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- PDB-5k4f: CAL PDZ mutant C319A with a peptide -

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Basic information

Entry
Database: PDB / ID: 5k4f
TitleCAL PDZ mutant C319A with a peptide
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • HPV18E6 peptide
KeywordsPEPTIDE BINDING PROTEIN / CAL PDZ mutant / C319A
Function / homology
Function and homology information


negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport ...negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / PDZ domain binding / : / protein transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / transmembrane transporter binding / postsynaptic density / lysosomal membrane / Golgi membrane / negative regulation of DNA-templated transcription / dendrite / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / Golgi apparatus / protein-containing complex / DNA binding / zinc ion binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Golgi-associated PDZ and coiled-coil motif-containing protein / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Golgi-associated PDZ and coiled-coil motif-containing protein / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein E6 / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsZhao, Y. / Madden, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK101541 United States
CitationJournal: To Be Published
Title: CAL PDZ domain mutant with a peptide
Authors: Zhao, Y. / Madden, D.R.
History
DepositionMay 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: HPV18E6 peptide
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: HPV18E6 peptide


Theoretical massNumber of molelcules
Total (without water)21,3344
Polymers21,3344
Non-polymers00
Water2,576143
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: HPV18E6 peptide


Theoretical massNumber of molelcules
Total (without water)10,6672
Polymers10,6672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: HPV18E6 peptide


Theoretical massNumber of molelcules
Total (without water)10,6672
Polymers10,6672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.730, 48.276, 51.435
Angle α, β, γ (deg.)90.00, 101.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Golgi-associated PDZ and coiled-coil motif-containing protein / CFTR-associated ligand / Fused in glioblastoma / PDZ protein interacting specifically with TC10 / PIST


Mass: 9321.656 Da / Num. of mol.: 2 / Fragment: UNP residues 284-370 / Mutation: C319A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HD26
#2: Protein/peptide HPV18E6 peptide


Mass: 1345.554 Da / Num. of mol.: 2 / Fragment: UNP residues 149-158 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 18 / References: UniProt: P06463
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.87 Å3/Da / Density % sol: 34.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 31% PEG3350, 125mM NaCl, 0.1M Tris7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.36→18.791 Å / Num. obs: 33527 / % possible obs: 99.19 % / Redundancy: 4.26 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.23
Reflection shellResolution: 1.36→1.46 Å / Redundancy: 4.26 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.09 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDS20151015data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+34 / Resolution: 1.36→18.791 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.84
RfactorNum. reflection% reflection
Rfree0.1833 1700 5.07 %
Rwork0.1536 --
obs0.1552 33527 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.36→18.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 0 143 1545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061646
X-RAY DIFFRACTIONf_angle_d0.8792254
X-RAY DIFFRACTIONf_dihedral_angle_d19.214643
X-RAY DIFFRACTIONf_chiral_restr0.077253
X-RAY DIFFRACTIONf_plane_restr0.007314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.40.25541700.21132578X-RAY DIFFRACTION99
1.4-1.44520.2381850.18472701X-RAY DIFFRACTION99
1.4452-1.49680.2411700.16732643X-RAY DIFFRACTION99
1.4968-1.55670.19851700.15392610X-RAY DIFFRACTION99
1.5567-1.62750.1989850.14472720X-RAY DIFFRACTION100
1.6275-1.71330.18141700.14252624X-RAY DIFFRACTION100
1.7133-1.82060.20451700.13922643X-RAY DIFFRACTION100
1.8206-1.9610.1674850.13952696X-RAY DIFFRACTION100
1.961-2.15810.1871700.13532652X-RAY DIFFRACTION100
2.1581-2.46980.18981700.14882625X-RAY DIFFRACTION100
2.4698-3.10940.1791850.16142738X-RAY DIFFRACTION100
3.1094-18.79280.16561700.15832597X-RAY DIFFRACTION95

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