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- PDB-7ep7: The complex structure of Gpsm2 and Whirlin -

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Basic information

Entry
Database: PDB / ID: 7ep7
TitleThe complex structure of Gpsm2 and Whirlin
Components
  • G-protein-signaling modulator 2
  • Whirlin
KeywordsPROTEIN BINDING / Gpsm2 / Whirlin / Complex
Function / homology
Function and homology information


paranodal junction maintenance / stereocilia ankle link / USH2 complex / periciliary membrane compartment / stereocilia ankle link complex / lateral cell cortex / cell cortex region / inner ear receptor cell differentiation / maintenance of centrosome location / sensory perception of light stimulus ...paranodal junction maintenance / stereocilia ankle link / USH2 complex / periciliary membrane compartment / stereocilia ankle link complex / lateral cell cortex / cell cortex region / inner ear receptor cell differentiation / maintenance of centrosome location / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / stereocilium tip / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / G alpha (i) signalling events / detection of mechanical stimulus involved in sensory perception of sound / positive regulation of spindle assembly / stereocilium / response to light intensity / retina homeostasis / auditory receptor cell stereocilium organization / Sensory processing of sound by outer hair cells of the cochlea / GDP-dissociation inhibitor activity / Sensory processing of sound by inner hair cells of the cochlea / neurotransmitter receptor localization to postsynaptic specialization membrane / mitotic spindle pole / dynein complex binding / establishment of mitotic spindle orientation / lateral plasma membrane / G-protein alpha-subunit binding / positive regulation of protein localization to cell cortex / photoreceptor inner segment / regulation of mitotic spindle organization / mitotic spindle organization / actin filament / establishment of localization in cell / establishment of protein localization / sensory perception of sound / growth cone / cell cortex / postsynaptic density / cilium / ciliary basal body / protein domain specific binding / cell division / nucleotide binding / synapse / centrosome / positive regulation of gene expression / protein-containing complex / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Whirlin / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat ...Whirlin / : / : / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / PDZ domain / Tetratricopeptide repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
G-protein-signaling modulator 2 / Whirlin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsLin, L. / Shi, Y. / Wang, C. / Zhu, J.
CitationJournal: Sci Adv / Year: 2022
Title: Promotion of row 1-specific tip complex condensates by Gpsm2-G alpha i provides insights into row identity of the tallest stereocilia.
Authors: Shi, Y. / Lin, L. / Wang, C. / Zhu, J.
History
DepositionApr 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-protein-signaling modulator 2
B: Whirlin


Theoretical massNumber of molelcules
Total (without water)41,0062
Polymers41,0062
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-5 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.885, 91.885, 177.202
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein G-protein-signaling modulator 2 / Pins homolog


Mass: 37497.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpsm2, Lgn, Pins / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8VDU0
#2: Protein/peptide Whirlin / Autosomal recessive deafness type 31 protein


Mass: 3507.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WHRN, DFNB31, KIAA1526 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P202
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.2 M Ammonium tartrate dibasic, 0.1 M Tris, pH 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45.94 Å / Num. obs: 14324 / % possible obs: 99.97 % / Redundancy: 15.93 % / Biso Wilson estimate: 73.68 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.087 / Χ2: 0.866 / Net I/σ(I): 22.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.6916.521.531.813930.7791.57999.71
2.69-2.816.061.0482.513850.8671.083100
2.8-2.9316.290.6714.113930.9490.692100
2.93-3.0816.350.446.314100.9740.454100
3.08-3.2716.520.3029.214080.9890.311100
3.27-3.5215.850.1715.314090.9970.175100
3.52-3.8816.020.11522.914230.9980.118100
3.88-4.4415.870.06438.314430.9990.066100
4.44-5.5915.780.05642.114640.9990.058100
5.59-45.9414.240.02575.9159610.02699.94

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ro2

3ro2


Resolution: 2.6→45.94 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2832 1433 10.01 %
Rwork0.2308 12888 -
obs0.2362 14321 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.59 Å2 / Biso mean: 85.0688 Å2 / Biso min: 34.24 Å2
Refinement stepCycle: final / Resolution: 2.6→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 0 31 2557
Biso mean---71.17 -
Num. residues----342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.690.43211390.352812531392
2.69-2.80.39661390.327912441383
2.8-2.920.3131390.275812541393
2.93-3.080.28761410.253212691410
3.08-3.270.30421410.259612661407
3.27-3.520.29381410.250112671408
3.52-3.880.31631430.228912821425
3.88-4.440.2741430.211612981441
4.44-5.590.29491470.234413191466
5.59-45.940.23711600.200614361596

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