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- PDB-7oks: X-ray structure of soluble EPCR in P212121 space group -

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Basic information

Entry
Database: PDB / ID: 7oks
TitleX-ray structure of soluble EPCR in P212121 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
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 1.0Apr 27, 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
Revision 1.3Nov 6, 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: Endothelial protein C receptor
B: Endothelial protein C receptor
C: Endothelial protein C receptor
D: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,74627
Polymers88,1864
Non-polymers8,56023
Water4,161231
1
A: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0596
Polymers22,0471
Non-polymers2,0125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1217
Polymers22,0471
Non-polymers2,0746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4457
Polymers22,0471
Non-polymers2,3996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1217
Polymers22,0471
Non-polymers2,0746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.437, 94.019, 124.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 9 through 10 and (name N...
d_2ens_1(chain "B" and (resid 9 through 19 or (resid 20...
d_3ens_1(chain "C" and ((resid 9 through 10 and (name N...
d_4ens_1(chain "D" and ((resid 9 through 10 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNASNA2 - 40
d_12ens_1THRPROA42 - 97
d_13ens_1SERSERA99 - 112
d_14ens_1PHEGLUA114 - 120
d_15ens_1ALATHRA122 - 159
d_16ens_1VALILEA161 - 168
d_17ens_1NAGNAGB
d_18ens_1NAGNAGE
d_21ens_1GLNASNJ1 - 39
d_22ens_1THRPROJ41 - 96
d_23ens_1SERSERJ98 - 111
d_24ens_1PHEGLUJ113 - 119
d_25ens_1ALATHRJ121 - 158
d_26ens_1VALILEJ160 - 167
d_27ens_1NAGNAGK
d_28ens_1NAGNAGN
d_31ens_1GLNASNT1 - 39
d_32ens_1THRSERT41 - 110
d_33ens_1PHEGLUT112 - 118
d_34ens_1ALATHRT120 - 157
d_35ens_1VALILET159 - 166
d_36ens_1NAGNAGU
d_37ens_1NAGNAGX
d_41ens_1GLNASND2 - 40
d_42ens_1THRPROD42 - 97
d_43ens_1SERSERD101 - 114
d_44ens_1PHEGLUD116 - 122
d_45ens_1ALATHRD124 - 161
d_46ens_1VALILED163 - 170
d_47ens_1NAGNAGN
d_48ens_1NAGNAGP

NCS oper:
IDCodeMatrixVector
1given(-0.98157086558, -0.178870815605, -0.0672596994422), (-0.181866324455, 0.982452591738, 0.0413708232513), (0.0586794331393, 0.0528406691101, -0.99687741865)39.0916686923, -0.279868852424, -64.446868065
2given(0.866204958737, -0.151136128513, 0.476284410954), (0.0558065242746, -0.91793887175, -0.392777111832), (0.496562786874, 0.366805259488, -0.786688820503)14.3774362346, 44.147878305, -64.3604087047
3given(-0.891641157795, -0.049650051219, -0.450012131104), (0.218446471959, -0.917794753525, -0.331562858731), (-0.396556660031, -0.393938653619, 0.829189455173)25.7221416147, 44.880496736, 5.27770655366

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 22046.562 Da / Num. of mol.: 4
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 , 4 types, 12 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb5-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+2)][a-L-Sorp5N]{[(5+1)][<C1O1>]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 242 molecules

#6: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 2.8 M sodium acetate pH 8.0, 0.1 M Tris pH 7.0 / PH range: 7.0-8.0

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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→41.53 Å / Num. obs: 67837 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 36.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Χ2: 0.89 / Net I/σ(I): 10.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.081 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4494 / CC1/2: 0.867 / Rpim(I) all: 0.447 / Χ2: 0.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSBUILT=20190315data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LQV

