[English] 日本語
Yorodumi
- PDB-4m7l: Crystal structure of the complex between human tissue factor extr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m7l
TitleCrystal structure of the complex between human tissue factor extracellular domain and antibody 10H10 FAB fragment
Components
  • 10H10 heavy chain
  • 10H10 light chain
  • Tissue factor
KeywordsBLOOD CLOTTING/IMMUNE SYSTEM / antibody / BLOOD CLOTTING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / 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 / protein processing / phospholipid binding / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: To be Published
Title: Crystal structure of the complex between human tissue factor extracellular domain and antibody 10H10 FAB fragment
Authors: Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Sep 20, 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
T: Tissue factor
L: 10H10 light chain
H: 10H10 heavy chain


Theoretical massNumber of molelcules
Total (without water)73,1243
Polymers73,1243
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-31 kcal/mol
Surface area28540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.860, 116.860, 106.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein Tissue factor / TF / Coagulation factor III / Thromboplastin


Mass: 24560.229 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 37-245)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Production host: Escherichia coli (E. coli) / References: UniProt: P13726
#2: Antibody 10H10 light chain


Mass: 24142.814 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Antibody 10H10 heavy chain


Mass: 24421.170 Da / Num. of mol.: 1 / Fragment: FD, SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
Sequence detailsHEAVY AND LIGHT CHAINS ARE CHIMERIC MOLECULES EACH COMPRISING A MOUSE VARIABLE DOMAIN AND HUMAN ...HEAVY AND LIGHT CHAINS ARE CHIMERIC MOLECULES EACH COMPRISING A MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1 M CAPS, pH 10.5, 24% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 12, 2010 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→28 Å / Num. all: 9573 / Num. obs: 9573 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 74.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 19.7
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 3.4 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UJ3

1uj3


Resolution: 3.4→15 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.868 / SU B: 95.278 / SU ML: 0.627 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.744 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28906 459 5 %RANDOM
Rwork0.24239 ---
all0.24466 9114 --
obs0.24466 9114 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 101.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2--1.12 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 3.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 0 0 4919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025041
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9526866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3445632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71424.926203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65215817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7531514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0213775
LS refinement shellResolution: 3.4→3.491 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.526 22 -
Rwork0.29 622 -
obs--97.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.85013.32294.20516.82924.12115.3242-0.00060.13640.7182-0.09550.1286-0.8175-0.89820.5747-0.1280.4398-0.01460.01521.3349-0.22020.887352.176314.522768.327
22.88963.3473-0.683314.5244-4.43189.00950.1879-1.2208-1.01940.7558-0.5643-0.30250.72490.20380.37650.5010.3352-0.38251.3263-0.13981.100235.5622-12.959873.9534
33.88010.0356-0.40121.5068-0.65083.82220.35260.42440.04890.00960.1504-0.16020.19150.3501-0.5030.07840.2083-0.0340.8156-0.23210.39122.7581-0.334649.8094
43.9227-2.81610.36572.3745-0.65484.8670.31630.1594-0.1566-0.59510.09310.2848-0.08420.2277-0.40930.503-0.1294-0.0531.13430.06450.6138.528214.507122.3261
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T6 - 107
2X-RAY DIFFRACTION2T108 - 210
3X-RAY DIFFRACTION3L1 - 113
4X-RAY DIFFRACTION3H1 - 120
5X-RAY DIFFRACTION4L114 - 220
6X-RAY DIFFRACTION4H121 - 223

+
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://pdbjlvh1.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