[English] 日本語
Yorodumi
- PDB-1m46: CRYSTAL STRUCTURE OF MLC1P BOUND TO IQ4 OF MYO2P, A CLASS V MYOSIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m46
TitleCRYSTAL STRUCTURE OF MLC1P BOUND TO IQ4 OF MYO2P, A CLASS V MYOSIN
Components
  • IQ4 Motif from MYO2P, A Class V Myosin
  • Myosin light chain
KeywordsCELL CYCLE PROTEIN / Protein-Peptide complex / IQ motif / myosin light chain
Function / homology
Function and homology information


protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / MIH complex / RHO GTPases activate PAKs / regulation of actomyosin contractile ring contraction / peroxisome inheritance / regulation of cell wall organization or biogenesis / myosin II heavy chain binding / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex ...protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / MIH complex / RHO GTPases activate PAKs / regulation of actomyosin contractile ring contraction / peroxisome inheritance / regulation of cell wall organization or biogenesis / myosin II heavy chain binding / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / membrane addition at site of cytokinesis / mitochondrion inheritance / site of polarized growth / mitotic actomyosin contractile ring assembly / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / cellular bud neck contractile ring / vesicle targeting / myosin V complex / vacuole inheritance / vesicle transport along actin filament / Golgi inheritance / incipient cellular bud site / septum digestion after cytokinesis / cellular bud tip / myosin V binding / cellular bud neck / mating projection tip / fungal-type vacuole membrane / vesicle docking involved in exocytosis / myosin II complex / microfilament motor activity / intracellular distribution of mitochondria / filamentous actin / actin filament bundle / establishment of mitotic spindle orientation / transport vesicle / vesicle-mediated transport / actin filament organization / regulation of cytokinesis / small GTPase binding / actin filament binding / protein transport / actin cytoskeleton / vesicle / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site ...: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / 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
Myosin-2 / Myosin light chain 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Molecular replacement, Based on another structure of a mutant of MLC1P bound to IQ4 that crystallized in a different space group, was determined in the lab by the se-met mad method / Resolution: 2.103 Å
AuthorsTerrak, M. / Dominguez, R.
Citation
Journal: Embo J. / Year: 2003
Title: Two distinct myosin light chain structures are induced by specific variations within the bound IQ motifs-functional implications
Authors: Terrak, M. / Wu, G. / Stafford, W.F. / Lu, R.C. / Dominguez, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallisation, X-ray characterization and selenomethionine phasing of Mlc1p bound to IQ motifs from myosin V
Authors: Terrak, M. / Otterbein, L.R. / Wu, G. / Palecanda, L.A. / Lu, R.C. / Dominguez, R.
History
DepositionJul 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin light chain
B: IQ4 Motif from MYO2P, A Class V Myosin


Theoretical massNumber of molelcules
Total (without water)19,4202
Polymers19,4202
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area11210 Å2
MethodPISA
2
A: Myosin light chain
B: IQ4 Motif from MYO2P, A Class V Myosin

A: Myosin light chain
B: IQ4 Motif from MYO2P, A Class V Myosin


Theoretical massNumber of molelcules
Total (without water)38,8404
Polymers38,8404
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6040 Å2
ΔGint-40 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.504, 121.504, 29.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Myosin light chain / M1c1p


Mass: 16332.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MLC1 / Plasmid: pAED4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P53141
#2: Protein/peptide IQ4 Motif from MYO2P, A Class V Myosin / IQ4


Mass: 3087.704 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Saccharomyces cerevisiae (Baker's yeast).
References: UniProt: P19524
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, potassium/sodium tartrate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.2 Mammonium sulfate11
20.2 Mpotassium sodium tartrate tetrahydrate11
30.1 Mtrisodium citrate dihydrate11pH5.6
45 mMsodium acetate12pH4.0
51 mM12CaCl2
61 mMdithiothreitol12
710 mMprotein12

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2000 / Details: Charles Supper Double Mirror X-ray Focusing System
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.103→45 Å / Num. all: 10540 / Num. obs: 10540 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15
Reflection shellResolution: 2.103→2.18 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 98.5
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 45 Å / % possible obs: 99.2 %
Reflection shell
*PLUS
Highest resolution: 2.1 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: Molecular replacement, Based on another structure of a mutant of MLC1P bound to IQ4 that crystallized in a different space group, was determined in the lab by the se-met mad method
Resolution: 2.103→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.782 / SU ML: 0.129 / Isotropic thermal model: overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CNS 1.0 was also used at the beginning of the refinement of this structure
RfactorNum. reflection% reflectionSelection details
Rfree0.23895 504 4.8 %RANDOM
Rwork0.19901 ---
obs0.2013 10035 99.2 %-
all-10035 --
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: 36.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.103→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 0 81 1469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221400
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9831883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9933177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49615285
X-RAY DIFFRACTIONr_chiral_restr0.1410.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021034
X-RAY DIFFRACTIONr_nbd_refined0.2270.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.215
X-RAY DIFFRACTIONr_mcbond_it1.5421.5873
X-RAY DIFFRACTIONr_mcangle_it2.93321409
X-RAY DIFFRACTIONr_scbond_it4.4463527
X-RAY DIFFRACTIONr_scangle_it7.5744.5474
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.286 36
Rwork0.258 685
obs-685
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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