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- PDB-3g7c: Structure of the Phosphorylation Mimetic of Occludin C-term Tail -

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Basic information

Entry
Database: PDB / ID: 3g7c
TitleStructure of the Phosphorylation Mimetic of Occludin C-term Tail
ComponentsOccludin
KeywordsCELL ADHESION / Occludin / Diabetic Retinopathy / ZO-1 / Tight Junction / Adhesion / Cell junction / Coiled coil / Membrane / Phosphoprotein / Transmembrane
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: 2 Å
AuthorsTash, B.R. / Sundstrom, J.M. / Murakami, T. / Flanagan, J.M. / Bewley, M.C. / Antonetii, D.A.
CitationJournal: J.PROTEOME RES. / Year: 2009
Title: Identification and analysis of occludin phosphosites: a combined mass spectrometry and bioinformatics approach.
Authors: Sundstrom, J.M. / Tash, B.R. / Murakami, T. / Flanagan, J.M. / Bewley, M.C. / Stanley, B.A. / Gonsar, K.B. / Antonetti, D.A.
History
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Occludin


Theoretical massNumber of molelcules
Total (without water)13,6361
Polymers13,6361
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.054, 35.591, 107.396
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: 13636.140 Da / Num. of mol.: 1 / Mutation: S490D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OCLN / Plasmid: pET28atev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21gold(DE3) / References: UniProt: Q16625
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium Citrate, 2.2M Ammonium Sulfate, 7% Glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 2006
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 9081 / Num. obs: 9081 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1WPA

1wpa


Resolution: 2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2513 896 RANDOM
Rwork0.2358 --
all0.24 9081 -
obs0.24 9081 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 0 90 1021

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