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- PDB-7x2e: Structure of USH1C PDZ2 and coiled-coil in complex with CDHR2 C-t... -

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Basic information

Entry
Database: PDB / ID: 7x2e
TitleStructure of USH1C PDZ2 and coiled-coil in complex with CDHR2 C-terminal tail
Components
  • Cadherin-related family member 2
  • Harmonin
KeywordsPROTEIN BINDING / CELL ADHESION / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of cell growth involved in contact inhibition / intermicrovillar adhesion / protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / retinal cone cell development ...negative regulation of cell growth involved in contact inhibition / intermicrovillar adhesion / protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / retinal cone cell development / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion mediated by cadherin / stereocilium / photoreceptor cell maintenance / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / anchoring junction / microvillus membrane / inner ear morphogenesis / spectrin binding / homophilic cell adhesion via plasma membrane adhesion molecules / brush border / microvillus / actin filament bundle assembly / photoreceptor outer segment / cell adhesion molecule binding / epithelial cell differentiation / photoreceptor inner segment / brush border membrane / sensory perception of sound / cilium / G2/M transition of mitotic cell cycle / apical part of cell / protein-containing complex assembly / cytoskeleton / cell adhesion / apical plasma membrane / synapse / calcium ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Harmonin, N-terminal domain / Harmonin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / PDZ domain ...Harmonin, N-terminal domain / Harmonin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Cadherin-related family member 2 / Harmonin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYan, W. / Chen, G. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Faseb J. / Year: 2022
Title: Structure of the Harmonin PDZ2 and coiled-coil domains in a complex with CDHR2 tail and its implications.
Authors: Yan, W. / Chen, G. / Li, J.
History
DepositionFeb 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 29, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Harmonin
B: Cadherin-related family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2444
Polymers22,0602
Non-polymers1842
Water3,675204
1
A: Harmonin
B: Cadherin-related family member 2
hetero molecules

A: Harmonin
B: Cadherin-related family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4888
Polymers44,1204
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5780 Å2
ΔGint-29 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.516, 50.681, 72.847
Angle α, β, γ (deg.)90.000, 107.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-648-

HOH

21A-655-

HOH

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Components

#1: Protein Harmonin / Usher syndrome type-1C protein


Mass: 20037.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USH1C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6N9
#2: Protein/peptide Cadherin-related family member 2


Mass: 2022.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: E9Q7P9
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% w/v polyethylene glycol 3000, 100 mM tri-sodium citrate, pH 5.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 16311 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.046 / Rrim(I) all: 0.117 / Χ2: 0.632 / Net I/σ(I): 5.2 / Num. measured all: 102320
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.886.50.8938090.7760.3690.9680.61199.8
1.88-1.926.50.7547800.8510.3130.8170.6199.7
1.92-1.956.40.5718510.8580.2390.620.76199.8
1.95-1.996.30.5527760.8970.2330.60.58199.7
1.99-2.046.20.3958190.930.1680.4290.55399.6
2.04-2.086.10.3368030.930.1460.3670.59699.6
2.08-2.145.70.2778080.9530.1260.3050.537100
2.14-2.195.90.2458430.9690.1090.2690.56299.8
2.19-2.266.20.2647770.960.1130.2880.965100
2.26-2.336.60.198350.9840.0780.2060.55999.8
2.33-2.416.50.1597850.9870.0660.1730.53399.7
2.41-2.516.40.1418260.9910.060.1530.533100
2.51-2.626.50.1188130.9920.050.1290.541100
2.62-2.765.80.1068120.9910.0480.1170.577100
2.76-2.946.10.0838130.9950.0360.0910.568100
2.94-3.166.70.0728360.9970.030.0780.61100
3.16-3.486.60.0578170.9970.0240.0620.679100
3.48-3.9860.0468220.9980.020.0510.75100
3.98-5.016.30.0388330.9990.0170.0420.771100
5.01-3060.048530.9990.0170.0440.75199.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KBS

2kbs


Resolution: 1.85→28.26 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 840 5.15 %
Rwork0.1806 15468 -
obs0.1825 16308 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.92 Å2 / Biso mean: 24.0993 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: final / Resolution: 1.85→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 12 204 1525
Biso mean--37.99 33.67 -
Num. residues----170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.960.261300.24212517264797
1.96-2.110.23591500.190925562706100
2.11-2.330.22011420.175325722714100
2.33-2.660.18791390.184625832722100
2.66-3.350.24511490.174525842733100
3.35-28.260.1941300.1726562786100

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