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- PDB-5c14: Crystal structure of PECAM-1 D1D2 domain -

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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


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
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

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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
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

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Components

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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

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Sugars , 1 types, 5 molecules

#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

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Non-polymers , 4 types, 34 molecules

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


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


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 / Tris


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


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

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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: 3.89 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

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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

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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

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