[English] 日本語
Yorodumi
- PDB-7q5d: Structure of EPCR in a non-canonical conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q5d
TitleStructure of EPCR in a non-canonical conformation
ComponentsEndothelial protein C receptor
KeywordsBLOOD CLOTTING / Endothelium / MHC-I-like / lipid receptor / conformational change
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
CYSTEINE / PHOSPHATIDYLETHANOLAMINE / Endothelial protein C receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLopez-Sagaseta, J. / Erausquin, E.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-094894-B-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2017-21683 Spain
CitationJournal: Biorxiv / Year: 2021
Title: Structure of EPCR in a non-canonical conformation
Authors: Erausquin, E. / Rodriguez-Fernandez, A. / Lopez-Sagaseta, J.
History
DepositionNov 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endothelial protein C receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9976
Polymers22,2011
Non-polymers1,7965
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-7 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.470, 70.470, 96.635
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

-
Components

-
Protein / Sugars , 2 types, 3 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: Remaning 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: 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

-
Non-polymers , 4 types, 69 molecules

#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium-potassium tartrate, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979182 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2020
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979182 Å / Relative weight: 1
ReflectionResolution: 1.8→96.64 Å / Num. obs: 26315 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 42.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.015 / Rrim(I) all: 0.036 / Net I/σ(I): 21.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6 % / Rmerge(I) obs: 1.004 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1531 / CC1/2: 0.644 / Rpim(I) all: 0.447 / Rrim(I) all: 1.101 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSBUILT=20200131data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8J

1l8j


Resolution: 1.8→37.88 Å / SU ML: 0.2053 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2201 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1946 1398 5.32 %
Rwork0.1835 24877 -
obs0.1841 26275 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 119 66 1563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01241551
X-RAY DIFFRACTIONf_angle_d1.16772108
X-RAY DIFFRACTIONf_chiral_restr0.0861237
X-RAY DIFFRACTIONf_plane_restr0.0081263
X-RAY DIFFRACTIONf_dihedral_angle_d7.89241204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.32421250.26432455X-RAY DIFFRACTION99.96
1.86-1.940.25651460.23682450X-RAY DIFFRACTION99.96
1.94-2.030.18011230.18622483X-RAY DIFFRACTION99.96
2.03-2.130.20341750.18952422X-RAY DIFFRACTION100
2.13-2.270.1891230.17952467X-RAY DIFFRACTION100
2.27-2.440.22581380.19332489X-RAY DIFFRACTION99.96
2.44-2.690.20611270.20072474X-RAY DIFFRACTION99.85
2.69-3.080.20241600.19632475X-RAY DIFFRACTION99.89
3.08-3.880.1811210.17192543X-RAY DIFFRACTION99.81
3.8-37.80.18731600.17662619X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: 29.2707127159 Å / Origin y: -13.0799160405 Å / Origin z: -3.12641730183 Å
111213212223313233
T0.480843682155 Å2-0.0576904520074 Å20.0331119174115 Å2-0.221960481952 Å20.0249055805861 Å2--0.363344135886 Å2
L3.7399549583 °22.09726444921 °20.188946798178 °2-5.13356710741 °2-0.722269630415 °2--3.30149949365 °2
S0.0275849893766 Å °-0.107305985025 Å °-0.159996795678 Å °-0.311404745933 Å °-0.0860297927679 Å °-0.209175844339 Å °0.109304048457 Å °-0.0256702333892 Å °0.0490685293526 Å °
Refinement TLS groupSelection details: all

+
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