[English] 日本語
Yorodumi
- PDB-7oks: X-ray structure of soluble EPCR in P212121 space group -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Non-polymers , 3 types, 242 molecules

#6: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / 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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more