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- PDB-1jps: Crystal structure of tissue factor in complex with humanized Fab D3h44 -

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Basic information

Entry
Database: PDB / ID: 1jps
TitleCrystal structure of tissue factor in complex with humanized Fab D3h44
Components
  • immunoglobulin Fab D3H44, heavy chain
  • immunoglobulin Fab D3H44, light chain
  • tissue factor
KeywordsIMMUNE SYSTEM / antigen-antibody recognition / humanized antibody / blood coagulation / interface water molecules
Function / homology
Function and homology information


activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of TOR signaling ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation / positive regulation of interleukin-8 production / phospholipid binding / protein processing / cytokine-mediated signaling pathway / positive regulation of angiogenesis / blood coagulation / : / protease binding / positive regulation of cell migration / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular space / membrane / plasma membrane
Similarity search - Function
Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold ...Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFaelber, K. / Kirchhofer, D. / Presta, L. / Kelley, R.F. / Muller, Y.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The 1.85 A resolution crystal structures of tissue factor in complex with humanized Fab D3h44 and of free humanized Fab D3h44: revisiting the solvation of antigen combining sites.
Authors: Faelber, K. / Kirchhofer, D. / Presta, L. / Kelley, R.F. / Muller, Y.A.
#1: Journal: THROMB.HAEMOST. / Year: 2001
Title: Generation of a humanized, high affinity anti-tissue factor antibody for use as a novel antithrombotic therapeutic
Authors: Presta, L. / Sims, P. / Meng, Y.G. / Moran, P. / Bullens, S. / Bunting, S. / Schoenfeld, J. / Lowe, D. / Lai, J. / Rancatore, P. / Iverson, M. / Lim, A. / Chisholm, V. / Kelley, R.F. / ...Authors: Presta, L. / Sims, P. / Meng, Y.G. / Moran, P. / Bullens, S. / Bunting, S. / Schoenfeld, J. / Lowe, D. / Lai, J. / Rancatore, P. / Iverson, M. / Lim, A. / Chisholm, V. / Kelley, R.F. / Riederer, M. / Kirchhofer, D.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: The crystal structure of the extracellulare domain of human tissue factor refined to 1.7 A resolution
Authors: Muller, Y.A. / Ultsch, M.H. / de Vos, A.M.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: immunoglobulin Fab D3H44, light chain
H: immunoglobulin Fab D3H44, heavy chain
T: tissue factor


Theoretical massNumber of molelcules
Total (without water)72,3933
Polymers72,3933
Non-polymers00
Water10,431579
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.25, 93.28, 110.01
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody immunoglobulin Fab D3H44, light chain


Mass: 23523.107 Da / Num. of mol.: 1 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEMX1 / Production host: Escherichia coli (E. coli)
#2: Antibody immunoglobulin Fab D3H44, heavy chain


Mass: 24043.805 Da / Num. of mol.: 1 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEMX1 / Production host: Escherichia coli (E. coli)
#3: Protein tissue factor


Mass: 24826.512 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEMX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13726
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 6000, sodium chloride, sodium-HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
220 mMHEPES1droppH7.5
30.01 %(w/v)1dropNaN3
411 %PEG60001reservoir
52.0 M1reservoirNaCl
60.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8428 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 2000 / Details: mirrors
RadiationMonochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8428 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 73056 / Num. obs: 73056 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 30.1 Å2 / Rsym value: 0.061 / Net I/σ(I): 12.6
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 11059 / Rsym value: 0.27 / % possible all: 94.4

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
CNS1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AHW

1ahw


Resolution: 1.85→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 5275 7.2207 %random
Rwork0.201 ---
all-73054 --
obs-73054 96.8 %-
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.352 Å20 Å20 Å2
2--3.94 Å20 Å2
3---0.413 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 0 579 5440
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.64
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.278 850 -
Rwork0.256 --
obs-11964 97.5 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 67779 / σ(F): 0 / % reflection Rfree: 7.221 % / Rfactor obs: 0.201 / Rfactor Rfree: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.2 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / Rfactor Rwork: 0.256

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