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- PDB-7okv: Crystal structure of soluble EPCR after exposure to the nonionic ... -

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Basic information

Entry
Database: PDB / ID: 7okv
TitleCrystal structure of soluble EPCR after exposure to the nonionic surfactant Polysorbate 20
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
DECANE / HEXANE / HEXADECANE / Endothelial protein C receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
CitationJournal: 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.
History
DepositionMay 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3818
Polymers22,2011
Non-polymers1,1817
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint17 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.051, 71.051, 103.153
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 / Sugars , 2 types, 4 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
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / 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 , 5 types, 60 molecules

#3: Chemical ChemComp-R16 / HEXADECANE / Hexadecane


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.39 Å3/Da / Density % sol: 63.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 3.5 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: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2020
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.85→35.53 Å / Num. obs: 26239 / % possible obs: 99.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 37.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.037 / Rrim(I) all: 0.105 / Χ2: 0.94 / Net I/σ(I): 10.6
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1589 / CC1/2: 0.543 / Χ2: 0.99 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSBUILT=20190315data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LQV

1lqv


Resolution: 1.85→35.53 Å / SU ML: 0.2524 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6203
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2335 1374 5.25 %
Rwork0.2131 24811 -
obs0.2142 26185 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.34 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1321 0 78 56 1455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051434
X-RAY DIFFRACTIONf_angle_d0.81011943
X-RAY DIFFRACTIONf_chiral_restr0.0533226
X-RAY DIFFRACTIONf_plane_restr0.0065243
X-RAY DIFFRACTIONf_dihedral_angle_d7.8471224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.361460.34982417X-RAY DIFFRACTION98.8
1.92-1.990.28631360.27512422X-RAY DIFFRACTION99.22
1.99-2.080.24561530.22972440X-RAY DIFFRACTION99.27
2.08-2.190.23061350.20752434X-RAY DIFFRACTION99.38
2.19-2.330.22581120.23022475X-RAY DIFFRACTION99.65
2.33-2.510.23481180.19882504X-RAY DIFFRACTION99.7
2.51-2.760.25781510.23852460X-RAY DIFFRACTION99.81
2.76-3.160.23741390.21992493X-RAY DIFFRACTION99.92
3.16-3.980.24531290.19762540X-RAY DIFFRACTION99.93
3.98-35.530.21131550.20282626X-RAY DIFFRACTION99.61
Refinement TLS params.Method: refined / Origin x: 26.1429228867 Å / Origin y: -21.6680897467 Å / Origin z: 3.05524115638 Å
111213212223313233
T0.382215614602 Å2-0.146399298802 Å20.00820370524233 Å2-0.269456584919 Å20.0370768447286 Å2--0.361218006307 Å2
L3.18323656826 °22.48319259468 °20.129042958716 °2-5.75251560164 °20.830484227547 °2--2.83920655653 °2
S0.0225361213296 Å °-0.149677885888 Å °-0.0625514852818 Å °-0.0154219444772 Å °4.35163761487E-5 Å °-0.0824403980506 Å °0.202492823382 Å °-0.0833337206444 Å °-0.012206003202 Å °
Refinement TLS groupSelection details: all

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