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- PDB-7oku: X-ray structure of soluble EPCR in P3121 space group -

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Basic information

Entry
Database: PDB / ID: 7oku
TitleX-ray structure of soluble EPCR in P3121 space group
ComponentsEndothelial protein C receptor
KeywordsLIPID BINDING PROTEIN / MHC class I-like / phospholipid / anticoagulant / endothelial cell membrane receptor
Function / homology
Function and homology information


negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space ...negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Endothelial protein C receptor / MHC-I family domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Endothelial protein C receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsErausquin, E. / Dichiara, M.G. / Lopez-Sagaseta, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-094894-B-I00 Spain
Citation
Journal: Sci Rep / Year: 2022
Title: Identification of a broad lipid repertoire associated to the endothelial cell protein C receptor (EPCR).
Authors: Erausquin, E. / Moran-Garrido, M. / Saiz, J. / Barbas, C. / Dichiara-Rodriguez, G. / Urdiciain, A. / Lopez-Sagaseta, J.
#1: Journal: Biorxiv / Year: 2021
Title: A novel alpha / beta T-cell subpopulation defined by recognition of EPCR
Authors: Erausquin, E. / Moran-Garrido, M. / Saiz, J. / Barbas, C. / Dichiara-Rodriguez, G. / Ramirez, N. / Lopez-Sagaseta, J.
History
DepositionMay 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_symm_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1297
Polymers22,2011
Non-polymers1,9286
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-2 kcal/mol
Surface area9600 Å2
Unit cell
Length a, b, c (Å)70.619, 70.619, 97.367
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 22200.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Remaining N-terminal GP motif from 3C site / Source: (gene. exp.) Homo sapiens (human) / Gene: PROCR, EPCR / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UNN8

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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.: 1 / 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, 56 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2.0 M Sodium formate, 0.1 M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2020
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.95→38.12 Å / Num. obs: 21046 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 52.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.023 / Rrim(I) all: 0.071 / Χ2: 0.91 / Net I/σ(I): 14.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1463 / CC1/2: 0.516 / Χ2: 0.78 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSBUILT=20190315data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LQV

1lqv


Resolution: 1.95→38.09 Å / SU ML: 0.2984 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.0911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 997 4.75 %RANDOM
Rwork0.1979 20012 --
obs0.1997 21009 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.96 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 123 53 1526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01441512
X-RAY DIFFRACTIONf_angle_d1.44432052
X-RAY DIFFRACTIONf_chiral_restr0.097239
X-RAY DIFFRACTIONf_plane_restr0.0142254
X-RAY DIFFRACTIONf_dihedral_angle_d12.5779253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.050.30721460.28552792X-RAY DIFFRACTION99.97
2.05-2.180.31071560.25422817X-RAY DIFFRACTION100
2.18-2.350.28131340.21682824X-RAY DIFFRACTION99.86
2.35-2.590.21551200.23152841X-RAY DIFFRACTION100
2.59-2.960.29591600.26722852X-RAY DIFFRACTION100
2.96-3.730.20851450.21082872X-RAY DIFFRACTION100
3.73-38.090.22531360.16563014X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.8797007934 Å / Origin y: -19.3138883521 Å / Origin z: 3.43537806534 Å
111213212223313233
T0.533947372786 Å2-0.183632647073 Å20.037997803734 Å2-0.519714486339 Å20.0227279916674 Å2--0.354090930799 Å2
L3.60099940658 °22.53355197728 °2-0.619363983259 °2-5.14266725335 °2-0.811591363639 °2--1.9659025617 °2
S0.0137975095369 Å °-0.287669878451 Å °-0.120089745127 Å °-0.424039008143 Å °-0.12156368957 Å °-0.317899845184 Å °-0.00450185123637 Å °0.030806560082 Å °0.0693950746648 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 8:204)A8 - 204
2X-RAY DIFFRACTION1(chain B and resseq 1:2)B1 - 2
3X-RAY DIFFRACTION1(chain C and resseq 1:2)C1 - 2

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