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- PDB-6m3c: hAPC-h1573 Fab complex -

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Basic information

Entry
Database: PDB / ID: 6m3c
TitlehAPC-h1573 Fab complex
Components
  • Vitamin K-dependent protein C heavy chain
  • Vitamin K-dependent protein C light chain
  • h1573 Fab H chain
  • h1573 Fab L chain
KeywordsBLOOD CLOTTING/IMMUNE SYSTEM / human APC / h1573 Fab / complex / BLOOD CLOTTING / BLOOD CLOTTING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


activated protein C (thrombin-activated peptidase) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall ...activated protein C (thrombin-activated peptidase) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / Golgi lumen / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / negative regulation of apoptotic process / endoplasmic reticulum / Golgi apparatus / proteolysis / extracellular space / extracellular region
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vitamin K-dependent protein C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsWang, X. / Wang, D. / Zhao, X. / Egner, U.
CitationJournal: Nat Commun / Year: 2020
Title: Targeted inhibition of activated protein C by a non-active-site inhibitory antibody to treat hemophilia.
Authors: Zhao, X.Y. / Wilmen, A. / Wang, D. / Wang, X. / Bauzon, M. / Kim, J.Y. / Linden, L. / Li, L. / Egner, U. / Marquardt, T. / Moosmayer, D. / Tebbe, J. / Gluck, J.M. / Ellinger, P. / McLean, K. ...Authors: Zhao, X.Y. / Wilmen, A. / Wang, D. / Wang, X. / Bauzon, M. / Kim, J.Y. / Linden, L. / Li, L. / Egner, U. / Marquardt, T. / Moosmayer, D. / Tebbe, J. / Gluck, J.M. / Ellinger, P. / McLean, K. / Yuan, S. / Yegneswaran, S. / Jiang, X. / Evans, V. / Gu, J.M. / Schneider, D. / Zhu, Y. / Xu, Y. / Mallari, C. / Hesslein, A. / Wang, Y. / Schmidt, N. / Gutberlet, K. / Ruehl-Fehlert, C. / Freyberger, A. / Hermiston, T. / Patel, C. / Sim, D. / Mosnier, L.O. / Laux, V.
History
DepositionMar 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 1.2Oct 16, 2024Group: Structure summary / Category: 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: Vitamin K-dependent protein C heavy chain
B: Vitamin K-dependent protein C light chain
L: h1573 Fab H chain
H: h1573 Fab L chain
C: Vitamin K-dependent protein C heavy chain
D: Vitamin K-dependent protein C light chain
E: h1573 Fab H chain
F: h1573 Fab L chain
G: Vitamin K-dependent protein C heavy chain
I: Vitamin K-dependent protein C light chain
J: h1573 Fab H chain
K: h1573 Fab L chain


Theoretical massNumber of molelcules
Total (without water)279,68412
Polymers279,68412
Non-polymers00
Water00
1
A: Vitamin K-dependent protein C heavy chain
B: Vitamin K-dependent protein C light chain
L: h1573 Fab H chain
H: h1573 Fab L chain


Theoretical massNumber of molelcules
Total (without water)93,2284
Polymers93,2284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Vitamin K-dependent protein C heavy chain
D: Vitamin K-dependent protein C light chain
E: h1573 Fab H chain
F: h1573 Fab L chain


Theoretical massNumber of molelcules
Total (without water)93,2284
Polymers93,2284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Vitamin K-dependent protein C heavy chain
I: Vitamin K-dependent protein C light chain
J: h1573 Fab H chain
K: h1573 Fab L chain


Theoretical massNumber of molelcules
Total (without water)93,2284
Polymers93,2284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.339, 124.339, 666.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain C and segid C
31chain G and segid G
12chain B and segid B
22chain D and segid D
32chain I and segid I
13chain E and segid E
23chain J and segid J
33chain L and segid L
14chain F and segid F
24chain H and segid H
34chain K and segid K

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain C and segid CC0
311chain G and segid GG0
112chain B and segid BB0
212chain D and segid DD0
312chain I and segid II0
113chain E and segid EE0
213chain J and segid JJ0
313chain L and segid LL0
114chain F and segid FF0
214chain H and segid HH0
314chain K and segid KK0

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Vitamin K-dependent protein C heavy chain / Anticoagulant protein C / Autoprothrombin IIA / Blood coagulation factor XIV


Mass: 28091.115 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PROC / Production host: Homo sapiens (human)
References: UniProt: P04070, activated protein C (thrombin-activated peptidase)
#2: Protein Vitamin K-dependent protein C light chain / Anticoagulant protein C / Autoprothrombin IIA / Blood coagulation factor XIV


Mass: 17607.980 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PROC / Production host: Homo sapiens (human)
References: UniProt: P04070, activated protein C (thrombin-activated peptidase)
#3: Antibody h1573 Fab H chain


Mass: 23749.223 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody h1573 Fab L chain


