[English] 日本語
Yorodumi
- PDB-5c14: Crystal structure of PECAM-1 D1D2 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c14
TitleCrystal structure of PECAM-1 D1D2 domain
Components(Platelet endothelial cell adhesion ...) x 2
KeywordsCELL ADHESION / Immunoglobulin / cell adhesion molecule
Function / homology
Function and homology information


diapedesis / cell recognition / positive regulation of protein localization to cell-cell junction / monocyte extravasation / glomerular endothelium development / cell-cell adhesion via plasma-membrane adhesion molecules / neutrophil extravasation / detection of mechanical stimulus / bicellular tight junction assembly / platelet alpha granule membrane ...diapedesis / cell recognition / positive regulation of protein localization to cell-cell junction / monocyte extravasation / glomerular endothelium development / cell-cell adhesion via plasma-membrane adhesion molecules / neutrophil extravasation / detection of mechanical stimulus / bicellular tight junction assembly / platelet alpha granule membrane / establishment of endothelial barrier / leukocyte cell-cell adhesion / Platelet sensitization by LDL / maintenance of blood-brain barrier / homophilic cell adhesion via plasma membrane adhesion molecules / PECAM1 interactions / positive regulation of intracellular signal transduction / Integrin cell surface interactions / phagocytosis / secretory granule membrane / Cell surface interactions at the vascular wall / cell-cell adhesion / cellular response to mechanical stimulus / vasodilation / transmembrane signaling receptor activity / cell-cell junction / Platelet degranulation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of MAPK cascade / immune response / positive regulation of cell migration / membrane raft / external side of plasma membrane / Neutrophil degranulation / nucleolus / signal transduction / protein homodimerization activity / protein-containing complex / extracellular space / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
C17orf99, Ig domain / C17orf99 Ig domain / : / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...C17orf99, Ig domain / C17orf99 Ig domain / : / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
COPPER (II) ION / Platelet endothelial cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsZhou, D. / Paddock, C. / Newman, P. / Zhu, J.
CitationJournal: Blood / Year: 2016
Title: Structural basis for PECAM-1 homophilic binding.
Authors: Paddock, C. / Zhou, D. / Lertkiatmongkol, P. / Newman, P.J. / Zhu, J.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Platelet endothelial cell adhesion molecule
B: Platelet endothelial cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,77314
Polymers49,0212
Non-polymers1,75212
Water48627
1
A: Platelet endothelial cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6599
Polymers24,5341
Non-polymers1,1268
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Platelet endothelial cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1135
Polymers24,4871
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Platelet endothelial cell adhesion molecule
B: Platelet endothelial cell adhesion molecule
hetero molecules

A: Platelet endothelial cell adhesion molecule
B: Platelet endothelial cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,54628
Polymers98,0414
Non-polymers3,50424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area20070 Å2
ΔGint-41 kcal/mol
Surface area40440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.010, 104.010, 281.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

-
Platelet endothelial cell adhesion ... , 2 types, 2 molecules AB

#1: Protein Platelet endothelial cell adhesion molecule / PECAM-1 / EndoCAM / GPIIA' / PECA1


Mass: 24533.736 Da / Num. of mol.: 1 / Fragment: D1D2 domain (UNP residues 28-229)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PECAM1 / Production host: Drosophila (fruit flies) / References: UniProt: P16284
#2: Protein Platelet endothelial cell adhesion molecule / PECAM-1 / EndoCAM / GPIIA' / PECA1


Mass: 24486.842 Da / Num. of mol.: 1 / Fragment: D1D2 domain (UNP residues 28-229)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PECAM1 / Production host: Drosophila (fruit flies) / References: UniProt: P16284

-
Sugars , 1 types, 5 molecules

#5: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
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 , 4 types, 34 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 0.1 M MgNO3, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97624, 0.97872
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976241
20.978721
ReflectionResolution: 2.8→20 Å / Num. obs: 36261 / % possible obs: 99.6 % / Redundancy: 6.17 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 11.76
Reflection shellResolution: 2.8→3.2 Å / Redundancy: 4.79 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.42 / Num. unique all: 11969 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.79 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 36.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 1014 2.8 %
Rwork0.238 --
obs0.239 36246 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 109 27 3368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153399
X-RAY DIFFRACTIONf_angle_d1.7144569
X-RAY DIFFRACTIONf_dihedral_angle_d17.3521292
X-RAY DIFFRACTIONf_chiral_restr0.066534
X-RAY DIFFRACTIONf_plane_restr0.009571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94720.45581450.39875038X-RAY DIFFRACTION100
2.9472-3.13110.38751440.35595046X-RAY DIFFRACTION100
3.1311-3.37180.37091450.30415023X-RAY DIFFRACTION100
3.3718-3.70910.30781430.24585015X-RAY DIFFRACTION100
3.7091-4.24120.22651410.19725042X-RAY DIFFRACTION100
4.2412-5.32620.20361480.17095039X-RAY DIFFRACTION100
5.3262-19.79410.26481480.22385029X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.9177 Å / Origin y: 33.0702 Å / Origin z: -0.8912 Å
111213212223313233
T0.6149 Å20.3242 Å20.0535 Å2-0.6443 Å20.0726 Å2--0.4905 Å2
L0.7233 °20.1936 °20.1711 °2-0.5571 °20.2333 °2--0.786 °2
S0.0602 Å °0.1525 Å °0.0919 Å °-0.0286 Å °-0.0226 Å °0.1266 Å °-0.0173 Å °-0.0746 Å °-0.0201 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