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- PDB-3k1r: Structure of harmonin NPDZ1 in complex with the SAM-PBM of Sans -

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Basic information

Entry
Database: PDB / ID: 3k1r
TitleStructure of harmonin NPDZ1 in complex with the SAM-PBM of Sans
Components
  • Harmonin
  • Usher syndrome type-1G protein
KeywordsSTRUCTURAL PROTEIN / PROTEIN-PROTEIN COMPLEX / Alternative splicing / Coiled coil / Deafness / Hearing / Non-syndromic deafness / Polymorphism / Retinitis pigmentosa / Sensory transduction / Usher syndrome / Vision / ANK repeat / Disease mutation
Function / homology
Function and homology information


photoreceptor cell cilium / protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / regulation of clathrin-dependent endocytosis / equilibrioception / sensory perception of light stimulus / retinal cone cell development ...photoreceptor cell cilium / protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / regulation of clathrin-dependent endocytosis / equilibrioception / sensory perception of light stimulus / retinal cone cell development / photoreceptor connecting cilium / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / 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 / ciliary base / inner ear morphogenesis / spectrin binding / brush border / microvillus / actin filament bundle assembly / photoreceptor outer segment / Cajal body / photoreceptor inner segment / ciliary basal body / sensory perception of sound / cilium / G2/M transition of mitotic cell cycle / actin cytoskeleton / apical part of cell / protein-containing complex assembly / cytoskeleton / nuclear speck / centrosome / synapse / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
USH1G, SAM domain / Paired amphipathic helix 2 (pah2 repeat) - #20 / Harmonin, N-terminal domain / Harmonin / Paired amphipathic helix 2 (pah2 repeat) / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / Sterile alpha motif. ...USH1G, SAM domain / Paired amphipathic helix 2 (pah2 repeat) - #20 / Harmonin, N-terminal domain / Harmonin / Paired amphipathic helix 2 (pah2 repeat) / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / DNA polymerase; domain 1 / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
pre-mRNA splicing regulator USH1G / Harmonin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPan, L. / Yan, J. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: The structure of the harmonin/sans complex reveals an unexpected interaction mode of the two Usher syndrome proteins
Authors: Yan, J. / Pan, L. / Chen, X. / Wu, L. / Zhang, M.
History
DepositionSep 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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: Harmonin
B: Usher syndrome type-1G protein


Theoretical massNumber of molelcules
Total (without water)30,3792
Polymers30,3792
Non-polymers00
Water4,306239
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-12 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.603, 57.775, 59.505
Angle α, β, γ (deg.)90.00, 104.63, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHOR STATES THAT THE BIOLOGICAL UNIT FOR THIS ENTRY IS UNKNOWN.

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Components

#1: Protein Harmonin / Harmonin scaffold protein / Usher syndrome type-1C protein / Autoimmune enteropathy-related antigen ...Harmonin scaffold protein / Usher syndrome type-1C protein / Autoimmune enteropathy-related antigen AIE-75 / Antigen NY-CO-38/NY-CO-37 / PDZ-73 protein / Renal carcinoma antigen NY-REN-3


Mass: 21964.311 Da / Num. of mol.: 1 / Fragment: NPDZ1 domain, residues 1-192 / Mutation: K157E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USH1C / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y6N9
#2: Protein Usher syndrome type-1G protein / Sans scaffold protein / Scaffold protein containing ankyrin repeats and SAM domain


Mass: 8414.734 Da / Num. of mol.: 1 / Fragment: SAM-PBM domain, residues 388-461 / Mutation: K437E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USH1G / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q495M9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M CaAc2, 0.1M HEPES, pH 7.5, 18% (w/v) polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 23, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30.8 Å / Num. obs: 16268 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.9 / Num. measured all: 61880
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 10.9 / Num. unique all: 16268 / Rsym value: 0.21 / % possible all: 93

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1)

2kbq

1qav

1kw4

1pk1


Resolution: 2.3→28.89 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.01 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(I): 3.3 / ESU R: 0.271 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25568 825 5.1 %RANDOM
Rwork0.21037 ---
obs0.21262 15430 92.53 %-
all-16268 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.719 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20.18 Å2
2---0.81 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 0 239 2378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222177
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.9952942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4345266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.18723.137102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66715409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8911523
X-RAY DIFFRACTIONr_chiral_restr0.0620.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211627
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 59 -
Rwork0.256 1113 -
obs--90.64 %

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