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- PDB-1wpa: 1.5 Angstrom crystal structure of human occludin fragment 413-522 -

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Basic information

Entry
Database: PDB / ID: 1wpa
Title1.5 Angstrom crystal structure of human occludin fragment 413-522
ComponentsOccludin
KeywordsCELL ADHESION / occludin / coiled-coil / ZO-1 binding / transmembrane protein
Function / homology
Function and homology information


protein localization to cell leading edge / positive regulation of blood-brain barrier permeability / RUNX1 regulates expression of components of tight junctions / regulation of D-glucose transmembrane transport / bicellular tight junction assembly / apicolateral plasma membrane / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / tight junction / positive regulation of wound healing ...protein localization to cell leading edge / positive regulation of blood-brain barrier permeability / RUNX1 regulates expression of components of tight junctions / regulation of D-glucose transmembrane transport / bicellular tight junction assembly / apicolateral plasma membrane / cell-cell junction organization / Apoptotic cleavage of cell adhesion proteins / tight junction / positive regulation of wound healing / maintenance of blood-brain barrier / cell leading edge / endocytic vesicle / bicellular tight junction / positive regulation of lamellipodium assembly / positive regulation of microtubule polymerization / positive regulation of D-glucose import / cell junction / cell-cell junction / protein-containing complex assembly / cytoplasmic vesicle / apical plasma membrane / protein domain specific binding / lysosomal membrane / negative regulation of gene expression / positive regulation of gene expression / protein-containing complex / plasma membrane
Similarity search - Function
Helix Hairpins - #340 / Occludin / Occludin homology domain / ELL/occludin family / Occludin homology domain / Occludin/ELL (OCEL) domain profile. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / Helix Hairpins ...Helix Hairpins - #340 / Occludin / Occludin homology domain / ELL/occludin family / Occludin homology domain / Occludin/ELL (OCEL) domain profile. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / Helix Hairpins / MFS transporter superfamily / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, Y. / Lavie, A. / Fanning, A.S. / Anderson, J.M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of the conserved cytoplasmic C-terminal domain of occludin: identification of the ZO-1 binding surface.
Authors: Li, Y. / Fanning, A.S. / Anderson, J.M. / Lavie, A.
History
DepositionSep 1, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 17, 2014Group: Database references
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Occludin


Theoretical massNumber of molelcules
Total (without water)13,6951
Polymers13,6951
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.020, 35.310, 107.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Occludin


Mass: 13695.207 Da / Num. of mol.: 1 / Fragment: residues 413-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q16625
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.6
Details: ammonium sulfate, pH 5.6, EVAPORATION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 21026 / Num. obs: 20588 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.5→1.58 Å / % possible all: 90.6

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.258 1064 random
Rwork0.237 --
all0.243 20942 -
obs0.24 20564 -
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 0 106 1012

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