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- PDB-5ic3: CAL PDZ domain with peptide and inhibitor -

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Basic information

Entry
Database: PDB / ID: 5ic3
TitleCAL PDZ domain with peptide and inhibitor
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • HPV18E6 Peptide
KeywordsPEPTIDE BINDING PROTEIN/INHIBITOR / inhibitor / complex / CAL PDZ / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-INHIBITOR complex
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 / symbiont-mediated perturbation of host apoptosis / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / trans-Golgi network transport vesicle / apical protein localization / molecular sequestering activity / RHOQ GTPase cycle ...negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / symbiont-mediated perturbation of host apoptosis / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / trans-Golgi network transport vesicle / apical protein localization / molecular sequestering activity / 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 / transmembrane transporter binding / host cell cytoplasm / postsynaptic density / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / lysosomal membrane / Golgi membrane / negative regulation of DNA-templated transcription / virus-mediated perturbation of host defense response / DNA-templated transcription / dendrite / host cell nucleus / Golgi apparatus / protein-containing complex / DNA binding / zinc ion binding / identical protein binding / membrane / 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
4-[methyl(nitroso)amino]benzene-1,2-diol / Protein E6 / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Alphapapillomavirus 7
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 with peptide and inhibitor
Authors: Zhao, Y. / Madden, D.R.
History
DepositionFeb 22, 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 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
B: Golgi-associated PDZ and coiled-coil motif-containing protein
C: HPV18E6 Peptide
D: HPV18E6 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5675
Polymers21,3994
Non-polymers1681
Water2,594144
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: HPV18E6 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8673
Polymers10,6992
Non-polymers1681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-5 kcal/mol
Surface area5120 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: HPV18E6 Peptide


Theoretical massNumber of molelcules
Total (without water)10,6992
Polymers10,6992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-2 kcal/mol
Surface area4990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.772, 48.252, 51.639
Angle α, β, γ (deg.)90.00, 101.47, 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: 9353.722 Da / Num. of mol.: 2 / Fragment: UNP residues 284-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 RIL / References: UniProt: Q9HD26
#2: Protein/peptide HPV18E6 Peptide


Mass: 1345.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Alphapapillomavirus 7 / References: UniProt: P06463*PLUS
#3: Chemical ChemComp-PQR / 4-[methyl(nitroso)amino]benzene-1,2-diol / Methyl-3,4-dephostatin


Mass: 168.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H8N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsthe numbering of the sequence is made according to the isofrom 2 of CAL

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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: 34.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 35% PEG3350, 100mM NaCl, 100mM Tris pH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 24, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→19.29 Å / Num. obs: 17472 / % possible obs: 99.9 % / Redundancy: 7.51 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.78
Reflection shellHighest resolution: 1.7 Å / Rmerge(I) obs: 0.686

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+34 / Resolution: 1.7→19.29 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.49
RfactorNum. reflection% reflection
Rfree0.226 858 4.91 %
Rwork0.174 --
obs0.177 17472 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 52.15 Å2 / ksol: 0.42 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.951 Å20 Å2-2.7544 Å2
2---1.7967 Å20 Å2
3----1.1543 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 12 144 1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071496
X-RAY DIFFRACTIONf_angle_d1.0592032
X-RAY DIFFRACTIONf_dihedral_angle_d15.708581
X-RAY DIFFRACTIONf_chiral_restr0.067233
X-RAY DIFFRACTIONf_plane_restr0.005272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.80640.28161280.24892742X-RAY DIFFRACTION100
1.8064-1.94580.24811710.19552734X-RAY DIFFRACTION100
1.9458-2.14140.23571290.16952767X-RAY DIFFRACTION100
2.1414-2.45070.21571290.17162776X-RAY DIFFRACTION100
2.4507-3.08560.24351720.16932753X-RAY DIFFRACTION100
3.0856-19.29120.19981290.16452842X-RAY DIFFRACTION100

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