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- PDB-6m3b: hAPC-c25k23 Fab complex -

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Basic information

Entry
Database: PDB / ID: 6m3b
TitlehAPC-c25k23 Fab complex
Components
  • (Vitamin K-dependent protein C ...) x 2
  • c25k23 Fab H chain
  • c25k23 Fab L chain
KeywordsBLOOD CLOTTING/IMMUNE SYSTEM / human APC / c25k23 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 / 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 ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / 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 / 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: 2.2 Å
AuthorsWang, X. / Li, L. / 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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 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
A: Vitamin K-dependent protein C heavy chain
D: Vitamin K-dependent protein C light chain
B: c25k23 Fab L chain
C: c25k23 Fab H chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5056
Polymers92,0634
Non-polymers4422
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.277, 94.889, 114.320
Angle α, β, γ (deg.)90.000, 105.490, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Vitamin K-dependent protein C ... , 2 types, 2 molecules AD

#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.: 1
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.: 1
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)

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Antibody , 2 types, 2 molecules BC

#3: Antibody c25k23 Fab L chain


Mass: 22472.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody c25k23 Fab H chain


Mass: 23890.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Sugars / Non-polymers , 2 types, 141 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.19 Å3/Da / Density % sol: 61.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1% n-Octyl-beta-D-glucoside, 0.1M sodium citrate tribasic dehydrate pH 5.5, 22% (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: Apr 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 57099 / % possible obs: 97.22 % / Redundancy: 4.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.096 / Net I/σ(I): 32.22
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 3.04 / Num. unique obs: 4288 / CC1/2: 0.825 / Rpim(I) all: 0.531

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUT

1aut


Resolution: 2.2→27.542 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.84
RfactorNum. reflection% reflection
Rfree0.2475 2920 5.11 %
Rwork0.2183 --
obs0.2198 57099 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 196.09 Å2 / Biso mean: 65.4415 Å2 / Biso min: 38.39 Å2
Refinement stepCycle: final / Resolution: 2.2→27.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5725 0 28 139 5892
Biso mean--88.89 61.04 -
Num. residues----756
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.23610.3841460.3514257897
2.2361-2.27460.41131410.3419254997
2.2746-2.31590.40081440.3272256997
2.3159-2.36050.35461560.3244254797
2.3605-2.40860.4051480.3046252497
2.4086-2.4610.32661310.2928261697
2.461-2.51820.34521290.2899254497
2.5182-2.58110.40441200.2815258398
2.5811-2.65080.32831100.2865264198
2.6508-2.72880.37061450.2692259298
2.7288-2.81680.30061270.2651256998
2.8168-2.91730.2641500.247258898
2.9173-3.0340.28041630.254256198
3.034-3.17190.28641490.2426259198
3.1719-3.33890.23331320.2306262098
3.3389-3.54760.24361230.2062261098
3.5476-3.82090.21571400.2014260498
3.8209-4.20420.18211500.1915258098
4.2042-4.80980.20651500.1582259998
4.8098-6.04920.2011340.178261997
6.0492-27.5420.23621320.2091249591

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