[English] 日本語
Yorodumi
- PDB-4dbp: Myosin VI nucleotide-free (MDINSERT2) D179Y crystal structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dbp
TitleMyosin VI nucleotide-free (MDINSERT2) D179Y crystal structure
Components
  • Calmodulin
  • Myosin-VI
Keywordsmotor protein/Calcium binding protein / motor protein / motor protein-Calcium 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 / regulation of secretion ...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 / regulation of secretion / myosin V complex / 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 / myosin complex / clathrin-coated vesicle / inner ear morphogenesis / myosin heavy chain binding / microfilament motor activity / muscle cell cellular homeostasis / mitotic spindle pole / filamentous actin / microvillus / centriole replication / cellular response to ethanol / cytoskeletal motor activity / enzyme regulator activity / ruffle / clathrin-coated pit / centriole / actin filament organization / actin filament / filopodium / DNA damage response, signal transduction by p53 class mediator / intracellular protein transport / sensory perception of sound / ADP binding / microtubule cytoskeleton organization / ruffle membrane / spindle / endocytosis / actin filament binding / mitotic spindle / sensory perception of smell / intracellular protein localization / protein transport / actin cytoskeleton / cytoplasmic vesicle / midbody / cell cortex / nuclear membrane / calmodulin binding / calcium ion binding / centrosome / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytoplasm / cytosol
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 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
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / TERTIARY-BUTYL ALCOHOL / Unconventional myosin-VI / 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
AuthorsPylypenko, O. / Sweeney, H.L. / Houdusse, A.
CitationJournal: To be Published
Title: Mutations in myosin VI that cause a loss of coordination between heads provide insights into the structural changes underlying force generation and the importance of gating
Authors: Song, L. / Pylypenko, O. / Yang, Z. / Houdusse, A. / Sweeney, L.H.
History
DepositionJan 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _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
C: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,39327
Polymers109,9072
Non-polymers1,48625
Water14,070781
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-23 kcal/mol
Surface area41020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.600, 104.390, 90.020
Angle α, β, γ (deg.)90.00, 91.15, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AC

#1: Protein Myosin-VI


Mass: 93081.164 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN-INSERT2, UNP residues 2-815 / Mutation: D179Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1RQI7, UniProt: Q29122*PLUS
#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) / Gene: Cam, CG8472 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62152

-
Non-polymers , 5 types, 806 molecules

#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#6: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.5% P8K, 50 mM MOPS pH7,3% I-prop, 3% tert-but,1mM TCEP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→19.9 Å / Num. all: 64374 / Num. obs: 63904 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.25 Å / % possible all: 98.8

-
Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BKH

2bkh


Resolution: 2.2→19.885 Å / SU ML: 0.65 / σ(F): 0 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3196 5 %RANDOM
Rwork0.1626 ---
obs0.1653 63899 99.41 %-
all-64374 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.641 Å2 / ksol: 0.314 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→19.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7403 0 90 781 8274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077684
X-RAY DIFFRACTIONf_angle_d0.99910341
X-RAY DIFFRACTIONf_dihedral_angle_d13.5962882
X-RAY DIFFRACTIONf_chiral_restr0.0711130
X-RAY DIFFRACTIONf_plane_restr0.0041348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27850.27493160.20785989X-RAY DIFFRACTION99
2.2785-2.36960.2673180.20196050X-RAY DIFFRACTION99
2.3696-2.47720.25623160.19316010X-RAY DIFFRACTION99
2.4772-2.60760.25263190.18366057X-RAY DIFFRACTION99
2.6076-2.77050.24813190.17086063X-RAY DIFFRACTION99
2.7705-2.98380.23433200.16136084X-RAY DIFFRACTION100
2.9838-3.28280.22673200.16296071X-RAY DIFFRACTION100
3.2828-3.75510.20563210.16286094X-RAY DIFFRACTION100
3.7551-4.72060.17253210.13076108X-RAY DIFFRACTION100
4.7206-19.8850.20683260.15846177X-RAY DIFFRACTION99
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)
10.07810.14330.08360.33230.35530.5973-0.1727-0.20460.10330.36140.1749-0.1527-0.08590.1291-0.01481.11410.4537-0.37910.5758-0.24730.047114.9308-7.241952.0317
21.2775-0.8742-0.49941.76771.1552.6989-0.1191-0.16170.01560.27320.15560.1842-0.3118-0.3365-0.00040.67740.31750.03050.3827-0.04230.1835-1.02343.295140.2895
31.0554-0.1687-0.40420.61810.58412.12780.0268-0.22880.19390.17940.1078-0.0251-0.2726-0.14730.07560.68690.2693-0.18850.3575-0.21370.09748.58390.490945.3747
40.6435-0.07380.19151.0705-0.40870.6271-0.05530.02850.0841-0.03120.13020.17230.0196-0.0723-0.0209-0.0279-0.00570.0317-0.0014-0.0220.0426-17.79260.092-0.6475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 80:147 )C80 - 147
2X-RAY DIFFRACTION2( CHAIN C AND RESID 3:72 )C3 - 72
3X-RAY DIFFRACTION3( CHAIN A AND RESID 784:815 )A784 - 815
4X-RAY DIFFRACTION4( CHAIN A AND RESID 3:783 )A3 - 783

+
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