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- PDB-4k76: CFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36-T... -

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Basic information

Entry
Database: PDB / ID: 4k76
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptide iCAL36-TRL (ANSRWPTTRL)
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • iCAL36-TRL peptide
KeywordsPEPTIDE BINDING PROTEIN/PROTEIN BINDING / PDZ domain / CAL / PIST / FIG / PDZ-peptide complex / CFTR Associated Ligand / CFTR / PEPTIDE BINDING PROTEIN-PROTEIN BINDING 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 / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / 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 / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / transmembrane transporter binding / postsynaptic density / lysosomal membrane / Golgi membrane / dendrite / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Golgi-associated PDZ and coiled-coil motif-containing protein / 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
Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionApr 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Golgi-associated PDZ and coiled-coil motif-containing protein
D: Golgi-associated PDZ and coiled-coil motif-containing protein
E: iCAL36-TRL peptide
F: iCAL36-TRL peptide
G: iCAL36-TRL peptide
H: iCAL36-TRL peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3209
Polymers42,2288
Non-polymers921
Water4,810267
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
E: iCAL36-TRL peptide


Theoretical massNumber of molelcules
Total (without water)10,5572
Polymers10,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-7 kcal/mol
Surface area9190 Å2
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
F: iCAL36-TRL peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6493
Polymers10,5572
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-7 kcal/mol
Surface area9050 Å2
3
C: Golgi-associated PDZ and coiled-coil motif-containing protein
G: iCAL36-TRL peptide


Theoretical massNumber of molelcules
Total (without water)10,5572
Polymers10,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Golgi-associated PDZ and coiled-coil motif-containing protein
H: iCAL36-TRL peptide


Theoretical massNumber of molelcules
Total (without water)10,5572
Polymers10,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.762, 50.169, 55.183
Angle α, β, γ (deg.)68.81, 75.79, 87.93
Int Tables number1
Space group name H-MP1

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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.: 4 / Fragment: 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
iCAL36-TRL peptide


Mass: 1203.351 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 1.94 Å3/Da / Density % sol: 36.53 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 27, 2011
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.75→19.262 Å / Num. all: 32071 / Num. obs: 30591 / % possible obs: 95.4 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 2.95 / Rsym value: 0.042 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
1.75-1.792.95246632.4194.6
1.8-1.924.28526722.1194.3
1.93-2.279.2889759.7195.7
2.28-2.5314.5238215.9195.3
2.54-2.9220.9535203.9196.8
2.93-3.5532.9928962.4195.5

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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 bound to iCAL36 peptide)

4e34


Resolution: 1.75→19.262 Å / SU ML: 0.23 / Cross valid method: Omit map / σ(F): 1.99 / σ(I): 2.95 / Phase error: 20.82 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 1493 4.88 %In thin shells
Rwork0.1724 ---
obs0.1747 30585 95.66 %-
all-20591 --
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.528 Å2 / ksol: 0.444 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2032 Å21.5367 Å2-2.2105 Å2
2---1.0738 Å21.4875 Å2
3---2.277 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 6 267 3174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062985
X-RAY DIFFRACTIONf_angle_d1.0664037
X-RAY DIFFRACTIONf_dihedral_angle_d14.7181122
X-RAY DIFFRACTIONf_chiral_restr0.066466
X-RAY DIFFRACTIONf_plane_restr0.005525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.27151430.21632623X-RAY DIFFRACTION94
1.8065-1.8710.27281250.20152632X-RAY DIFFRACTION96
1.871-1.94590.2381360.17712612X-RAY DIFFRACTION94
1.9459-2.03430.20571340.16762648X-RAY DIFFRACTION95
2.0343-2.14150.221300.16262643X-RAY DIFFRACTION96
2.1415-2.27540.22061320.1642664X-RAY DIFFRACTION96
2.2754-2.45080.2511440.18482619X-RAY DIFFRACTION96
2.4508-2.69680.21621290.18792673X-RAY DIFFRACTION96
2.6968-3.08570.21991370.16472658X-RAY DIFFRACTION96
3.0857-3.88240.1981270.15692662X-RAY DIFFRACTION96
3.8824-19.26310.20851560.17082658X-RAY DIFFRACTION97
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)
10.08930.0122-0.29340.63030.04470.8467-0.0149-0.05410.05070.0189-0.02690.055-0.023-0.02340.01160.0375-0.01180.00810.06940.00430.071329.548513.552620.2438
20.29550.0778-0.09580.21770.16610.18530.03780.1434-0.0351-0.0204-0.02150.04410.031-0.0477-0.00930.05620.0091-0.00520.0878-0.00580.067917.067832.62540.8823
30.3491-0.03330.13120.0769-0.13620.609-0.0064-0.0145-0.0719-0.01330.03240.0202-0.12820.0512-0.00710.07930.02380.01740.09980.02510.068734.39497.3351-4.1271
40.1738-0.1589-0.01380.5523-0.42390.4201-0.21640.12820.00340.38610.0385-0.3442-0.4179-0.3820.03310.0106-0.09970.0354-0.14640.0983-0.008711.931240.274223.8198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 284:370
2X-RAY DIFFRACTION2CHAIN B AND RESID 284:370
3X-RAY DIFFRACTION3CHAIN C AND RESID 284:370
4X-RAY DIFFRACTION4CHAIN D AND RESID 284:370

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