Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

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

Macromolecule Content

• Total Structure Weight: 241640.13 
• Atom Count: 16725 
• Residue Count: 2204 
• Unique protein chains: 3

4KXZ

crystal structure of tgfb2 in complex with GC2008.

• DOI: 10.2210/pdb4KXZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli


• Deposited: 2013-05-28 Released: 2014-09-24 
• Deposition Author(s): Mathieu, M., Moulin, A.G., Wei, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.222 
• R-Value Work: 0.183 

Literature

Structures of a pan-specific antagonist antibody complexed to different isoforms of TGF beta reveal structural plasticity of antibody-antigen interactions.

Moulin, A., Mathieu, M., Lawrence, C., Bigelow, R., Levine, M., Hamel, C., Marquette, J.P., Le Parc, J., Loux, C., Ferrari, P., Capdevila, C., Dumas, J., Dumas, B., Rak, A., Bird, J., Qiu, H., Pan, C.Q., Edmunds, T., Wei, R.R.

(2014) Protein Sci. 23: 1698-1707

• PubMed: 25209176 
• DOI: 10.1002/pro.2548
• Primary Citation of Related Structures:  
  4KV5
• Also Cited By: 6I9J


• PubMed Abstract: 
  

Various important biological pathways are modulated by TGFβ isoforms; as such they are potential targets for therapeutic intervention. Fresolimumab, also known as GC1008, is a pan-TGFβ neutralizing antibody that has been tested clinically for several indications including an ongoing trial for focal segmental glomerulosclerosis. The structure of the antigen-binding fragment of fresolimumab (GC1008 Fab) in complex with TGFβ3 has been reported previously, but the structural capacity of fresolimumab to accommodate tight interactions with TGFβ1 and TGFβ2 was insufficiently understood. We report the crystal structure of the single-chain variable fragment of fresolimumab (GC1008 scFv) in complex with target TGFβ1 to a resolution of 3.00 Å and the crystal structure of GC1008 Fab in complex with TGFβ2 to 2.83 Å. The structures provide further insight into the details of TGFβ recognition by fresolimumab, give a clear indication of the determinants of fresolimumab pan-specificity and provide potential starting points for the development of isoform-specific antibodies using a fresolimumab scaffold.

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Organizational Affiliation: 

Sanofi Biotherapeutics, Framingham, Massachusetts, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transforming growth factor beta-2	A, B, D, E	112	Homo sapiens	Mutation(s): 0  Gene Names: TGFB2
Find proteins for P61812 (Homo sapiens) Go to Gene View: TGFB2 Go to UniProtKB:  P61812

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
GC1008 Heavy Chain	H, J, N, Q	224	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
GC1008 Light Chain	I, L, M, P	215	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PE5	P	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL, POLYETHYLENE GLYCOL PEG400 C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
MES	A, E, J, M, Q	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.222 
• R-Value Work: 0.183 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 131.200	α = 90.00
b = 359.680	β = 90.00
c = 64.630	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
PHASER	phasing
XSCALE	data scaling
BUSTER	refinement
BUSTER-TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-28 
• Released Date: 2014-09-24 
• Deposition Author(s): Mathieu, M., Moulin, A.G., Wei, R.

Revision History 

• Version 1.0: 2014-09-24
  Type: Initial release
• Version 1.1: 2014-12-03
  Type: Database references