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- PDB-4q2n: INADL PDZ3 in Complex with a Phage-Derived Peptide -

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Basic information

Entry
Database: PDB / ID: 4q2n
TitleINADL PDZ3 in Complex with a Phage-Derived Peptide
ComponentsInaD-like protein
KeywordsPROTEIN BINDING / PDZ
Function / homology
Function and homology information


tight junction assembly / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of apical/basal cell polarity / establishment or maintenance of epithelial cell apical/basal polarity / apical junction complex / bicellular tight junction / centriolar satellite / apical part of cell / cell junction ...tight junction assembly / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of apical/basal cell polarity / establishment or maintenance of epithelial cell apical/basal polarity / apical junction complex / bicellular tight junction / centriolar satellite / apical part of cell / cell junction / intracellular signal transduction / apical plasma membrane / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
L27-2 / L27_2 / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain ...L27-2 / L27_2 / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAppleton, B.A. / Wiesmann, C.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: A structural portrait of the PDZ domain family.
Authors: Ernst, A. / Appleton, B.A. / Ivarsson, Y. / Zhang, Y. / Gfeller, D. / Wiesmann, C. / Sidhu, S.S.
History
DepositionApr 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: InaD-like protein
B: InaD-like protein
C: InaD-like protein
D: InaD-like protein
E: InaD-like protein
F: InaD-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,75912
Polymers66,3876
Non-polymers3726
Water5,873326
1
A: InaD-like protein
B: InaD-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1913
Polymers22,1292
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-11 kcal/mol
Surface area10620 Å2
MethodPISA
2
C: InaD-like protein
D: InaD-like protein


Theoretical massNumber of molelcules
Total (without water)22,1292
Polymers22,1292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-13 kcal/mol
Surface area10420 Å2
MethodPISA
3
E: InaD-like protein
F: InaD-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4397
Polymers22,1292
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-3 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.957, 65.156, 82.543
Angle α, β, γ (deg.)90.000, 101.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
InaD-like protein / Inadl protein / hINADL / Pals1-associated tight junction protein / Protein associated to tight junctions


Mass: 11064.448 Da / Num. of mol.: 6 / Fragment: unp residues 362-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INADL, PATJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NI35
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPHAGE-DERIVED PEPTIDE LIGAND WAS FUSED TO THE C TERMINUS OF THE LINKER

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG monomethyl ether 5000, 0.1 M bis-tris (pH 6.5), VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 40881 / % possible obs: 98.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Χ2: 1.043 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2-2.0750.5962.639860.92896.8
2.07-2.1550.45340001.01797.3
2.15-2.255.10.34340611.03897.5
2.25-2.375.10.26240711.05998.4
2.37-2.525.20.23340541.11198.2
2.52-2.715.20.16640801.09298.7
2.71-2.995.20.1241451.08199.4
2.99-3.425.20.08741351.04299.6
3.42-4.35.10.06641651.07299.8
4.3-2550.05241840.97897.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2iwn

2iwn


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.823 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 2057 5 %RANDOM
Rwork0.2012 ---
obs0.2038 40875 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.04 Å2 / Biso mean: 36.154 Å2 / Biso min: 14.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0.2 Å2
2---0.21 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 24 326 4741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214542
X-RAY DIFFRACTIONr_bond_other_d0.0010.022946
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9246150
X-RAY DIFFRACTIONr_angle_other_deg0.9437166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06523.649211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40815736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5431530
X-RAY DIFFRACTIONr_chiral_restr0.0870.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02935
X-RAY DIFFRACTIONr_nbd_refined0.1880.2727
X-RAY DIFFRACTIONr_nbd_other0.2050.22927
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22082
X-RAY DIFFRACTIONr_nbtor_other0.0830.22434
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.212
X-RAY DIFFRACTIONr_mcbond_it3.6522.53661
X-RAY DIFFRACTIONr_mcbond_other0.7862.51217
X-RAY DIFFRACTIONr_mcangle_it4.26954527
X-RAY DIFFRACTIONr_scbond_it3.5932.51982
X-RAY DIFFRACTIONr_scangle_it4.75551613
LS refinement shellResolution: 2.001→2.041 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.376 109 -
Rwork0.259 2207 -
all-2316 -
obs--94.84 %
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)
13.52611.90320.68182.2746-0.09531.39780.0978-0.1734-0.0820.1385-0.0778-0.13810.09160.0015-0.02-0.1174-0.0234-0.0138-0.07980.0058-0.077618.2576-1.37137.103
23.39061.482-0.51374.93691.2323.7726-0.06330.18650.27470.1998-0.04370.36890.1659-0.33150.107-0.0887-0.05440.005-0.05970.0204-0.081519.829216.506320.0536
33.2286-0.16341.28096.46240.29973.25630.17750.0567-0.22690.3429-0.20380.16920.102-0.21590.0263-0.07270.0246-0.0069-0.0477-0.0173-0.08329.8707-8.4587-9.886
43.33671.1404-0.58112.57931.00344.3865-0.10930.0485-0.0973-0.03320.0082-0.049-0.0260.11960.10110.0191-0.0364-0.0109-0.0013-0.081-0.030228.10798.165-3.6486
54.2289-0.0949-0.81461.53830.42770.8857-0.0486-0.30990.20710.03150.10270.0031-0.02620.1155-0.0541-0.15680.0172-0.0012-0.0874-0.0239-0.10849.31978.630238.6566
62.066-1.47270.3753.3555-1.3283.29120.0754-0.09110.03010.1597-0.00120.0154-0.00560.1137-0.0742-0.05090.06370.0407-0.08670.008-0.123239.76518.937559.6822
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A359 - 454
2X-RAY DIFFRACTION1B455 - 460
3X-RAY DIFFRACTION2B360 - 454
4X-RAY DIFFRACTION2A455 - 460
5X-RAY DIFFRACTION3C360 - 454
6X-RAY DIFFRACTION3D455 - 460
7X-RAY DIFFRACTION4D358 - 454
8X-RAY DIFFRACTION4C455 - 460
9X-RAY DIFFRACTION5E359 - 454
10X-RAY DIFFRACTION5F455 - 460
11X-RAY DIFFRACTION6F359 - 454
12X-RAY DIFFRACTION6E455 - 460

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