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- PDB-4jop: CFTR Associated Ligand (CAL) PDZ bound to HPV16 E6 oncoprotein C-... -

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Basic information

Entry
Database: PDB / ID: 4jop
TitleCFTR Associated Ligand (CAL) PDZ bound to HPV16 E6 oncoprotein C-terminal peptide (TRRETQL)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • Protein E6
KeywordsPEPTIDE BINDING PROTEIN / PDZ / CFTR Associated Ligand / CAL / FIG / PIST / Human papillomavirus type 16 / HPV16 / E6 oncoprotein
Function / homology
Function and homology information


negative regulation of anion channel activity / symbiont-mediated suppression of host transcription / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / regulation of proteolysis ...negative regulation of anion channel activity / symbiont-mediated suppression of host transcription / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / regulation of proteolysis / activation of GTPase 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 / virus-mediated perturbation of host defense response / DNA-templated transcription / dendrite / host cell nucleus / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / identical protein binding / membrane / metal ion 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 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Sep 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


Theoretical massNumber of molelcules
Total (without water)20,5174
Polymers20,5174
Non-polymers00
Water2,684149
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: Protein E6


Theoretical massNumber of molelcules
Total (without water)10,2592
Polymers10,2592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-5 kcal/mol
Surface area5200 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: Protein E6


Theoretical massNumber of molelcules
Total (without water)10,2592
Polymers10,2592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-2 kcal/mol
Surface area5220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.083, 48.396, 51.966
Angle α, β, γ (deg.)90.00, 101.55, 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: 905.011 Da / Num. of mol.: 2 / Fragment: HPV16 E6 peptide / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16 / References: UniProt: P03126
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 32% (w/v) polyethylene glycol (PEG), 0.125 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: 1.8→19.39 Å / Num. all: 15041 / Num. obs: 14956 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.16 / Rsym value: 0.059 / Net I/σ(I): 20.37
Reflection shell
Resolution (Å)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.8-1.93.1653.9198.1
1.91-2.035.8928.3199.9
2.04-2.198.9317.8199.7
2.2-2.413.3111.7199.8
2.41-2.6818.487.71100
2.69-3.0826.594.9199.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E34 (CAL PDZ domain bound to iCAL36 peptide)

4e34


Resolution: 1.8→19.39 Å / SU ML: 0.19 / Cross valid method: Omit map / σ(F): 2 / σ(I): 3.16 / Phase error: 20.7 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 758 5.07 %In thin shells
Rwork0.1794 ---
obs0.1811 14953 99.83 %-
all-14956 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.443 Å2 / ksol: 0.412 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7438 Å2-0 Å2-3.0251 Å2
2---3.9458 Å2-0 Å2
3----0.798 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 0 149 1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071470
X-RAY DIFFRACTIONf_angle_d1.0531985
X-RAY DIFFRACTIONf_dihedral_angle_d14.882558
X-RAY DIFFRACTIONf_chiral_restr0.067231
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.94110.24641500.21512807X-RAY DIFFRACTION100
1.9411-2.13620.24681520.1762812X-RAY DIFFRACTION100
2.1362-2.44480.23021520.17832846X-RAY DIFFRACTION100
2.4448-3.07820.23061520.17852842X-RAY DIFFRACTION100
3.0782-19.39160.19271520.17382888X-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)
10.6745-0.5955-0.32191.3451-0.00641.0891-0.0735-0.14240.06380.22110.09950.0268-0.018-0.11260.00790.08570.01990.00440.1094-0.01590.099530.349625.19115.751
20.4794-0.07140.27870.4159-0.05390.72990.2382-0.055-0.2510.049-0.07890.08220.3305-0.13030.12750.1382-0.0697-0.09460.0502-0.00930.109726.421327.3361-8.213
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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