Mass: 23779.533 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
Has protein modificationY

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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: 4.6 Å3/Da / Density % sol: 73.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium fluoride, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 56425 / % possible obs: 98.42 % / Redundancy: 5.5 % / Biso Wilson estimate: 69.9 Å2 / Rpim(I) all: 0.149 / Net I/σ(I): 6.14
Reflection shellResolution: 3.7→3.79 Å / Num. unique obs: 3756 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUT

1aut


Resolution: 3.7→33.385 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3022 2811 4.98 %
Rwork0.2784 53614 -
obs0.2796 56425 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 243.12 Å2 / Biso mean: 107.9789 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.7→33.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16911 0 0 0 16911
Num. residues----2193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417340
X-RAY DIFFRACTIONf_angle_d1.10123502
X-RAY DIFFRACTIONf_chiral_restr0.0432589
X-RAY DIFFRACTIONf_plane_restr0.0073024
X-RAY DIFFRACTIONf_dihedral_angle_d14.7926249
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3302X-RAY DIFFRACTION8.641TORSIONAL
12C3302X-RAY DIFFRACTION8.641TORSIONAL
13G3302X-RAY DIFFRACTION8.641TORSIONAL
21B717X-RAY DIFFRACTION8.641TORSIONAL
22D717X-RAY DIFFRACTION8.641TORSIONAL
23I717X-RAY DIFFRACTION8.641TORSIONAL
31E3042X-RAY DIFFRACTION8.641TORSIONAL
32J3042X-RAY DIFFRACTION8.641TORSIONAL
33L3042X-RAY DIFFRACTION8.641TORSIONAL
41F3006X-RAY DIFFRACTION8.641TORSIONAL
42H3006X-RAY DIFFRACTION8.641TORSIONAL
43K3006X-RAY DIFFRACTION8.641TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.7-3.76370.43611420.37932679100
3.7637-3.83210.34511340.37792640100
3.8321-3.90570.5695970.5887216780
3.9057-3.98530.40461250.425249793
3.9853-4.07180.40871320.31282643100
4.0718-4.16630.29371570.30192670100
4.1663-4.27030.33311340.27882704100
4.2703-4.38550.32361350.26072653100
4.3855-4.51430.27451470.25922682100
4.5143-4.65960.2611390.25712693100
4.6596-4.82570.3321250.25062709100
4.8257-5.01830.26671620.24732700100
5.0183-5.24590.2661670.23462686100
5.2459-5.52130.25781270.23822723100
5.5213-5.86540.28271510.24542744100
5.8654-6.31550.30671370.25532739100
6.3155-6.94590.27581450.25242767100
6.9459-7.93920.2761490.25682771100
7.9392-9.95830.23791400.217281999
9.9583-33.3850.281660.2541292897
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)
12.15140.2649-0.21752.33950.65623.85810.17210.14810.0298-0.0056-0.2261-0.1668-0.1621-0.46720.00011.0736-0.2889-0.04060.80120.06610.887815.9873-45.600919.8096
21.80990.2714-0.84614.4847-0.9782.89740.07970.4120.1075-0.5415-0.06340.5612-0.2552-0.397-0.01971.0162-0.1933-0.18051.07940.09411.0416-8.6257-68.054-36.353
32.8613-0.09950.8042.7793-0.77963.9651-0.2190.4582-0.1654-0.07910.28620.05380.16630.3398-0.03890.9374-0.07680.02871.1773-0.03330.87413.7529-82.928174.8262
42.08210.22680.63532.8240.92092.32040.216-0.1593-0.44990.0417-0.0968-0.23270.05180.02130.00020.6394-0.3214-0.0120.81160.10311.0643-0.1446-93.7991-3.477
51.79531.7362-1.2454.0828-1.83541.48760.2455-0.16290.03380.5255-0.09750.0369-0.3748-0.00190.0011.2364-0.1545-0.01851.10440.04250.908127.4332-28.6764-54.1242
62.0523-0.9970.29563.5556-2.26424.06870.0536-0.33920.31210.55930.17370.2319-1.3758-0.62280.0041.7819-0.14160.06311.0755-0.08091.14991.4178-30.851856.9087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 212:450)) or chain 'B' and ((resseq 136:187))A0
2X-RAY DIFFRACTION2chain 'C' and ((resseq 212:450)) or chain 'D' and ((resseq 136:187))C0
3X-RAY DIFFRACTION3chain 'G' and ((resseq 212:450)) or chain 'I' and ((resseq 136:187))G0
4X-RAY DIFFRACTION4chain 'L' and ((resseq 1:218)) or chain 'H' and ((resseq 1:221))L0
5X-RAY DIFFRACTION5chain 'E' and ((resseq 1:218)) or chain 'F' and ((resseq 1:221))E0
6X-RAY DIFFRACTION6chain 'J' and ((resseq 1:218)) or chain 'K' and ((resseq 1:221))J0

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