[English] 日本語
Yorodumi
- PDB-5f3x: Crystal structure of Harmonin NPDZ1 in complex with ANKS4B SAM-PBM -

+
Open data


ID or keywords:

Loading...

-
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
  • HarmoninUSH1C
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 / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / retinal cone cell development / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization ...protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / retinal cone cell development / equilibrioception / sensory perception of light stimulus / 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 / inner ear morphogenesis / spectrin binding / actin filament bundle assembly / microvillus / brush border / photoreceptor outer segment / photoreceptor inner segment / response to endoplasmic reticulum stress / sensory perception of sound / cilium / G2/M transition of mitotic cell cycle / apical part of cell / protein-containing complex assembly / cell differentiation / cytoskeleton / synapse / endoplasmic reticulum membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ANKS4B, 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. ...ANKS4B, 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Harmonin / USH1C


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 / Chloride


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more