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- PDB-8cn9: Factor VII binding Fab of the bispecific antibody HMB-001 in comp... -

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Basic information

Entry
Database: PDB / ID: 8cn9
TitleFactor VII binding Fab of the bispecific antibody HMB-001 in complex with Factor VII
Components
  • (Coagulation factor ...Coagulation) x 2
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Tissue factor
KeywordsBLOOD CLOTTING / Factor VII / Fab / Bispecific Antibody / HMB-001
Function / homology
Function and homology information


activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / positive regulation of leukocyte chemotaxis / NGF-stimulated transcription / response to cholesterol / response to growth hormone / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of interleukin-8 production / phospholipid binding / protein processing / Golgi lumen / cytokine-mediated signaling pathway / circadian rhythm / response to estrogen / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / blood coagulation / response to estradiol / collagen-containing extracellular matrix / protease binding / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / 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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site ...Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Fibronectin type III / Fibronectin type III superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold
Similarity search - Domain/homology
beta-D-glucopyranose / : / Coagulation factor VII / Tissue factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSchluckebier, G. / Johansson, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Cardiovasc Res / Year: 2023
Title: A bispecific antibody approach for the potential prophylactic treatment of inherited bleeding disorders
Authors: Gandhi, P.S. / Zivkovic, M. / Oestergaard, H. / Bonde, A.C. / Loevgreen, M.N. / Schluckebier, G. / Johansson, E. / Rea, C.J. / Soerensen, B. / Schutgens, R.E. / Urbanus, R.T. / Faber, J.H.
History
DepositionFeb 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab light chain
B: Fab heavy chain
C: Coagulation factor VII
D: Coagulation factor VII
E: Tissue factor
F: Fab light chain
G: Fab heavy chain
H: Coagulation factor VII
I: Coagulation factor VII
J: Tissue factor
K: Fab light chain
L: Fab heavy chain
M: Coagulation factor VII
N: Coagulation factor VII
O: Tissue factor
P: Fab light chain
Q: Fab heavy chain
R: Coagulation factor VII
S: Coagulation factor VII
T: Tissue factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,75434
Polymers445,67920
Non-polymers1,07414
Water0
1
A: Fab light chain
B: Fab heavy chain
C: Coagulation factor VII
D: Coagulation factor VII
E: Tissue factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6808
Polymers111,4205
Non-polymers2603
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Fab light chain
G: Fab heavy chain
H: Coagulation factor VII
I: Coagulation factor VII
J: Tissue factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7209
Polymers111,4205
Non-polymers3004
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: Fab light chain
L: Fab heavy chain
M: Coagulation factor VII
N: Coagulation factor VII
O: Tissue factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5408
Polymers111,4205
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: Fab light chain
Q: Fab heavy chain
R: Coagulation factor VII
S: Coagulation factor VII
T: Tissue factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8139
Polymers111,4205
Non-polymers3934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.782, 100.794, 181.739
Angle α, β, γ (deg.)90.000, 101.220, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999666969866, -0.0148689503937, -0.0210917915953), (-0.0148039230484, 0.99988517992, -0.00323586753636), (0.021137483788, -0.00292254863523, -0.999772306822)-72.7320505951, -26.4516343682, 0.230755181716
2given(0.922788990252, 0.00516209654217, 0.385271115228), (0.00801696034193, -0.999951019683, -0.00580401423669), (0.385222283645, 0.00844458368855, -0.922785176078)-17.5593633856, -29.8908204572, 89.2647321384
3given(-0.923373158697, -0.000459678317079, -0.383903371297), (0.00695055771373, -0.999855392496, -0.0155204330886), (-0.383840721582, -0.016999493864, 0.923242827031)-89.9657202543, -56.5452559461, 89.1425544585
4given(-0.999982179659, 1.26182700489E-5, -0.00596994188384), (2.43540938443E-5, 0.999998067615, -0.00196575015449), (0.00596990554324, -0.00196586051668, -0.999980247615)-72.4369932984, -26.2080388592, -0.0363563323219
5given(0.924358898801, 0.000555103772763, 0.381523679562), (0.000961923967199, -0.999999154019, -0.000875593557598), (0.381522870755, 0.00117635946812, -0.924358650779)-17.7285216948, -29.8328238711, 89.1302614092
6given(-0.926953681679, -0.00905407783575, -0.375066521696), (0.013667135317, -0.999860121159, -0.00964092988597), (-0.374926768096, -0.0140627803575, 0.926947763778)-89.6919572524, -56.3177428109, 89.4746025994
7given(-0.99997154862, 0.00470112216215, -0.00589927127536), (0.00466922970534, 0.999974473718, 0.00540834607803), (0.0059245459845, 0.00538064715044, -0.999967973683)-72.277070308, -26.1250183924, 0.0673726617053
8given(0.920551100833, -0.000271996003906, 0.390622063859), (0.00101873477489, -0.99999468509, -0.00309709073983), (0.390620830135, 0.00324897057022, -0.920545931095)-17.6492962487, -29.8570026961, 89.2011771201
9given(-0.916343110626, -0.010542445927, -0.400255119195), (0.0111027747442, -0.999937939976, 0.000919015146008), (-0.40023996802, -0.00360180923104, 0.916403292754)-90.1049061177, -56.0740428815, 88.9779407689
10given(-0.999989284425, -0.00456209135285, -0.000786357300422), (-0.0045603085642, 0.999987060945, -0.00225422442251), (0.000796631103447, -0.00225061423527, -0.999997150053)-72.4693358926, -26.1799927908, 0.0571141055669
11given(0.921242540622, 0.00226836188061, 0.388982050849), (0.000599188520196, -0.999990085834, 0.00441239237977), (0.388988203319, -0.00383180998673, -0.921234766447)-17.619941808, -29.9004140554, 89.2826380885
12given(-0.90818321058, -0.0109827099009, -0.418428770645), (0.00801708201478, -0.999928744797, 0.00884486990764), (-0.418496096059, 0.00467818457828, 0.908206547088)-90.0265019299, -56.2344089514, 88.50527348
13given(-0.999976133309, -0.00673696094488, 0.00153172118719), (-0.0067447448834, 0.999964070691, -0.00513475833446), (-0.00149707348714, -0.00514496685341, -0.99998564394)-72.4175394593, -26.1018506384, 0.0831921660682
14given(0.929958206439, -0.00377434430007, 0.367645873909), (-0.000314680769937, -0.999955110873, -0.00946980547235), (0.367665112913, 0.00869083222573, -0.92991764914)-16.8764328373, -29.6977448085, 89.2564204435

