[English] 日本語
Yorodumi
- PDB-2bkh: Myosin VI nucleotide-free (MDInsert2) crystal structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bkh
TitleMyosin VI nucleotide-free (MDInsert2) crystal structure
Components
  • CALMODULIN
  • UNCONVENTIONAL MYOSIN
KeywordsMOTOR PROTEIN/METAL-BINDING PROTEIN / COMPLEX (MOTOR PROTEIN-CALMODULIN) / MYOSIN VI / REVERSE MYOSIN / CALMODULIN / NON-CONVENTIONAL MYOSIN / NUCLEOTIDE-FREE CONFORMATION / MUSCLE PROTEIN / MOTOR PROTEIN-METAL-BINDING PROTEIN complex
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 / cellular response to ethanol / myosin complex / clathrin-coated vesicle / muscle cell cellular homeostasis / inner ear morphogenesis / microfilament motor activity / myosin heavy chain binding / mitotic spindle pole / channel regulator activity / filamentous actin / centriole replication / cytoskeletal motor activity / microvillus / DNA damage response, signal transduction by p53 class mediator / enzyme regulator activity / ruffle / centriole / actin filament organization / filopodium / actin filament / intracellular protein transport / sensory perception of sound / ADP binding / mitotic spindle / microtubule cytoskeleton organization / spindle / ruffle membrane / endocytosis / actin filament binding / sensory perception of smell / actin cytoskeleton / protein localization / cell cortex / midbody / 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
Myosin VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / 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 VI, cargo binding domain / Class VI myosin, motor domain / : / Myosin VI cargo binding domain / Myosin VI, lever arm / 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. / : / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
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: 2.4 Å
AuthorsMenetrey, J. / Bahloul, A. / Yengo, C. / Wells, A. / Morris, C. / Sweeney, H.L. / Houdusse, A.
CitationJournal: Nature / Year: 2005
Title: The Structure of the Myosin Vi Motor Reveals the Mechanism of Directionality Reversal
Authors: Menetrey, J. / Bahloul, A. / Wells, A. / Yengo, C. / Morris, C. / Sweeney, H.L. / Houdusse, A.
History
DepositionFeb 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
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_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UNCONVENTIONAL MYOSIN
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,57112
Polymers109,8592
Non-polymers71310
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.570, 104.437, 90.284
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein UNCONVENTIONAL MYOSIN / MYOSIN VI


Mass: 93033.078 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN-INSERT2, RESIDUES 2-816
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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY ...THE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY INCORRECT BECAUSE THE CHANGES THAT ARE IN THEIR CLONE (LYS DELETION AND THE 6 MUTATIONS) ARE CONSERVED ACROSS THE MYOSIN VI FAMILY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.5 %
Crystal growDetails: 8-10% PEG 8000, 50MM MES PH 6.7, 150MM NH4.SO4, 3% ISO-PROPANOL, 3% TERT-BUTANOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 49721 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OE9

1oe9


Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.454 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS 356-360 AND 623-639 IN CHAIN A AND 73-80 IN CHAIN B WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2520 5.1 %RANDOM
Rwork0.206 ---
obs0.208 47177 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å2-0.09 Å2
2---1.2 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7403 0 40 285 7728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217574
X-RAY DIFFRACTIONr_bond_other_d0.0020.026796
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.95610189
X-RAY DIFFRACTIONr_angle_other_deg0.776315878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835919
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.21112
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028381
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021540
X-RAY DIFFRACTIONr_nbd_refined0.1980.21687
X-RAY DIFFRACTIONr_nbd_other0.2230.27773
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.24394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6171.54586
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17927387
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51232988
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6534.52802
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.53 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.317 352
Rwork0.259 6855

+
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