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- PDB-4m7l: Crystal structure of the complex between human tissue factor extr... -

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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 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)
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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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)
Has protein modificationY
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.

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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: 2.5 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

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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

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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

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