[English] 日本語
Yorodumi
- PDB-5f3y: Crystal Structure of Myo7b N-MyTH4-FERM-SH3 in complex with Anks4b CEN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f3y
TitleCrystal Structure of Myo7b N-MyTH4-FERM-SH3 in complex with Anks4b CEN
Components
  • Ankyrin repeat and SAM domain-containing protein 4B
  • Unconventional myosin-VIIb
KeywordsMOTOR PROTEIN/PROTEIN BINDING / MOTOR PROTEIN / PROTEIN BINDING / STRUCTURAL PROTEIN / PROTEIN TRANSPORT / MOTOR PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


apical cytoplasm / protein localization to microvillus / microfilament motor activity => GO:0000146 / brush border assembly / sensory organ development / vesicle transport along actin filament / myosin complex / microfilament motor activity / brush border / microvillus ...apical cytoplasm / protein localization to microvillus / microfilament motor activity => GO:0000146 / brush border assembly / sensory organ development / vesicle transport along actin filament / myosin complex / microfilament motor activity / brush border / microvillus / response to endoplasmic reticulum stress / actin filament organization / sensory perception of sound / actin filament binding / actin cytoskeleton / protein-containing complex assembly / vesicle / cell differentiation / endoplasmic reticulum membrane / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
ANKS4B, SAM domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Acyl-CoA Binding Protein - #10 ...ANKS4B, SAM domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / IQ calmodulin-binding motif / Myosin S1 fragment, N-terminal / SAM domain (Sterile alpha motif) / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / SH3 Domains / PH-domain like / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Sterile alpha motif. / Sterile alpha motif domain / Kinesin motor domain superfamily / Sterile alpha motif/pointed domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Src homology 3 domains / Ubiquitin-like (UB roll) / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ankyrin repeat and SAM domain-containing protein 4B / Unconventional myosin-VIIb
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.409 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: Unconventional myosin-VIIb
B: Ankyrin repeat and SAM domain-containing protein 4B


Theoretical massNumber of molelcules
Total (without water)81,5982
Polymers81,5982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-14 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.516, 197.516, 97.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Unconventional myosin-VIIb


Mass: 69985.125 Da / Num. of mol.: 1 / Fragment: N-MyTH4-FERM-SH3, UNP residues 962-1578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo7b / Production host: Escherichia coli (E. coli) / References: UniProt: Q99MZ6
#2: Protein Ankyrin repeat and SAM domain-containing protein 4B / ANKS4B


Mass: 11613.118 Da / Num. of mol.: 1 / Fragment: CEN, UNP residues 252-352
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.84 Å3/Da / Density % sol: 78.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25%(w/v) Pentaerythritol ethoxylate (3/4 EO/OH), 0.1 M MES
PH range: 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2015
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 24972 / % possible obs: 92.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 92.1 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.04 / Rrim(I) all: 0.109 / Χ2: 1.651 / Net I/av σ(I): 19.612 / Net I/σ(I): 8.7 / Num. measured all: 169291
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.464.90.88812620.6570.4190.9871.46495.7
3.46-3.525.10.70112510.7240.3250.7781.60495.5
3.52-3.595.20.49412750.690.2290.5481.70495.4
3.59-3.665.30.35312280.7480.1690.3952.12694.5
3.66-3.745.30.3112490.8340.1480.3461.96993.9
3.74-3.835.30.3312270.8670.1540.3661.68694.2
3.83-3.925.90.43612470.8960.1880.4781.66693.9
3.92-4.036.30.32312500.9480.1340.3521.694.3
4.03-4.156.40.26812390.970.1090.2911.63193.7
4.15-4.286.70.22612110.9760.0910.2441.60491.3
4.28-4.446.80.16712320.9740.070.1822.01893
4.44-4.617.10.12512250.9860.050.1361.72791.3
4.61-4.827.30.12312290.9930.0470.1331.67292.5
4.82-5.087.60.11112760.9950.040.1191.53694
5.08-5.480.09912520.9960.0340.1051.51593.8
5.4-5.818.30.10112580.9960.0340.1071.62393.3
5.81-6.48.60.09912630.9970.0330.1051.77993
6.4-7.328.60.07512700.9970.0250.0791.64492
7.32-9.218.60.03912690.9990.0130.0421.34290.8
9.21-508.20.03112590.9990.0110.0331.44984.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX(1.10_2142: ???)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PVL

3pvl


Resolution: 3.409→30.718 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 1288 5.2 %
Rwork0.2411 23493 -
obs0.2432 24781 92.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.33 Å2 / Biso mean: 93.211 Å2 / Biso min: 38.97 Å2
Refinement stepCycle: final / Resolution: 3.409→30.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4041 0 0 0 4041
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084143
X-RAY DIFFRACTIONf_angle_d1.1115700
X-RAY DIFFRACTIONf_chiral_restr0.062697
X-RAY DIFFRACTIONf_plane_restr0.008719
X-RAY DIFFRACTIONf_dihedral_angle_d13.9432401
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4088-3.54510.38651320.36022515264791
3.5451-3.70620.34951390.29972664280395
3.7062-3.90120.34021410.29912611275294
3.9012-4.14510.36341340.3052571270592
4.1451-4.46430.27921490.25732554270391
4.4643-4.91190.23751500.19322584273492
4.9119-5.61890.27231480.2122650279894
5.6189-7.0650.29481480.24092673282193
7.065-30.71890.21951470.19352671281889
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)
12.76251.00251.20580.5460.16070.8920.10370.1651-0.6675-0.30460.1597-0.16860.36440.3477-0.40770.4570.0583-0.05231.0982-0.06381.06234.26151.2034-4.7002
22.1260.91991.30151.95581.09831.79830.0284-0.82120.02580.0764-0.1914-0.1055-0.3162-0.1583-0.06620.5054-0.1445-0.09110.6951-0.01360.5979-36.732152.1259-9.9929
32.1426-1.00811.07474.6048-2.82772.6009-1.7857-1.5105-0.39520.72210.39060.1832-0.2988-0.18760.58241.4607-0.2864-0.31141.91090.41351.8086-24.796558.29055.4387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 972 through 1251 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1252 through 1559 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 263 through 275 )B0

+
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://pdbjlvh1.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