Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 185.71 kDa 
• Atom Count: 13317 
• Modelled Residue Count: 1712 
• Deposited Residue Count: 1720 
• Unique protein chains: 4

1PG7

Murine 6A6 Fab in complex with humanized anti-Tissue Factor D3H44 Fab

• PDB DOI: 10.2210/pdb1PG7/pdb

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


• Deposited: 2003-05-27 Released: 2003-08-26 
• Deposition Author(s): Eigenbrot, C., Meng, Y.G., Krishnamurthy, R., Lipari, M.T., Presta, L., Devaux, B., Wong, T., Moran, P., Bullens, S., Kirchhofer, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

Structural insight into how an anti-idiotypic antibody against D3H44 (anti-tissue factor antibody) restores normal coagulation.

Eigenbrot, C., Meng, Y.G., Krishnamurthy, R., Lipari, M.T., Presta, L., Devaux, B., Wong, T., Moran, P., Bullens, S., Kirchhofer, D.

(2003) J Mol Biol 331: 433-446

• PubMed: 12888350 
• DOI: 10.1016/s0022-2836(03)00735-6
• Primary Citation of Related Structures:  
  1PG7


• PubMed Abstract: 
  

6A6 is a murine monoclonal antibody raised against the humanized anti-tissue factor antibody D3H44. 6A6 is able to completely neutralize the anticoagulant activity of D3H44 in tissue factor-dependent functional assays, such as endotoxin-induced whole blood clotting, prothrombin time, as well as factor X and factor IX activation. ELISA-type assays further showed that 6A6 binds to an epitope with critical determinants on the V(L) domain of D3H44. The possibility that the anti-idiotypic 6A6 might carry an "internal image" of the original antigen (tissue factor) was examined using the X-ray structure of the 6A6-Fab/D3H44-Fab complex determined at 2.5A resolution. We find that 6A6 structurally mimics tissue factor only so far as it combines with the antigen recognition surface of D3H44. While 6A6 contacts both V(L) and V(H) domains of D3H44, as does tissue factor, there is more contact with the D3H44 V(L) domain and less with the D3H44 V(H) domain relative to the tissue factor contacts on D3H44. Additionally, there is an almost total lack of correspondence between 6A6 and tissue factor at the level of amino acid side-chain functional groups. Despite the fact that both tissue factor and 6A6 are composed largely of beta-sheets, they present fundamentally different elements of secondary structure to D3H44; tissue factor presents beta-sheets edge-on, while 6A6 uses mostly loops. Finally, the finding that 6A6 competes with tissue factor for D3H44 binding raises the possibility of using 6A6 as an antidote for D3H44 anticoagulant therapy. To this end, we constructed a chimeric murine/human 6A6-Fab, which effectively neutralized D3H44 and fully restored tissue factor function in enzymatic assays.

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Organizational Affiliation: 

Department of Protein, Genentech Inc, South San Francisco, CA 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
humanized antibody D3H44	A [auth H], B [auth I]	217	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
humanized antibody D3H44	C [auth L], D [auth M]	213	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for Q7Z3Y4 (Homo sapiens) Explore Q7Z3Y4  Go to UniProtKB:  Q7Z3Y4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
murine antibody 6A6 Fab fragment	E [auth W], G [auth Y]	210	Mus musculus	Mutation(s): 0
UniProt
Find proteins for G0YP42 (Mus musculus) Explore G0YP42  Go to UniProtKB:  G0YP42

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
murine antibody 6A6 Fab fragment	F [auth X], H [auth Z]	220	Mus musculus	Mutation(s): 0  Gene Names: Ighg
UniProt
Find proteins for P01863 (Mus musculus) Explore P01863  Go to UniProtKB:  P01863

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.89	α = 77.48
b = 85.78	β = 75.92
c = 92.37	γ = 63.33

Software Package:

Software Name	Purpose
X-PLOR	refinement
HKL-2000	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-27 
• Released Date: 2003-08-26 
Deposition Author(s): Eigenbrot, C., Meng, Y.G., Krishnamurthy, R., Lipari, M.T., Presta, L., Devaux, B., Wong, T., Moran, P., Bullens, S., Kirchhofer, D.

Revision History  

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-02-05
  Changes: Source and taxonomy