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- PDB-1lqv: Crystal structure of the Endothelial protein C receptor with phos... -

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Basic information

Entry
Database: PDB / ID: 1lqv
TitleCrystal structure of the Endothelial protein C receptor with phospholipid in the groove in complex with Gla domain of protein C.
Components
  • Endothelial protein C receptor
  • Vitamin-K dependent protein C
KeywordsBLOOD CLOTTING / Gla (gamma-carboxyglutamic acid) residues / phospholipid binding groove / Ca ion binding
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 / signaling receptor activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / focal adhesion / calcium ion binding / centrosome / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Endothelial protein C receptor / MHC-I family domain / 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 calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Endothelial protein C receptor / MHC-I family domain / 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 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. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Vitamin K-dependent protein C / Endothelial protein C receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOganesyan, V. / Oganesyan, N. / Terzyan, S. / Dongfeng, Q. / Dauter, Z. / Esmon, N.L. / Esmon, C.T.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The crystal structure of the endothelial protein C receptor and a bound phospholipid.
Authors: Oganesyan, V. / Oganesyan, N. / Terzyan, S. / Qu, D. / Dauter, Z. / Esmon, N.L. / Esmon, C.T.
History
DepositionMay 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothelial protein C receptor
B: Endothelial protein C receptor
C: Vitamin-K dependent protein C
D: Vitamin-K dependent protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,16826
Polymers52,8124
Non-polymers3,35622
Water7,728429
1
A: Endothelial protein C receptor
C: Vitamin-K dependent protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,08413
Polymers26,4062
Non-polymers1,67811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-88 kcal/mol
Surface area11470 Å2
MethodPISA
2
B: Endothelial protein C receptor
D: Vitamin-K dependent protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,08413
Polymers26,4062
Non-polymers1,67811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-88 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.220, 62.360, 71.030
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide / Sugars , 3 types, 10 molecules ABCD

#1: Protein Endothelial protein C receptor / Endothelial cell protein C receptor / Activated protein C receptor / APC receptor


Mass: 22046.562 Da / Num. of mol.: 2 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEE EPCR / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO lecI / References: UniProt: Q9UNN8
#2: Protein/peptide Vitamin-K dependent protein C / Autoprothrombin IIA / Anticoagulant protein C / Blood coagulation factor XIV


Mass: 4359.409 Da / Num. of mol.: 2 / Fragment: Protein C Gla domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Cleavage happened during crystallization and the crystal contains only the N-terminal domain (Gla domain) of protein C.
References: UniProt: P04070
#3: 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.: 6 / Source method: obtained synthetically / 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

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Non-polymers , 3 types, 445 molecules

#4: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: peg 400, potassium chloride, magnesium chloride, calcium chloride, hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM11CaCl2
20.02 %11NaN3
320 mg/mlprotein11
420 mMTris-HCl11pH7.5
5100 mM11NaCl
6100 mM12KCl
710 mM12MgCl2
810 mM12CaCl2
950 mMHEPES12pH7.0
105 %(v/v)polyethylene glycol12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2001 / Details: mirrors
RadiationMonochromator: CuKa / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 73694 / Num. obs: 66375 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.041 / Net I/σ(I): 27
Reflection shellResolution: 1.55→1.61 Å / % possible obs: 49.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 27 / Num. unique all: 66000 / Rsym value: 0.043 / % possible all: 91
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 98 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 83.8 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Endothelial protein C receptor

Resolution: 1.6→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3000 -random 5%
Rwork0.189 ---
all0.189 66336 --
obs0.189 66335 100 %-
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-0.282 Å20 Å2-5.177 Å2
2---3.316 Å20 Å2
3---3.033 Å2
Refinement stepCycle: LAST / Resolution: 1.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 198 429 4048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d1.73
X-RAY DIFFRACTIONc_angle_deg1.73
LS refinement shellResolution: 1.6→12 Å
RfactorNum. reflection% reflection
Rfree0.222 3000 -
Rwork0.189 --
obs-66335 100 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_d
LS refinement shell
*PLUS
Rfactor obs: 0.189

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