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- PDB-4jor: CFTR Associated Ligand (CAL) PDZ domain bound to HPV18 E6 oncopro... -

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Basic information

Entry
Database: PDB / ID: 4jor
TitleCFTR Associated Ligand (CAL) PDZ domain bound to HPV18 E6 oncoprotein C-terminal peptide (RLQRRRETQV)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • Protein E6
KeywordsPEPTIDE BINDING PROTEIN / PDZ / CFTR Associated Ligand / CAL / PIST / FIG / Human papillomavirus type 18 / HPV18 / E6 oncoprotein
Function / homology
Function and homology information


negative regulation of anion channel activity / symbiont-mediated perturbation of host apoptosis / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / apical protein localization / RHOQ GTPase cycle / molecular sequestering activity ...negative regulation of anion channel activity / symbiont-mediated perturbation of host apoptosis / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / apical protein localization / RHOQ GTPase cycle / molecular sequestering activity / 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 / Golgi membrane / lysosomal membrane / negative regulation of DNA-templated transcription / 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
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: 1.34 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: Structure / Year: 2014
Title: Stereochemical Preferences Modulate Affinity and Selectivity among Five PDZ Domains that Bind CFTR: Comparative Structural and Sequence Analyses.
Authors: Amacher, J.F. / Cushing, P.R. / Brooks, L. / Boisguerin, P. / Madden, D.R.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Data collection / Derived calculations / Category: reflns_shell / struct_site
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value ..._reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 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
B: Golgi-associated PDZ and coiled-coil motif-containing protein
C: Protein E6
D: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5836
Polymers21,3994
Non-polymers1842
Water4,648258
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8834
Polymers10,6992
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: Protein E6


Theoretical massNumber of molelcules
Total (without water)10,6992
Polymers10,6992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-3 kcal/mol
Surface area5200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.205, 47.960, 52.852
Angle α, β, γ (deg.)90.00, 101.98, 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


Mass: 9353.722 Da / Num. of mol.: 2 / Fragment: CAL PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9HD26
#2: Protein/peptide Protein E6


Mass: 1345.554 Da / Num. of mol.: 2 / Fragment: HPV18 E6 peptide / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 18 / References: UniProt: P06463
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 29% (w/v) polyethylene glycol (PEG), 0.075 M sodium chloride, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 29, 2012
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→19.29 Å / Num. all: 36592 / Num. obs: 34483 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 7.53 / Rmerge(I) obs: 0.05 / Rsym value: 0.038 / Net I/σ(I): 36.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.34-1.420.2477.530.265177.8
1.43-1.510.14911.350.193196.1
1.52-1.640.09316.780.128196.8
1.65-1.790.06224.070.083197.6
1.8-20.03438.030.048197.8
2.01-2.310.0256.420.03198.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E34 (CAL PDZ domain bound to iCAL36 peptide)

4e34


Resolution: 1.34→19.29 Å / SU ML: 0.16 / Cross valid method: Omit map / σ(F): 2 / σ(I): 7.53 / Phase error: 17.36 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1811 1729 5.01 %In thin shells
Rwork0.1709 ---
obs0.1722 34482 95.17 %-
all-34483 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.62 Å2 / ksol: 0.45 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1791 Å2-0 Å2-1.3967 Å2
2---1.5159 Å20 Å2
3---0.3368 Å2
Refinement stepCycle: LAST / Resolution: 1.34→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 12 258 1722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071541
X-RAY DIFFRACTIONf_angle_d1.1662084
X-RAY DIFFRACTIONf_dihedral_angle_d14.567594
X-RAY DIFFRACTIONf_chiral_restr0.064239
X-RAY DIFFRACTIONf_plane_restr0.006278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.38380.25661340.23972009X-RAY DIFFRACTION71
1.3838-1.42840.2439840.19652690X-RAY DIFFRACTION93
1.4284-1.47950.21391760.19242680X-RAY DIFFRACTION96
1.4795-1.53870.19191760.1652728X-RAY DIFFRACTION96
1.5387-1.60870.1865890.15922835X-RAY DIFFRACTION97
1.6087-1.69350.19771760.16652724X-RAY DIFFRACTION97
1.6935-1.79950.20531780.16592767X-RAY DIFFRACTION98
1.7995-1.93830.1575890.1652894X-RAY DIFFRACTION98
1.9383-2.13310.16591770.16762774X-RAY DIFFRACTION98
2.1331-2.44130.17951800.16352819X-RAY DIFFRACTION99
2.4413-3.07370.1868900.17752939X-RAY DIFFRACTION99
3.0737-19.29410.15771800.1632894X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1502-0.0993-0.06850.1843-0.00460.2739-0.0354-0.02610.01770.01290.00950.0032-0.0005-0.00550.01330.02770.0065-0.00310.0369-0.00310.032630.911524.535816.0734
20.10870.0532-0.03510.2191-0.02940.15460.0399-0.014100.0126-0.01950.04510.0306-0-0.0010.0372-0.0139-0.00650.028-0.00470.035726.467526.1783-8.3825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 284:370
2X-RAY DIFFRACTION2CHAIN B AND RESID 284:370

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