[English] 日本語
Yorodumi
- PDB-2x51: M6 delta Insert1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x51
TitleM6 delta Insert1
Components
  • CALMODULIN
  • MYOSIN-VI
KeywordsMOTOR PROTEIN/SIGNALING PROTEIN / MOTOR PROTEIN-SIGNALING PROTEIN COMPLEX / ENDOCYTOSIS / PROTEIN TRANSPORT / CALMODULIN-BINDING / TRANSPORT / ACTIN-BINDING / GOLGI APPARATUS
Function / homology
Function and homology information


negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex ...negative regulation of phospholipase C-activating phototransduction signaling pathway / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere development / rhabdomere / detection of chemical stimulus involved in sensory perception of smell / myosin V complex / regulation of secretion / kinetochore organization / autophagic cell death / G protein-coupled opsin signaling pathway / inner ear auditory receptor cell differentiation / actin filament-based movement / myosin V binding / channel regulator activity / cellular response to ethanol / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / muscle cell cellular homeostasis / microfilament motor activity / myosin heavy chain binding / mitotic spindle pole / filamentous actin / centriole replication / cytoskeletal motor activity / microvillus / enzyme regulator activity / ruffle / centriole / DNA damage response, signal transduction by p53 class mediator / actin filament organization / filopodium / actin filament / intracellular protein transport / sensory perception of sound / ADP binding / microtubule cytoskeleton organization / spindle / ruffle membrane / endocytosis / actin filament binding / mitotic spindle / sensory perception of smell / intracellular protein localization / actin cytoskeleton / midbody / cell cortex / cytoplasmic vesicle / nuclear membrane / calmodulin binding / centrosome / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2980 / Alpha-Beta Plaits - #1590 / Arc Repressor Mutant, subunit A - #820 / Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2980 / Alpha-Beta Plaits - #1590 / Arc Repressor Mutant, subunit A - #820 / Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Kinesin motor domain superfamily / : / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / EF-hand domain pair / Special / EF-hand, calcium binding motif / SH3 type barrels. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Arc Repressor Mutant, subunit A / Roll / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calmodulin / Unconventional myosin-VI
Similarity search - Component
Biological speciesSUS SCROFA (pig)
DROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSquires, G. / Houdusse, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Role of Insert-1 of Myosin Vi in Modulating Nucleotide Affinity.
Authors: Pylypenko, O. / Song, L. / Squires, G. / Liu, X. / Zong, A.B. / Houdusse, A. / Sweeney, H.L.
History
DepositionFeb 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYOSIN-VI
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,71713
Polymers106,8562
Non-polymers86111
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-88 kcal/mol
Surface area39570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.888, 61.017, 133.274
Angle α, β, γ (deg.)90.00, 116.19, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein MYOSIN-VI / UNCONVENTIONAL MYOSIN VI


Mass: 90030.672 Da / Num. of mol.: 1 / Fragment: MYOSIN VI DELTA INSERT1,RESIDUES 1-277,303-817
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q29122
#2: Protein CALMODULIN / CAM


Mass: 16825.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62152

-
Non-polymers , 4 types, 262 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 303 TO GLY ENGINEERED RESIDUE IN CHAIN A, GLY 548 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, ALA 303 TO GLY ENGINEERED RESIDUE IN CHAIN A, GLY 548 TO VAL ENGINEERED RESIDUE IN CHAIN A, ALA 573 TO ARG ENGINEERED RESIDUE IN CHAIN A, TYR 574 TO ASP ENGINEERED RESIDUE IN CHAIN A, VAL 715 TO LEU ENGINEERED RESIDUE IN CHAIN A, SER 722 TO TYR ENGINEERED RESIDUE IN CHAIN A, LEU 723 TO MET

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.37 % / Description: NONE
Crystal growpH: 6.75
Details: 10.8% PEG 8000, 50 MM MES PH 6.75, 175 MM AMMONIUM SULFATE, 3% ISO-PROPANOL, 3% TERT-BUTANOL, 4 MM EGTA. SOLUTION OF PROTEIN AT 18 MG/ML.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 60348 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.068 / Net I/σ(I): 14.44
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.92 / Rsym value: 0.437 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BKH

2bkh


Resolution: 2.2→26.818 Å / SU ML: 0.28 / σ(F): 1.39 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2723 3015 5 %
Rwork0.2158 --
obs0.2186 60296 99.88 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1--15.5861 Å20 Å2-5.5933 Å2
2--18.639 Å20 Å2
3----0.6774 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 0 50 251 7401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087272
X-RAY DIFFRACTIONf_angle_d1.0229778
X-RAY DIFFRACTIONf_dihedral_angle_d14.5652720
X-RAY DIFFRACTIONf_chiral_restr0.0721064
X-RAY DIFFRACTIONf_plane_restr0.0041272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27860.29733000.24125693X-RAY DIFFRACTION100
2.2786-2.36980.2942990.23725696X-RAY DIFFRACTION100
2.3698-2.47760.32052970.23495643X-RAY DIFFRACTION100
2.4776-2.60810.28833010.22825710X-RAY DIFFRACTION100
2.6081-2.77140.30673000.23325701X-RAY DIFFRACTION100
2.7714-2.98510.30423020.23835724X-RAY DIFFRACTION100
2.9851-3.2850.30013010.24485720X-RAY DIFFRACTION100
3.285-3.75930.26523020.22235745X-RAY DIFFRACTION100
3.7593-4.73210.24393040.18685764X-RAY DIFFRACTION100
4.7321-26.81960.24943090.19825885X-RAY DIFFRACTION99

+
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