[English] 日本語
Yorodumi
- PDB-6ixq: Structure of Myo2-GTD in complex with Smy1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ixq
TitleStructure of Myo2-GTD in complex with Smy1
Components
  • Kinesin-related protein SMY1
  • Myosin-2
KeywordsPROTEIN BINDING / Cargo binding domain
Function / homology
Function and homology information


peroxisome inheritance / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / RHOT2 GTPase cycle / membrane addition at site of cytokinesis / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance ...peroxisome inheritance / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / RHOT2 GTPase cycle / membrane addition at site of cytokinesis / mitochondrion inheritance / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance / vesicle transport along actin filament / incipient cellular bud site / cytoskeleton-dependent intracellular transport / cellular bud tip / Golgi inheritance / cellular bud neck / mating projection tip / plus-end-directed microtubule motor activity / fungal-type vacuole membrane / vesicle docking involved in exocytosis / kinesin complex / microtubule-based movement / microfilament motor activity / actin filament bundle / filamentous actin / intracellular distribution of mitochondria / establishment of mitotic spindle orientation / cytoskeletal motor activity / transport vesicle / vesicle-mediated transport / actin filament organization / small GTPase binding / actin filament binding / protein transport / actin cytoskeleton / microtubule binding / vesicle / microtubule / calmodulin binding / ATP hydrolysis activity / ATP binding / membrane / cytoplasm
Similarity search - Function
: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Kinesin-like protein / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Kinesin motor domain signature. ...: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Kinesin-like protein / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-2 / Kinesin-related protein SMY1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsTang, K. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770791 China
National Natural Science Foundation of China31570741 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural mechanism for versatile cargo recognition by the yeast class V myosin Myo2.
Authors: Tang, K. / Li, Y. / Yu, C. / Wei, Z.
History
DepositionDec 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin-2
B: Kinesin-related protein SMY1


Theoretical massNumber of molelcules
Total (without water)53,7702
Polymers53,7702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-13 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.510, 93.510, 204.136
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Myosin-2 / Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain ...Cell division control protein 66 / Class V unconventional myosin MYO2 / Type V myosin heavy chain MYO2 / Myosin V MYO2


Mass: 48747.227 Da / Num. of mol.: 1 / Mutation: Deletions 1342-1347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MYO2, CDC66, YOR326W, O6167 / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19524
#2: Protein/peptide Kinesin-related protein SMY1 / Suppressor protein SMY1


Mass: 5022.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SMY1, YKL079W, YKL409 / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32364

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.79 Å3/Da / Density % sol: 74.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8% w/v PEG 8000, 0.1M sodium dihydrogen phosphate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.06→75.28 Å / Num. obs: 20270 / % possible obs: 99.7 % / Redundancy: 18.7 % / Biso Wilson estimate: 125.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.017 / Rrim(I) all: 0.071 / Net I/σ(I): 20.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.06-3.2220.71.69329110.9780.3781.736100
9.66-75.2815.70.0437380.9970.0110.04599.5

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F6H

2f6h


Resolution: 3.06→39.717 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.1
RfactorNum. reflection% reflection
Rfree0.2233 976 4.87 %
Rwork0.2031 --
obs0.2041 20042 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 345.96 Å2 / Biso mean: 172.9546 Å2 / Biso min: 75.68 Å2
Refinement stepCycle: final / Resolution: 3.06→39.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 0 0 3258
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043321
X-RAY DIFFRACTIONf_angle_d0.6254510
X-RAY DIFFRACTIONf_chiral_restr0.023536
X-RAY DIFFRACTIONf_plane_restr0.003563
X-RAY DIFFRACTIONf_dihedral_angle_d12.6731206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0556-3.21670.39351290.35742662279198
3.2167-3.41810.40041630.32862603276698
3.4181-3.68180.25461030.27772737284099
3.6818-4.0520.27761260.24112715284199
4.052-4.63760.23991540.19162693284799
4.6376-5.83990.21211550.20492746290199
5.8399-39.72060.18831460.171829103056100
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)
12.09320.50950.76724.30631.75562.9513-0.0197-0.094-0.25970.316-0.171-0.09990.4708-0.9368-01.4787-0.13210.11421.4827-0.08671.454379.938152.8928222.632
21.6144-2.38821.54890.59250.56930.7201-0.37020.42410.1033-0.89340.00180.0169-0.7120.30110.00061.5182-0.36680.22361.0884-0.21361.376988.809365.0336228.4236
31.67192.21531.15592.47340.08671.99010.1155-0.1049-0.38420.67480.0901-0.49780.7689-0.2583-1.00321.16940.2215-0.20941.025-0.08171.110895.205572.269255.6039
4-0.8618-0.10560.3212.58660.92191.70390.1763-0.3941-0.07550.2816-0.5799-0.15680.3997-0.5261-0.01531.3608-0.11410.10041.5808-0.13641.528494.312869.9593242.6787
55.56583.2142-3.89086.4842-4.98544.1198-0.79730.6792-0.1971-1.41911.4205-0.06272.9552-0.491-0.27732.396-0.1876-0.12081.561-0.18361.918283.682339.7059215.9284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1152 through 1280 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1281 through 1326 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1327 through 1462 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1463 through 1572 )
5X-RAY DIFFRACTION5chain 'B' and (resid 633 through 647 )

+
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