[English] 日本語
Yorodumi
- PDB-1uj3: Crystal structure of a humanized Fab fragment of anti-tissue-fact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uj3
TitleCrystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor
Components
  • IgG Fab heavy chain
  • IgG Fab light chain
  • tissue factor
KeywordsIMMUNE SYSTEM/BLOOD CLOTTING / tissue factor / antigen / antibody / Fab / IMMUNE SYSTEM-BLOOD CLOTTING COMPLEX
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 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 / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / 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: 2.1 Å
AuthorsOhto, U. / Mizutani, R. / Nakamura, M. / Adachi, H. / Satow, Y.
CitationJournal: J.Synchrotron Radiat. / Year: 2004
Title: Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor.
Authors: Ohto, U. / Mizutani, R. / Nakamura, M. / Adachi, H. / Satow, Y.
History
DepositionJul 25, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IgG Fab light chain
B: IgG Fab heavy chain
C: tissue factor


Theoretical massNumber of molelcules
Total (without water)70,0353
Polymers70,0353
Non-polymers00
Water8,359464
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.054, 265.996, 42.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Antibody IgG Fab light chain


Mass: 23475.979 Da / Num. of mol.: 1 / Fragment: anti-tissue-factor antibody hATR-5 Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody IgG Fab heavy chain


Mass: 23255.990 Da / Num. of mol.: 1 / Fragment: anti-tissue-factor antibody hATR-5 Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein tissue factor / / TF / Coagulation factor III / Thromboplastin / CD142 antigen / blood coagulation factor


Mass: 23302.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 606-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13726
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 3.85 Å3/Da / Density % sol: 67.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2-propanol, PEG4000, HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2002
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→37.1 Å / Num. all: 69013 / Num. obs: 64872 / % possible obs: 94 % / Observed criterion σ(F): 3 / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.1→2.2 Å / % possible all: 81

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2HFT AND 1JPT

2hft

1jpt


Resolution: 2.1→37.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1947766.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 6352 10.1 %RANDOM
Rwork0.196 ---
all0.2 69013 --
obs0.196 62792 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9528 Å2 / ksol: 0.339345 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2--1.86 Å20 Å2
3----3.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4913 0 0 464 5377
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it31.5
X-RAY DIFFRACTIONc_mcangle_it4.362
X-RAY DIFFRACTIONc_scbond_it3.642
X-RAY DIFFRACTIONc_scangle_it4.892.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 926 10.8 %
Rwork0.205 7659 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

+
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