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- PDB-4q6s: CFTR Associated Ligand (CAL) PDZ bound to biotinylated peptide BT... -

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Basic information

Entry
Database: PDB / ID: 4q6s
TitleCFTR Associated Ligand (CAL) PDZ bound to biotinylated peptide BT-L-iCAL36
Components
  • BT-L-iCAL36 peptide
  • Golgi-associated PDZ and coiled-coil motif-containing protein
KeywordsTRANSPORT PROTEIN / PDZ-peptide 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: 1.45 Å
AuthorsAmacher, J.F. / Madden, D.R.
CitationJournal: To be Published
Title: Modulator Preferences are Critical Co-Determinants of PDZ Network Wiring
Authors: Amacher, J.F. / Cushing, P.R. / Cullati, S.N. / Gerber, S.A. / Madden, D.R.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: 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 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: BT-L-iCAL36 peptide
D: BT-L-iCAL36 peptide


Theoretical massNumber of molelcules
Total (without water)22,8024
Polymers22,8024
Non-polymers00
Water4,360242
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: BT-L-iCAL36 peptide


Theoretical massNumber of molelcules
Total (without water)11,4012
Polymers11,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-4 kcal/mol
Surface area6050 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: BT-L-iCAL36 peptide


Theoretical massNumber of molelcules
Total (without water)11,4012
Polymers11,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-6 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.599, 48.167, 101.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCAL PDZ domain bound to peptide, BT-L-iCAL36

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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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q9HD26
#2: Protein/peptide BT-L-iCAL36 peptide


Mass: 2047.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: peptide synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 1.96 Å3/Da / Density % sol: 37.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.95
Details: 16% (w/v) polyethylene glycol (PEG), 0.15 M sodium chloride, 0.01 M Tris HCl pH 7.95, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9181 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 26, 2010
RadiationMonochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionResolution: 1.45→19.732 Å / Num. all: 32531 / Num. obs: 32353 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 8.27 / Redundancy: 13.9 % / Rmerge(I) obs: 0.055 / Rsym value: 0.074 / Net I/σ(I): 24.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.41-2.9313.50.02341.7332080.054100
2.09-2.413.80.02936.9237950.066100
1.87-2.0814.20.04527.5242770.092100
1.71-1.8614.40.07918.2946230.15399.9
1.58-1.714.50.1212.9752180.23899.7
1.45-1.5714.10.2068.2772060.39599.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4E34 without peptide

4e34


Resolution: 1.45→19.732 Å / SU ML: 0.17 / Cross valid method: Omit map / σ(F): 2 / σ(I): 8.27 / Phase error: 17.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 1615 4.99 %In thin shells
Rwork0.177 ---
obs0.1779 32353 99.5 %-
all-32531 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.439 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2854 Å2-0 Å2-0 Å2
2---0.6816 Å2-0 Å2
3----1.6038 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 0 242 1845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081674
X-RAY DIFFRACTIONf_angle_d1.4972264
X-RAY DIFFRACTIONf_dihedral_angle_d19.707663
X-RAY DIFFRACTIONf_chiral_restr0.109258
X-RAY DIFFRACTIONf_plane_restr0.008292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.50180.25721610.2142992X-RAY DIFFRACTION99
1.5018-1.56190.20761620.18173032X-RAY DIFFRACTION99
1.5619-1.6330.21171610.1813032X-RAY DIFFRACTION100
1.633-1.7190.23161600.17543048X-RAY DIFFRACTION100
1.719-1.82660.17661610.17323040X-RAY DIFFRACTION100
1.8266-1.96760.20051620.16413061X-RAY DIFFRACTION100
1.9676-2.16530.18041620.16953090X-RAY DIFFRACTION100
2.1653-2.47820.20491620.17313087X-RAY DIFFRACTION100
2.4782-3.12020.18261620.18333142X-RAY DIFFRACTION100
3.1202-19.73390.18461620.17683214X-RAY DIFFRACTION98
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)
10.2833-0.14990.20640.5662-0.18510.58320.0079-0.0383-0.0177-0.01970.01420.04230.05880.0064-0.01790.04450.0007-0.00050.0501-0.00370.04842.701621.766640.9308
20.1288-0.18780.12111.66670.44560.39170.02140.1074-0.00390.0684-0.0268-0.25570.06930.0689-0.04430.07610.01-0.0020.118-0.01160.146217.122317.611845.9583
30.47260.39560.09780.3782-0.09610.78030.0367-0.02460.0260.0561-0.0381-0.0026-0.04380.07140.00550.0667-0.0156-0.00110.05540.00450.06046.289119.598116.809
41.15650.634-0.62490.6019-0.15640.47350.0644-0.2551-0.27170.0576-0.088-0.21740.04920.2835-0.06030.1002-0.01620.00380.1582-0.02750.165221.952224.560217.0502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A and resid 284:370
2X-RAY DIFFRACTION2Chain C and resid 0:15
3X-RAY DIFFRACTION3Chain B and resid 284:370
4X-RAY DIFFRACTION4Chain D and resid 0:15

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