[English] 日本語
Yorodumi
- PDB-4xa3: Crystal structure of the coiled-coil surrounding Skip 2 of MYH7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xa3
TitleCrystal structure of the coiled-coil surrounding Skip 2 of MYH7
ComponentsGp7-MYH7(1361-1425)-Eb1 chimera protein
KeywordsMOTOR PROTEIN / Myosin / coiled coil / skip residue / Fusion / Gp7 / Eb1 / Cardiac
Function / homology
Function and homology information


viral scaffold / protein localization to astral microtubule / regulation of slow-twitch skeletal muscle fiber contraction / cortical microtubule cytoskeleton / regulation of the force of skeletal muscle contraction / mitotic spindle astral microtubule end / protein localization to microtubule / muscle myosin complex / microtubule plus-end / muscle filament sliding ...viral scaffold / protein localization to astral microtubule / regulation of slow-twitch skeletal muscle fiber contraction / cortical microtubule cytoskeleton / regulation of the force of skeletal muscle contraction / mitotic spindle astral microtubule end / protein localization to microtubule / muscle myosin complex / microtubule plus-end / muscle filament sliding / cell projection membrane / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / myosin II complex / non-motile cilium assembly / adult heart development / microtubule bundle formation / cardiac muscle hypertrophy in response to stress / protein localization to centrosome / myosin complex / sarcomere organization / microtubule organizing center / virion assembly / negative regulation of microtubule polymerization / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myofibril / mitotic spindle pole / microtubule polymerization / establishment of mitotic spindle orientation / skeletal muscle contraction / striated muscle contraction / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / stress fiber / ATP metabolic process / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of heart rate / sarcomere / AURKA Activation by TPX2 / ciliary basal body / muscle contraction / RHO GTPases Activate Formins / protein localization / Z disc / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / actin filament binding / cell migration / microtubule / molecular adaptor activity / calmodulin binding / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / DNA binding / RNA binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / DNA repair protein XRCC4-like, C-terminal / Myosin tail ...Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Calponin homology (CH) domain / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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 / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-7 / Capsid assembly scaffolding protein / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.548 Å
AuthorsTaylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinz, N.T. / Qiang, C. / Leinwand, L.A. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL111237 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly.
Authors: Taylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinze, N.T. / Cui, Q. / Leinwand, L.A. / Rayment, I.
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Gp7-MYH7(1361-1425)-Eb1 chimera protein
B: Gp7-MYH7(1361-1425)-Eb1 chimera protein


Theoretical massNumber of molelcules
Total (without water)35,5312
Polymers35,5312
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-72 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.462, 146.115, 153.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Gp7-MYH7(1361-1425)-Eb1 chimera protein / chimera protein of Head morphogenesis protein / Myosin-7 and Microtubule-associated protein RP/EB ...chimera protein of Head morphogenesis protein / Myosin-7 and Microtubule-associated protein RP/EB family member 1


Mass: 17765.717 Da / Num. of mol.: 2
Fragment: UNP P13848 residues 1-49,UNP P12883 residues 1361-1425,UNP Q15691 residues 215-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human)
Plasmid: pET28 / Gene: MYH7, MYHCB, MAPRE1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P13848, UniProt: P12883, UniProt: Q15691
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 4.5% (w/v) polyethylene glycol 8000, 100 mM sodium acetate pH 5.0, 50 mM CaCl2, 2.5% (w/v) 3-methoxy-3-methyl-1-butanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2012
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 11019 / % possible obs: 87 % / Redundancy: 6.4 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.09 / Net I/av σ(I): 24.1 / Net I/σ(I): 16.3
Reflection shellResolution: 2.54→2.58 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / % possible all: 53

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1819)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NO4, 1YIB

1no4

1yib


Resolution: 2.548→29.726 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3114 547 4.97 %Random Selection
Rwork0.2668 ---
obs0.269 11005 76.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.6 Å2
Refinement stepCycle: LAST / Resolution: 2.548→29.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 0 17 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032340
X-RAY DIFFRACTIONf_angle_d0.6563148
X-RAY DIFFRACTIONf_dihedral_angle_d16.47919
X-RAY DIFFRACTIONf_chiral_restr0.025354
X-RAY DIFFRACTIONf_plane_restr0.003414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5477-2.80390.3167550.33441072X-RAY DIFFRACTION32
2.8039-3.20920.39231360.32442478X-RAY DIFFRACTION74
3.2092-4.04170.29991700.26793385X-RAY DIFFRACTION100
4.0417-29.72810.29081860.23833523X-RAY DIFFRACTION100

+
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