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- PDB-5gni: The crystal structure of PECAM-1 IgL1-2 trans-homophilic dimer -

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Basic information

Entry
Database: PDB / ID: 5gni
TitleThe crystal structure of PECAM-1 IgL1-2 trans-homophilic dimer
ComponentsPlatelet endothelial cell adhesion molecule
KeywordsCELL ADHESION / Cell adhesion molecule / Immunoglobulin-like domain / Trans-homophilic dimer
Function / homology
Function and homology information


positive regulation of protein localization to cell-cell junction / diapedesis / cell recognition / glomerular endothelium development / monocyte extravasation / neutrophil extravasation / platelet alpha granule membrane / cell-cell adhesion via plasma-membrane adhesion molecules / bicellular tight junction assembly / negative regulation of immune response ...positive regulation of protein localization to cell-cell junction / diapedesis / cell recognition / glomerular endothelium development / monocyte extravasation / neutrophil extravasation / platelet alpha granule membrane / cell-cell adhesion via plasma-membrane adhesion molecules / bicellular tight junction assembly / negative regulation of immune response / establishment of endothelial barrier / leukocyte cell-cell adhesion / maintenance of blood-brain barrier / Platelet sensitization by LDL / homophilic cell adhesion via plasma membrane adhesion molecules / PECAM1 interactions / Integrin cell surface interactions / phagocytosis / secretory granule membrane / Cell surface interactions at the vascular wall / cell-cell adhesion / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / Platelet degranulation / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / membrane raft / positive regulation of protein phosphorylation / external side of plasma membrane / Neutrophil degranulation / signal transduction / protein homodimerization activity / protein-containing complex / extracellular space / extracellular exosome / plasma membrane
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. / Immunoglobulin-like domain ...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
Platelet endothelial cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.008 Å
AuthorsHu, M. / Zhang, H. / Liu, Q. / Hao, Q.
CitationJournal: Sci Rep / Year: 2016
Title: Structural Basis for Human PECAM-1-Mediated Trans-homophilic Cell Adhesion
Authors: Hu, M. / Zhang, H. / Liu, Q. / Hao, Q.
History
DepositionJul 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,1002
Polymers49,1002
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-0 kcal/mol
Surface area19930 Å2
Unit cell
Length a, b, c (Å)60.522, 141.496, 169.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 24549.855 Da / Num. of mol.: 2 / Fragment: UNP residues 28-232 / Mutation: N52Q, N84Q, N151Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PECAM1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P16284

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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: 3.7 Å3/Da / Density % sol: 66.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH6.5, 1.8M (NH4)2SO4, 0.01M CoCl2 / PH range: 6.2-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0719 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0719 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14823 / % possible obs: 99.7 % / Redundancy: 7.9 % / Rsym value: 0.086 / Net I/σ(I): 25.12

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.008→45.447 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.58
RfactorNum. reflection% reflection
Rfree0.2806 557 4.7 %
Rwork0.2205 --
obs0.2234 11839 79.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.008→45.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 0 0 3170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013226
X-RAY DIFFRACTIONf_angle_d1.3434354
X-RAY DIFFRACTIONf_dihedral_angle_d16.4422012
X-RAY DIFFRACTIONf_chiral_restr0.065504
X-RAY DIFFRACTIONf_plane_restr0.007552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0077-3.31020.3025860.27151869X-RAY DIFFRACTION54
3.3102-3.7890.35321090.23772499X-RAY DIFFRACTION71
3.789-4.7730.27351680.21253286X-RAY DIFFRACTION93
4.773-45.45220.25771940.20963628X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.5017 Å / Origin y: 35.2888 Å / Origin z: 35.3553 Å
111213212223313233
T0.1685 Å2-0.0154 Å20.0271 Å2-0.5182 Å2-0.1063 Å2--0.3158 Å2
L1.2805 °2-0.2059 °20.5778 °2-1.3591 °2-1.3009 °2--5.4861 °2
S-0.006 Å °0.1281 Å °-0.0386 Å °-0.0332 Å °0.0093 Å °0.0826 Å °0.0971 Å °0.6982 Å °0.0254 Å °
Refinement TLS groupSelection details: all

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