[English] 日本語
Yorodumi
- PDB-1jps: Crystal structure of tissue factor in complex with humanized Fab D3h44 -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / cytokine receptor activity / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation ...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 / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / cytokine receptor activity / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / blood coagulation / collagen-containing extracellular matrix / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more