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- PDB-1xaw: crystal structure of the cytoplasmic distal C-terminal domain of ... -

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Basic information

Entry
Database: PDB / ID: 1xaw
Titlecrystal structure of the cytoplasmic distal C-terminal domain of occludin
ComponentsOccludin
KeywordsCELL ADHESION / coiled-coil
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 / MAD / Resolution: 1.45 Å
AuthorsLi, Y. / Fanning, A.S. / Anderson, J.M. / Lavie, A.
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
DepositionAug 26, 2004Deposition site: RCSB / Processing site: RCSB
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 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)16,6011
Polymers16,6011
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.960, 109.570, 48.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Occludin


Mass: 16601.273 Da / Num. of mol.: 1 / Fragment: residues 383-522 / Mutation: E449V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OCLN / Production host: Escherichia coli (E. coli) / References: UniProt: Q16625
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.44 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.6
Details: amonium sulfate, pH 5.6, VAPOR DIFFUSION, temperature 295.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C10.9
SYNCHROTRONCHESS F221
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2002
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
211
ReflectionResolution: 1.45→50 Å / Num. all: 22450 / Num. obs: 22041 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.063
Reflection shellResolution: 1.45→1.5 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.45→24.73 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 1127 RANDOM
Rwork0.261 --
all0.275 22447 -
obs0.265 20914 -
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.45→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 0 83 987

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