[English] 日本語
Yorodumi
- PDB-4pk4: Myosin VI motor domain in the PPS state - from a Pi release state... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pk4
TitleMyosin VI motor domain in the PPS state - from a Pi release state crystal, space group P212121 after long soaking with PO4
ComponentsUnconventional myosin-VI
KeywordsMOTOR PROTEIN / motor domain / Pre powerstroke state
Function / homology
Function and homology information


myosin complex / clathrin-coated vesicle / microvillus / cytoskeletal motor activity / clathrin-coated pit / filopodium / sensory perception of sound / ruffle membrane / endocytosis / actin filament binding ...myosin complex / clathrin-coated vesicle / microvillus / cytoskeletal motor activity / clathrin-coated pit / filopodium / sensory perception of sound / ruffle membrane / endocytosis / actin filament binding / protein transport / calmodulin binding / perinuclear region of cytoplasm / Golgi apparatus / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
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 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / Kinesin motor domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / SH3 type barrels. / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Unconventional myosin-VI
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsIsabet, T. / Benisty, H. / Llinas, P. / Sweeney, H.L. / Houdusse, A.
Funding support France, United States, 3items
OrganizationGrant numberCountry
French National Research AgencyBLAN07 France
French National Research AgencyBLAN10 France
National Institutes of HealthRO01DC009100 United States
CitationJournal: Dev.Cell / Year: 2015
Title: How actin initiates the motor activity of Myosin.
Authors: Llinas, P. / Isabet, T. / Song, L. / Ropars, V. / Zong, B. / Benisty, H. / Sirigu, S. / Morris, C. / Kikuti, C. / Safer, D. / Sweeney, H.L. / Houdusse, A.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 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: Unconventional myosin-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3944
Polymers89,8471
Non-polymers5463
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-28 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.590, 94.790, 101.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Unconventional myosin-VI


Mass: 89847.180 Da / Num. of mol.: 1 / Fragment: residues 2-789
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MYO6 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1RQI7
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 6,6% PEG8k, 50mM Tris pH8,5, 1mM TCEP, 3% Glycerol then soaked during 45 minutes with 100mM NaH2PO4 pH7,5
PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 23205 / % possible obs: 99.3 % / Redundancy: 7.23 % / Biso Wilson estimate: 84.54 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 16.53
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.125 / Mean I/σ(I) obs: 1.35 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
Cootmodel building
PHASERphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v26

2v26


Resolution: 2.78→31 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.8992 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.361
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1161 5 %RANDOM
Rwork0.1871 ---
obs0.1908 23205 99.08 %-
Displacement parametersBiso mean: 104.44 Å2
Baniso -1Baniso -2Baniso -3
1--16.6649 Å20 Å20 Å2
2---5.5072 Å20 Å2
3---22.1721 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: 1 / Resolution: 2.78→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 33 15 6052
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016168HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.178353HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2159SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes166HARMONIC2
X-RAY DIFFRACTIONt_gen_planes914HARMONIC5
X-RAY DIFFRACTIONt_it6168HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion20.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion800SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7117SEMIHARMONIC4
LS refinement shellResolution: 2.78→2.9 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2955 140 5.03 %
Rwork0.2414 2641 -
all0.244 2781 -
obs--99.08 %
Refinement TLS params.Method: refined / Origin x: 18.9055 Å / Origin y: -21.9872 Å / Origin z: -10.6339 Å
111213212223313233
T-0.3792 Å2-0.1094 Å2-0.1112 Å2--0.2942 Å20.0455 Å2---0.3149 Å2
L1.5168 °2-0.2438 °20.4323 °2-2.3935 °2-1.0327 °2--3.7703 °2
S0.3069 Å °0.0195 Å °-0.0345 Å °-0.0511 Å °-0.2108 Å °0.3129 Å °0.2652 Å °0.2458 Å °-0.0961 Å °
Refinement TLS groupSelection details: { A|* }

+
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