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- PDB-5f3x: Crystal structure of Harmonin NPDZ1 in complex with ANKS4B SAM-PBM -

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Basic information

Entry
Database: PDB / ID: 5f3x
TitleCrystal structure of Harmonin NPDZ1 in complex with ANKS4B SAM-PBM
Components
  • Ankyrin repeat and SAM domain-containing protein 4B
  • Harmonin
KeywordsSTRUCTURAL PROTEIN/PROTEIN BINDING / COMPLEX / STRUCTURAL PROTEIN / PROTEIN BINDING / STRUCTURAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


protein localization to microvillus / brush border assembly / stereocilia ankle link complex / regulation of microvillus length / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / stereocilium tip / retinal cone cell development / auditory receptor cell morphogenesis ...protein localization to microvillus / brush border assembly / stereocilia ankle link complex / regulation of microvillus length / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / stereocilium tip / retinal cone cell development / auditory receptor cell morphogenesis / 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 / inner ear morphogenesis / spectrin binding / microvillus / brush border / actin filament bundle assembly / photoreceptor outer segment / photoreceptor inner segment / response to endoplasmic reticulum stress / sensory perception of sound / G2/M transition of mitotic cell cycle / apical part of cell / protein-containing complex assembly / cell differentiation / cytoskeleton / cilium / synapse / endoplasmic reticulum membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ANKS4B, SAM domain / Paired amphipathic helix 2 (pah2 repeat) - #20 / Harmonin / Harmonin, N-terminal domain / Paired amphipathic helix 2 (pah2 repeat) / : / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain ...ANKS4B, SAM domain / Paired amphipathic helix 2 (pah2 repeat) - #20 / Harmonin / Harmonin, N-terminal domain / 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 / PDZ superfamily / Ankyrin repeats (3 copies) / 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
Ankyrin repeat and SAM domain-containing protein 4B / Harmonin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.649 Å
AuthorsLi, J. / He, Y. / Lu, Q. / Zhang, M.
CitationJournal: Dev.Cell / Year: 2016
Title: Mechanistic Basis of Organization of the Harmonin/USH1C-Mediated Brush Border Microvilli Tip-Link Complex
Authors: Li, J. / He, Y. / Lu, Q. / Zhang, M.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Harmonin
B: Ankyrin repeat and SAM domain-containing protein 4B
C: Harmonin
D: Ankyrin repeat and SAM domain-containing protein 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9356
Polymers62,8644
Non-polymers712
Water34219
1
A: Harmonin
B: Ankyrin repeat and SAM domain-containing protein 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4683
Polymers31,4322
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-24 kcal/mol
Surface area14120 Å2
MethodPISA
2
C: Harmonin
D: Ankyrin repeat and SAM domain-containing protein 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4683
Polymers31,4322
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-24 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.566, 124.566, 49.654
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Harmonin


Mass: 22222.609 Da / Num. of mol.: 2 / Fragment: NPDZ1, UNP residues 1-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USH1C, AIE75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6N9
#2: Protein Ankyrin repeat and SAM domain-containing protein 4B / ANKS4B


Mass: 9209.466 Da / Num. of mol.: 2 / Fragment: SAM-PBM, UNP residues 345-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Anks4b, Harp / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K3X6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 3.0 M NaCl, 0.1 M Bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 14, 2015
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.649→31.511 Å / Num. obs: 24978 / % possible obs: 99.5 % / Redundancy: 5.7 % / Net I/σ(I): 38.2
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K1R

3k1r


Resolution: 2.649→31.511 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 1133 4.55 %
Rwork0.2274 --
obs0.2291 24922 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.649→31.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 2 19 4081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084133
X-RAY DIFFRACTIONf_angle_d0.9945622
X-RAY DIFFRACTIONf_dihedral_angle_d14.6172506
X-RAY DIFFRACTIONf_chiral_restr0.058672
X-RAY DIFFRACTIONf_plane_restr0.008728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6485-2.7690.43441540.39583019X-RAY DIFFRACTION100
2.769-2.91490.41160.31942998X-RAY DIFFRACTION100
2.9149-3.09740.3481500.29772947X-RAY DIFFRACTION100
3.0974-3.33630.24781420.25352995X-RAY DIFFRACTION100
3.3363-3.67160.29941690.24692928X-RAY DIFFRACTION100
3.6716-4.20180.22371260.18643020X-RAY DIFFRACTION100
4.2018-5.28970.23631380.1852984X-RAY DIFFRACTION100
5.2897-31.51340.23781380.21252898X-RAY DIFFRACTION97
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)
15.8735-2.69171.39542.593-0.47591.4508-0.1461-0.6006-0.63770.01780.34390.12610.46230.2476-0.20341.31370.32-0.02240.82980.03270.478723.723616.60293.6715
27.5645-0.02461.55355.4641-2.54254.3036-0.1222-0.8558-0.6340.22120.13530.34510.584-0.23530.01760.87670.1314-0.06080.527-0.08670.51412.853930.57810.5348
34.4883-2.52030.62439.0738-6.28994.9458-0.2433-0.24580.62140.75830.4246-0.7435-0.1445-0.2796-0.11720.60650.02240.00080.4247-0.22770.53940.520250.5996-6.8796
41.30870.25010.7837.4855-0.65271.0038-0.05840.2566-0.18260.42250.37550.50720.4863-0.3823-0.29821.1404-0.30320.01660.91280.06350.4322-35.912823.9211.9431
55.336-1.293-1.31656.2437-2.76143.6674-0.2033-0.1906-0.05650.86970.20840.6303-0.067-0.61470.03630.7395-0.2177-0.11910.6848-0.0040.508-34.55748.97638.9127
65.29532.1203-4.30647.046-2.36074.60560.5768-0.3175-0.52790.8001-0.2302-1.1161-0.26620.0916-0.21430.4938-0.1021-0.21060.5058-0.10840.5975-18.297160.94111.3075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 190 )
3X-RAY DIFFRACTION3chain 'B' and (resid 387 through 423 )
4X-RAY DIFFRACTION4chain 'C' and (resid 2 through 90 )
5X-RAY DIFFRACTION5chain 'C' and (resid 91 through 192 )
6X-RAY DIFFRACTION6chain 'D' and (resid 387 through 423 )

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