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Components

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Coagulation factor ... , 2 types, 8 molecules CHMRDINS

#3: Protein
Coagulation factor VII / / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 28103.256 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa
#4: Protein
Coagulation factor VII / / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 11670.991 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa

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Antibody , 2 types, 8 molecules AFKPBGLQ

#1: Antibody
Fab light chain / Fragment antigen-binding


Mass: 23384.982 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
Fab heavy chain / Fragment antigen-binding


Mass: 23434.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 7 molecules EJOT

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


Mass: 24826.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Production host: Homo sapiens (human) / References: UniProt: P13726
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 11 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs

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Details

Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.15 M Cesium chloride 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: May 8, 2018 / Details: na
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→48.5 Å / Num. obs: 69059 / % possible obs: 96.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 63.86 Å2 / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.15 / Rrim(I) all: 0.35 / Net I/σ(I): 3.6
Reflection shellResolution: 3.4→3.522 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 6423 / CC1/2: 0.697 / CC star: 0.906 / Rrim(I) all: 1.21 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.5 Å / SU ML: 0.6377 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.0162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3557 3677 2.85 %Random
Rwork0.3032 125179 --
obs0.3047 68416 93.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.3 Å2
Refinement stepCycle: LAST / Resolution: 3.4→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29476 0 44 0 29520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001930191
X-RAY DIFFRACTIONf_angle_d0.494441086
X-RAY DIFFRACTIONf_chiral_restr0.04084646
X-RAY DIFFRACTIONf_plane_restr0.00415257
X-RAY DIFFRACTIONf_dihedral_angle_d3.93844100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.440.42741210.39324145X-RAY DIFFRACTION81.35
3.44-3.490.42291300.39634624X-RAY DIFFRACTION88.43
3.49-3.540.61961180.47854192X-RAY DIFFRACTION81.46
3.54-3.590.6277910.50943519X-RAY DIFFRACTION67.01
3.59-3.650.46031450.40454685X-RAY DIFFRACTION91.77
3.65-3.710.49521480.41664802X-RAY DIFFRACTION91.85
3.71-3.770.38671370.38994718X-RAY DIFFRACTION91.62
3.77-3.840.43531450.36224918X-RAY DIFFRACTION94.74
3.84-3.920.34721440.32034884X-RAY DIFFRACTION94.67
3.92-40.45121420.3464936X-RAY DIFFRACTION94.42
4-4.080.36981460.31814844X-RAY DIFFRACTION94.06
4.08-4.180.2851440.27464880X-RAY DIFFRACTION94.97
4.18-4.280.32181470.26674879X-RAY DIFFRACTION94.46
4.28-4.40.30671450.26174919X-RAY DIFFRACTION94.62
4.4-4.530.31571510.24914923X-RAY DIFFRACTION94.45
4.53-4.670.27781390.25734835X-RAY DIFFRACTION94.06
4.67-4.840.2771470.24944947X-RAY DIFFRACTION94.98
4.84-5.030.30381460.24454981X-RAY DIFFRACTION95.83
5.04-5.260.31141490.24445060X-RAY DIFFRACTION98.47
5.26-5.540.32681500.27285128X-RAY DIFFRACTION98.91
5.54-5.890.36331500.26955108X-RAY DIFFRACTION98.5
5.89-6.340.34431500.26685117X-RAY DIFFRACTION99.21
6.34-6.980.3241510.29395127X-RAY DIFFRACTION99.06
6.98-7.980.29691490.28545114X-RAY DIFFRACTION98.43
7.98-10.040.29991430.26864953X-RAY DIFFRACTION95.83
10.05-48.50.35681490.28024941X-RAY DIFFRACTION95.57

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