1lqv


Resolution: 1.95→40.32 Å / SU ML: 0.2598 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 3289 4.87 %RANDOM
Rwork0.199 64310 --
obs0.201 67599 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.89 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 0 549 231 6093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00946036
X-RAY DIFFRACTIONf_angle_d1.07738181
X-RAY DIFFRACTIONf_chiral_restr0.0605973
X-RAY DIFFRACTIONf_plane_restr0.0103994
X-RAY DIFFRACTIONf_dihedral_angle_d12.68491050
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS3.28233804157
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS3.66824818752
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS3.24801280178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.37331320.33732771X-RAY DIFFRACTION99.52
1.98-2.010.32751370.29992802X-RAY DIFFRACTION99.83
2.01-2.040.2911290.26342730X-RAY DIFFRACTION99.55
2.04-2.080.31391480.25362775X-RAY DIFFRACTION99.32
2.08-2.120.27031250.24732717X-RAY DIFFRACTION99.27
2.12-2.160.29181530.23352760X-RAY DIFFRACTION99.49
2.16-2.20.25881280.22342741X-RAY DIFFRACTION98.79
2.2-2.250.26281480.21282760X-RAY DIFFRACTION99.49
2.25-2.30.25321480.20752807X-RAY DIFFRACTION99.86
2.3-2.360.27571210.20532765X-RAY DIFFRACTION99.55
2.36-2.420.26931550.21292733X-RAY DIFFRACTION99.48
2.42-2.490.2621680.22492765X-RAY DIFFRACTION99.56
2.49-2.570.27871470.22022767X-RAY DIFFRACTION99.83
2.57-2.670.30661580.2162787X-RAY DIFFRACTION99.83
2.67-2.770.27491490.21412789X-RAY DIFFRACTION99.73
2.77-2.90.32971340.22632810X-RAY DIFFRACTION99.86
2.9-3.050.26651260.23722806X-RAY DIFFRACTION99.97
3.05-3.240.24891310.20712833X-RAY DIFFRACTION100
3.24-3.490.26061480.18812818X-RAY DIFFRACTION99.9
3.49-3.840.22151770.17372794X-RAY DIFFRACTION99.97
3.84-4.40.14341430.15542851X-RAY DIFFRACTION99.93
4.4-5.540.18061450.16462906X-RAY DIFFRACTION99.93
5.54-40.320.25391390.20373023X-RAY DIFFRACTION99.94
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)
13.07683157763-0.713837092788-0.6443409369382.25957856627-0.1023835461642.767930668980.07934294001530.07341947846780.176174950365-0.1883627713560.0398717806398-0.0405546030019-0.0547579269907-0.0322865098247-0.1190241510330.262031722922-0.006139687369930.0215582959320.204850321590.01107385731250.244673147408-0.17935227893416.7058450278-18.4486993093
22.331765740350.693487666067-0.6468048271082.779278702520.5068691153683.500385353440.0863467514732-0.1408745133660.03000811788110.215797474242-0.03806607658190.008500131216220.0127403765675-0.060990914989-0.04867185433320.279744180610.03372802482370.01080023586240.2442607603380.008565882830360.22869182044337.480516609215.0209534231-45.3358140457
32.087931100940.5151804710550.6532663110071.670772638830.02603625855223.09036439923-0.0225970474541-0.0118791093651-0.04064575585980.09054077793940.08600051645920.04086084167060.0803269322644-0.17162298591-0.06472287245050.292267442848-0.000691100101354-0.03391965888410.256514978220.009322213218620.2732550984752.9294107021436.1793267142-44.241249117
41.61394239077-0.224447938440.8087502295742.28113807052-0.2738631592974.09911852258-0.04250852676860.080816845367-0.0911207157743-0.03067512150550.1305723916960.02546919608230.266389346668-0.137019290775-0.08568904622720.303215622463-0.0437804133347-0.03397049501090.252080174896-0.01618511427260.24827304819233.16073844335.7351331261-16.2221207674
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 8:177)AA - F8 - 1771
22(chain B and resseq 9:177)BB - H9 - 1771
33(chain C and resseq 9:177)CC - AA9 - 1771
44(chain D and resseq 9:177)DD - P9 - 1772
51(chain E and resseq 201)E201
61(chain F and resseq 203)F203
71(chain F and resseq 206)F206
81(chain G and resseq 204)G204
92(chain H and resseq 201)H201
102(chain H and resseq 206)H206
112(chain I and resseq 202)I202
122(chain J and resseq 205)J205
133(chain K and resseq 201)K201
143(chain K and resseq 202)K202
153(chain L and resseq 203)L203
163(chain L and resseq 208)L208
173(chain M and resseq 204)M204
184(chain N and resseq 201)N201
194(chain N and resseq 207)N207
204(chain O and resseq 202)O202
214(chain O and resseq 206)O206
224(chain P and resseq 205)P205
234(chain P and resseq 208)P208

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