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- PDB-7jzr: CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic L... -

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Basic information

Entry
Database: PDB / ID: 7jzr
TitleCFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALAEB
Components
  • Golgi-associated PDZ and coiled-coil motif-containing protein
  • LyCALAEB peptide core
KeywordsPEPTIDE BINDING PROTEIN / PDZ domain / inhibitor / complex / peptidomimetic
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 / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / 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 / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / 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 / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Golgi-associated PDZ and coiled-coil motif-containing protein / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
4-(2-aminoethyl)benzoic acid / Golgi-associated PDZ and coiled-coil motif-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsGill, N.P. / Madden, D.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK101541 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008704 United States
CitationJournal: To Be Published
Title: CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALAEB
Authors: Gill, N.P.
History
DepositionSep 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 2.0Feb 2, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.asym_id ..._entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _software.version / _struct_conn.pdbx_dist_value / _struct_sheet.number_strands
Description: Polymer geometry
Details: Improved geometry (lower RMSD values for bond lengths and angles) obtained from additional refinement using simulated annealing.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: LyCALAEB peptide core
D: LyCALAEB peptide core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2146
Polymers20,8844
Non-polymers3302
Water3,531196
1
A: Golgi-associated PDZ and coiled-coil motif-containing protein
C: LyCALAEB peptide core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6073
Polymers10,4422
Non-polymers1651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-5 kcal/mol
Surface area5440 Å2
MethodPISA
2
B: Golgi-associated PDZ and coiled-coil motif-containing protein
D: LyCALAEB peptide core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6073
Polymers10,4422
Non-polymers1651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-5 kcal/mol
Surface area5060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.362, 47.468, 98.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9HD26
#2: Protein/peptide LyCALAEB peptide core


Mass: 1088.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-VU4 / 4-(2-aminoethyl)benzoic acid


Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5.5 mg/mL CAL PDZ, 1 mM LyCALAEB, 30% (w/v) PEG 8000, 100 mM NaCl, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.8263 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2017
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8263 Å / Relative weight: 1
ReflectionResolution: 1.54→42.72 Å / Num. obs: 23523 / % possible obs: 93.4 % / Redundancy: 8.66 % / Biso Wilson estimate: 18.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.075 / Net I/σ(I): 17.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
8-108.940.04231.331030.9990.044100
7-89.330.04930.64980.9990.052100
6-79.570.04831.531730.9970.051100
5-69.110.05530.243360.9950.05899.7
3.26-58.880.05829.819870.9970.06199.7
2.66-3.269.670.06828.4422670.9970.07299.8
2.31-2.669.550.07824.226010.9960.08399.7
2.06-2.319.430.0921.0730340.9960.09599.6
1.89-2.06100.11117.3530480.9950.11799.3
1.75-1.8910.360.15911.8334560.9920.16899.3
1.63-1.757.360.2066.8739320.9820.2298
1.54-1.633.330.2382.9223750.9220.28161.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSVersion November 1, 2016data reduction
XSCALEVersion November 1, 2016data scaling
PHENIXv1.17.1-3660phasing
PHENIXv1.17.1-3660model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NMO

4nmo


Resolution: 1.54→42.72 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 2359 10.03 %
Rwork0.1751 21164 -
obs0.1783 23523 93.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.47 Å2 / Biso mean: 21.7966 Å2 / Biso min: 12.04 Å2
Refinement stepCycle: final / Resolution: 1.54→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 0 197 1644
Biso mean---29.01 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081469
X-RAY DIFFRACTIONf_angle_d1.1051979
X-RAY DIFFRACTIONf_dihedral_angle_d16.201553
X-RAY DIFFRACTIONf_chiral_restr0.079231
X-RAY DIFFRACTIONf_plane_restr0.007256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.54-1.5740028
1.57-1.610.29211180.238297473
1.61-1.640.27441180.2067122494
1.64-1.680.23692360.1857120097
1.68-1.730.22781180.1937130199
1.73-1.780.24331170.1853133199
1.78-1.840.22161180.1907132399
1.84-1.90.22912210.1876123799
1.9-1.980.19641330.1776134299
1.98-2.070.19631180.17111333100
2.07-2.180.22761180.17421346100
2.18-2.320.20632030.17181269100
2.32-2.490.19941510.18281346100
2.49-2.740.20351180.18481374100
2.75-3.140.19141180.18611378100
3.14-3.960.17632360.16521296100
3.96-42.720.25181180.15181490100

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