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- PDB-1ahw: A COMPLEX OF EXTRACELLULAR DOMAIN OF TISSUE FACTOR WITH AN INHIBI... -

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Basic information

Entry
Database: PDB / ID: 1ahw
TitleA COMPLEX OF EXTRACELLULAR DOMAIN OF TISSUE FACTOR WITH AN INHIBITORY FAB (5G9)
Components
  • IMMUNOGLOBULIN FAB 5G9 (HEAVY CHAIN)
  • IMMUNOGLOBULIN FAB 5G9 (LIGHT CHAIN)
  • TISSUE FACTOR
KeywordsCOMPLEX (IMMUNOGLOBULIN/TISSUE FACTOR) / BLOOD COAGULATION / TISSUE FACTOR / FAB / COMPLEX / ANTIBODY / COMPLEX (IMMUNOGLOBULIN-TISSUE FACTOR) / COMPLEX (IMMUNOGLOBULIN-TISSUE FACTOR) 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 / immunoglobulin complex / positive regulation of endothelial cell proliferation / B cell differentiation / positive regulation of interleukin-8 production / protein processing / phospholipid binding / cytokine-mediated signaling pathway / positive regulation of angiogenesis / blood coagulation / : / protease binding / adaptive immune response / positive regulation of cell migration / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular space / extracellular region / 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 / : / : / Immunoglobulin V-Type ...Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / : / : / Immunoglobulin V-Type / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa constant / Tissue factor / IgM heavy chain VDJ region
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHuang, M. / Syed, R. / Stura, E.A. / Stone, M.J. / Stefanko, R.S. / Ruf, W. / Edgington, T.S. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF.5G9 complex.
Authors: Huang, M. / Syed, R. / Stura, E.A. / Stone, M.J. / Stefanko, R.S. / Ruf, W. / Edgington, T.S. / Wilson, I.A.
History
DepositionApr 10, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: IMMUNOGLOBULIN FAB 5G9 (LIGHT CHAIN)
B: IMMUNOGLOBULIN FAB 5G9 (HEAVY CHAIN)
C: TISSUE FACTOR
D: IMMUNOGLOBULIN FAB 5G9 (LIGHT CHAIN)
E: IMMUNOGLOBULIN FAB 5G9 (HEAVY CHAIN)
F: TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)143,6256
Polymers143,6256
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.304, 73.312, 115.826
Angle α, β, γ (deg.)90.00, 90.89, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (-0.253131, -0.068772, 0.964984), (-0.082161, 0.995394, 0.049387), (-0.963937, -0.066783, -0.257616)
Vector: 71.38972, 59.62823, 57.18087)

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Components

#1: Antibody IMMUNOGLOBULIN FAB 5G9 (LIGHT CHAIN) / FAB / FAB LIGHT CHAIN / FAB HEAVY CHAIN


Mass: 23810.203 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN RESIDUES 1 - 214 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: BL21 / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P01837
#2: Antibody IMMUNOGLOBULIN FAB 5G9 (HEAVY CHAIN) / FAB / FAB LIGHT CHAIN / FAB HEAVY CHAIN


Mass: 23175.799 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN RESIDUES 1 - 214 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: BL21 / Organ: BLOOD / Tissue: BLOOD / References: PIR: S49220, UniProt: X5J519*PLUS
#3: Protein TISSUE FACTOR / TF / THROMBOPLASTIN / COAGULATION FACTOR III


Mass: 24826.512 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: HUMAN TISSUE FACTOR EXTRACELLU / Organ: BLOOD / Plasmid: PTRCHISC (INVITROGEN) / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODIES
Gene (production host): HUMAN TISSUE FACTOR EXTRACELLULAR DOMAIN
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13726
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 64 %
Crystal growpH: 7
Details: TF-5G9 CRYSTAL WERE GROWN IN 1.7-2.0M AMMONIUM SULFATE, 0.1M SODIUM CITRATE, PH 5.0-5.5, 0.2% 2-METHYL-2,4-PENTANE-DIOL (MPD), AND 2% PEG 600 AT AN EQUIMOLAR 5G9:TF RATIO. THE CRYSTALS GREW ...Details: TF-5G9 CRYSTAL WERE GROWN IN 1.7-2.0M AMMONIUM SULFATE, 0.1M SODIUM CITRATE, PH 5.0-5.5, 0.2% 2-METHYL-2,4-PENTANE-DIOL (MPD), AND 2% PEG 600 AT AN EQUIMOLAR 5G9:TF RATIO. THE CRYSTALS GREW EXTREMELY SLOWLY, TAKING 6-9 MONTHS TO REACH A MAXIMAL SIZE OF 0.4 X 0.4 X 0.8 MM3., pH 7.0
PH range: 5.0-5.5
Crystal grow
*PLUS
Method: unknown / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7-2.0 Mammonium sulfate11
20.1 Msodium citrate11
30.2 %MPD11
42 %PEG60011

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→47 Å / Num. obs: 42650 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 42.4 Å2 / Rsym value: 0.135 / Net I/σ(I): 7.2
Reflection shellResolution: 3→3.19 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 0.9 / Rsym value: 0.43 / % possible all: 87
Reflection
*PLUS
Num. measured all: 118598 / Rmerge(I) obs: 0.135
Reflection shell
*PLUS
% possible obs: 87 % / Rmerge(I) obs: 0.446

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
TFFCmodel building
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
TFFCphasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TISSUE FACTOR (PDB ENTRY 1TFH) AND FAB 5G9 (PDB ENTRY 1FGN)

1tfh

1fgn


Resolution: 3→7 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.285 889 2.6 %RANDOM
Rwork0.217 ---
obs0.217 34656 78.1 %-
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å25.05 Å2
2--1.68 Å20 Å2
3----1.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9834 0 0 0 9834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.84
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.281.5
X-RAY DIFFRACTIONx_mcangle_it6.912
X-RAY DIFFRACTIONx_scbond_it6.832
X-RAY DIFFRACTIONx_scangle_it10.322.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.30.1
22X-RAY DIFFRACTION0.290.1
33X-RAY DIFFRACTION0.40.3
44X-RAY DIFFRACTION0.40.3
LS refinement shellResolution: 3→3.17 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 77 1.9 %
Rwork0.309 3983 -
obs--55.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.84

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