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- PDB-1g8x: STRUCTURE OF A GENETICALLY ENGINEERED MOLECULAR MOTOR -

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Basic information

Entry
Database: PDB / ID: 1g8x
TitleSTRUCTURE OF A GENETICALLY ENGINEERED MOLECULAR MOTOR
ComponentsMYOSIN II HEAVY CHAIN FUSED TO ALPHA-ACTININ 3
KeywordsSTRUCTURAL PROTEIN / myosin / motor / alpha-actinin / dictyostelium / lever arm / protein engineering
Function / homology
Function and homology information


contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / sorocarp development / calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole ...contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / sorocarp development / calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / RHO GTPases activate PAKs / contractile actin filament bundle assembly / Neutrophil degranulation / cell trailing edge / contractile vacuole organization / macropinocytic cup / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / adenyl nucleotide binding / actomyosin contractile ring / hypotonic response / uropod / actin-myosin filament sliding / actin crosslink formation / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / myosin filament / filopodium assembly / myosin II complex / early phagosome / hyperosmotic response / microfilament motor activity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / cell leading edge / pseudopodium / actin filament bundle assembly / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / phagocytic vesicle / phagocytosis / response to mechanical stimulus / response to cAMP / cellular response to starvation / extracellular matrix / 14-3-3 protein binding / cell projection / actin filament / cell motility / response to hydrogen peroxide / protein localization / structural constituent of cytoskeleton / chemotaxis / actin filament binding / protein-macromolecule adaptor activity / cell junction / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / cytoskeleton / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #820 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Kinesin motor domain / Kinesin ...Arc Repressor Mutant, subunit A - #820 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Kinesin motor domain / Kinesin / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Spectrin/alpha-actinin / Spectrin repeats / Myosin S1 fragment, N-terminal / Calponin homology domain / Calponin homology (CH) domain / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand domain pair / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Alpha-actinin A / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsKliche, W. / Fujita-Becker, S. / Kollmar, M. / Manstein, D.J. / Kull, F.J.
CitationJournal: EMBO J. / Year: 2001
Title: Structure of a genetically engineered molecular motor.
Authors: Kliche, W. / Fujita-Becker, S. / Kollmar, M. / Manstein, D.J. / Kull, F.J.
History
DepositionNov 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOSIN II HEAVY CHAIN FUSED TO ALPHA-ACTININ 3
B: MYOSIN II HEAVY CHAIN FUSED TO ALPHA-ACTININ 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,3216
Polymers230,4182
Non-polymers9034
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.423, 155.420, 143.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MYOSIN II HEAVY CHAIN FUSED TO ALPHA-ACTININ 3


Mass: 115208.867 Da / Num. of mol.: 2
Fragment: MYOSIN II HEAVY CHAIN, MOTOR DOMAIN RESIDUES 1-761, AND ALPHA-ACTININ 3, REPEATS 1 AND 2 RESIDUES 765-1002
Mutation: ARG238GLU
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Plasmid: PDH12 / Production host: Dictyostelium discoideum (eukaryote) / Strain (production host): AX3-ORF+ / References: UniProt: P08799, UniProt: P05095
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 12% PEGM 5000; 170 mM NaCl; 50 mM HEPES (NaOH) pH 7.2; 5 mM MgCl2; 5 mM DTT; 0.5 mM EGTA; and 2% 2-methyl-1,3-propanediol, at 280 K, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
Temperature: 7 ℃ / pH: 7.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
230 mMHEPES-NaOH1drop
30.5 mMEDTA1drop
42 mMdithiothreitol1drop
51 mMbenzamidine1drop
61 mM1dropMgCl2
73 %sucrose1drop
812 %mPEG50001reservoir
9170 mM1reservoirNaCl
1050 mMHEPES-NaOH1reservoir
115 mM1reservoirMgCl2
125 mMdithiothreitol1reservoir
130.5 mMEGTA1reservoir
142 %2-methyl-1,3-propanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 52.3 Å2
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Num. obs: 73355 / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 98 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 3.09

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MAR345data collection
XDSdata scaling
RefinementResolution: 2.8→41.15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 304957.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 5989 8.2 %RANDOM
Rwork0.232 ---
obs0.232 73283 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.13 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 52.7 Å2
Baniso -1Baniso -2Baniso -3
1--11.56 Å20 Å20 Å2
2---7.69 Å20 Å2
3---19.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16222 0 56 14 16292
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.572.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 962 8 %
Rwork0.328 11122 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PA
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4TOP
X-RAY DIFFRACTION5WATER_REP.PARA
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8.2 % / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.379 / % reflection Rfree: 8 % / Rfactor Rwork: 0.328

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