Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.03 kDa 
• Atom Count: 5377 
• Modelled Residue Count: 636 
• Deposited Residue Count: 637 
• Unique protein chains: 3

1UJ3

Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor

• DOI: 10.2210/pdb1UJ3/pdb

• Classification: IMMUNE SYSTEM/BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-07-25 Released: 2004-07-25 
• Deposition Author(s): Ohto, U., Mizutani, R., Nakamura, M., Adachi, H., Satow, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor.

Ohto, U., Mizutani, R., Nakamura, M., Adachi, H., Satow, Y.

(2004) J Synchrotron Radiat 11: 105-108

• PubMed: 14646147 
• DOI: 10.1107/s0909049503023513
• Primary Citation of Related Structures:  
  1UJ3


• PubMed Abstract: 
  

Tissue factor (TF) is a membrane-anchored protein that initiates the extrinsic cascade of blood coagulation. TF forms a complex with serine protease Factor VIIa, and then activates Factor X zymogen to Factor Xa, leading to the blood coagulation. Humanized anti-TF antibody hATR-5 strongly inhibits TF-initiated blood coagulation, and is of potential use for various thrombotic diseases. The Fab fragment of antibody hATR-5 is obtained for crystallization. The crystal structure of the complex of the Fab with extracellular domains of human TF was determined with the molecular replacement method, and refined to an R factor of 0.196 at 2.1 A resolution. All the complementarity-determining regions (CDRs) of the Fab are involved in interaction with the C-terminal-side extracellular domain of TF through 19 hydrogen bonds. The interface between the Fab and TF molecules contains 15 water molecules, and yields buried surface areas as wide as 2000 A2. The TF surface in the interface is possibly involved in the activation of Factor X, by forming a transient ternary complex of Factor X-TF-Factor VIIa. Electrostatic interactions are predominantly observed between the heavy-chain CDRs and TF. These hydrogen-bonding and electrostatic interactions together with the wide buried areas contribute to the high affinity of the antibody toward TF, leading to the effective inhibition of the TF-initiated blood coagulation.

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Organizational Affiliation: 

Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG Fab light chain	A	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG Fab heavy chain	B	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
tissue factor	C	205	Homo sapiens	Mutation(s): 0  Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726  Go to UniProtKB:  P13726
PHAROS:  P13726 GTEx:  ENSG00000117525

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.054	α = 90
b = 265.996	β = 90
c = 42.254	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-25 
• Released Date: 2004-07-25 
Deposition Author(s): Ohto, U., Mizutani, R., Nakamura, M., Adachi, H., Satow, Y.

Revision History  

• Version 1.0: 2004-07-25
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-06
  Changes: Data collection, Database references