4KXZ

crystal structure of tgfb2 in complex with GC2008.

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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

  • DOI: 10.1002/pro.2548
  • Primary Citation of Related Structures:  
    4KV5, 4KXZ

  • 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 ...

    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.

    Organizational Affiliation: 

    Sanofi Biotherapeutics, Framingham, Massachusetts, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transforming growth factor beta-2A,
B,
C [auth D],
D [auth E]		112Homo sapiensMutation(s): 0 
Gene Names: TGFB2
UniProt & NIH Common Fund Data Resources
Find proteins for P61812 (Homo sapiens)
Explore P61812 
Go to UniProtKB:  P61812
PHAROS:  P61812
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61812
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GC1008 Heavy ChainE [auth H],
F [auth J],
G [auth N],
H [auth Q]		224Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GC1008 Light ChainI,
J [auth L],
K [auth M],
L [auth P]		215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE5
Query on PE5
Download Ideal Coordinates CCD File 
R [auth P]3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N		 Ligand Interaction
MES
Query on MES
Download Ideal Coordinates CCD File 
M [auth A],
N [auth E],
O [auth J],
P [auth Q],
Q [auth M]		2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
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 = 131.2α = 90
b = 359.68β = 90
c = 64.63γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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