[English] 日本語
Yorodumi
- PDB-7okt: X-ray structure of soluble EPCR in C2221 space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7okt
TitleX-ray structure of soluble EPCR in C2221 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,40511
Polymers44,4012
Non-polymers3,0049
Water3,765209
1
A: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6606
Polymers22,2011
Non-polymers1,4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7455
Polymers22,2011
Non-polymers1,5444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.295, 91.602, 123.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 10 and (name N or name...
d_2ens_1(chain "B" and (resid 10 through 22 or (resid 23...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGHISA2 - 76
d_12ens_1GLUGLUA78
d_13ens_1THRPROA80 - 96
d_14ens_1HISASPA100 - 125
d_15ens_1GLNVALA127 - 128
d_16ens_1GLYGLYA130
d_17ens_1VALILEA132 - 165
d_18ens_1NAGNAGB
d_19ens_1NAGNAGC
d_110ens_1NAGNAGE
d_111ens_1PTYPTYF
d_21ens_1ARGHISG2 - 76
d_22ens_1GLUGLYG78 - 124
d_23ens_1VALILEG126 - 159
d_24ens_1NAGNAGH
d_25ens_1NAGNAGI
d_26ens_1NAGNAGK
d_27ens_1PTYPTYL

NCS oper: (Code: givenMatrix: (-0.92376346297, -0.0961031747764, 0.370709110057), (-0.0662558766436, -0.913298092764, -0.401866585527), (0.377188577891, -0.395791325765, 0.837304008803)Vector: -45. ...NCS oper: (Code: given
Matrix: (-0.92376346297, -0.0961031747764, 0.370709110057), (-0.0662558766436, -0.913298092764, -0.401866585527), (0.377188577891, -0.395791325765, 0.837304008803)
Vector: -45.7275036887, 0.385452512025, 3.658884202)

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 22200.730 Da / Num. of mol.: 2
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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UNN8

-
Sugars , 2 types, 6 molecules

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


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}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 / N-Acetylglucosamine


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

-
Non-polymers , 3 types, 212 molecules

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8 M Sodium acetate pH 7.0

-
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→45.8 Å / Num. obs: 31475 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 45.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Χ2: 0.91 / Net I/σ(I): 11.7
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.549 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2191 / CC1/2: 0.514 / Rpim(I) all: 0.684 / Rrim(I) all: 1.696 / Χ2: 0.87 / % possible all: 100

-
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→45.8 Å / SU ML: 0.2714 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 1532 4.88 %
Rwork0.2206 29881 -
obs0.2223 31413 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.34 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 183 209 2872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01422727
X-RAY DIFFRACTIONf_angle_d1.22763701
X-RAY DIFFRACTIONf_chiral_restr0.077433
X-RAY DIFFRACTIONf_plane_restr0.0114456
X-RAY DIFFRACTIONf_dihedral_angle_d9.9726458
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.20055650219 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.36981280.35972682X-RAY DIFFRACTION99.89
2.01-2.080.35491350.32892688X-RAY DIFFRACTION99.96
2.08-2.170.32341740.292642X-RAY DIFFRACTION99.75
2.17-2.270.32521470.24642672X-RAY DIFFRACTION99.79
2.27-2.390.29141190.23862712X-RAY DIFFRACTION99.86
2.39-2.540.26091390.22962691X-RAY DIFFRACTION99.86
2.54-2.730.28961460.24832700X-RAY DIFFRACTION99.93
2.73-3.010.28141140.2312742X-RAY DIFFRACTION99.96
3.01-3.440.26311430.21742725X-RAY DIFFRACTION99.97
3.44-4.340.23821490.18732753X-RAY DIFFRACTION100
4.34-45.80.22591380.21312874X-RAY DIFFRACTION99.83
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)
13.131999921351.106296523550.2275761130914.9965325825-0.7424837236585.716817267250.121682982129-0.19948032218-0.2512176996910.1940362838630.1789723664610.03716719871660.499416400662-0.206352608452-0.2179606374540.412254671711-0.0506972612474-0.1317532737270.3387850351570.09083439579470.428686631276-17.2736027135-16.57263183916.9124223922
21.92254142996-0.7366349933250.2475861845692.63812445916-0.153658589395.013774103770.0635117664865-0.2753934170460.1146678263150.3813727008360.3868591538060.167989345556-0.817855251527-0.432076424454-0.4007903702480.5365311300140.08992747988320.1631189635370.4113667043150.04252753993750.383934074271-21.67952288099.8350291664817.1608627629
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain A and resseq 9:205)AA - D9 - 205
22(chain B and resseq 9:203)BG - L9 - 203

+
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