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- PDB-4q6h: CFTR Associated Ligand (CAL) bound to last 6 residues of CFTR (de... -

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Basic information

Entry
Database: PDB / ID: 4q6h
TitleCFTR Associated Ligand (CAL) bound to last 6 residues of CFTR (decameric peptide: iCAL36VQDTRL)
Components
  • CFTR-associated ligand
  • iCAL36-VQDTRL peptide
KeywordsTRANSPORT PROTEIN / PDZ-peptide complex / cystic fibrosis transmembrane conductance regulator
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 / 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 ...negative regulation of anion channel activity / 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 / protein transport / transmembrane transporter binding / postsynaptic density / Golgi membrane / lysosomal 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
SULFITE ION / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: TO BE PUBLISHED
Title: Understanding PDZ Affinity and Selectivity: All Residues Considered
Authors: Amacher, J.F.
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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 / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: CFTR-associated ligand
B: iCAL36-VQDTRL peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1663
Polymers10,0862
Non-polymers801
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-5 kcal/mol
Surface area4960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.394, 61.394, 97.786
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-331-

HIS

21A-402-

HOH

31A-409-

HOH

41A-414-

HOH

51A-433-

HOH

61A-434-

HOH

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Components

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


Mass: 9353.722 Da / Num. of mol.: 1
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) RIL / References: UniProt: Q9HD26
#2: Protein/peptide iCAL36-VQDTRL peptide


Mass: 731.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide synthesis
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 37% (w/v) polyethylene glycol (PEG) 1000, 0.07 M sodium thiosulfate pentahydrate, 0.1 M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 8, 2013
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.9→19.123 Å / Num. all: 9142 / Num. obs: 9041 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 9.08 / Rsym value: 0.085 / Net I/σ(I): 48.39
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.84-3.254163.749270.07198.9
2.54-2.8341.543.0710620.114198.9
2.32-2.5341.727.8811750.193199.3
2.15-2.3141.922.6112520.248199.9
2.02-2.1441.815.4412610.371199.9
1.9-2.0141.49.0814300.644196.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4E34 (CAL PDZ, no peptide included in search model)

4e34


Resolution: 1.903→19.123 Å / SU ML: 0.12 / σ(F): 1.36 / σ(I): 9.08 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 460 5.09 %
Rwork0.1983 --
all0.1996 9142 -
obs0.1996 9041 99.47 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.784 Å2 / ksol: 0.431 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0242 Å2-0 Å20 Å2
2--5.0242 Å2-0 Å2
3----10.0484 Å2
Refinement stepCycle: LAST / Resolution: 1.903→19.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms708 0 4 51 763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007755
X-RAY DIFFRACTIONf_angle_d1.1791025
X-RAY DIFFRACTIONf_dihedral_angle_d15.259286
X-RAY DIFFRACTIONf_chiral_restr0.079117
X-RAY DIFFRACTIONf_plane_restr0.005136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9031-2.17810.2071380.17362790X-RAY DIFFRACTION100
2.1781-2.74290.23181610.19142785X-RAY DIFFRACTION99
2.7429-19.12420.2211610.20752998X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.4388 Å / Origin y: 22.9653 Å / Origin z: 36.4886 Å
111213212223313233
T0.1532 Å20.0234 Å2-0.0237 Å2-0.153 Å2-0.0025 Å2--0.1347 Å2
L0.6895 °2-0.5315 °20.2649 °2-0.5132 °2-0.3401 °2--1.1777 °2
S0.0603 Å °-0.0453 Å °-0.1077 Å °0.0187 Å °-0.001 Å °-0.0533 Å °0.199 Å °0.1536 Å °-0.0273 Å °
Refinement TLS groupSelection details: chain A and resid 284:370

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