [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H, J [auth L], K [auth L], L, M [auth A], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	E [auth C], F [auth D]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.203 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.174	α = 90
b = 84.421	β = 90
c = 151.885	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Dobritzsch, D., Ge, C., Holmdahl, R.

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Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	KAW 2010.0148
Swedish Research Council	Sweden	K2011-52X-07931-25-5, K2009-75SX-21029-01-3, K2012-75SX-22072-01-3, 2015-02662

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary