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- PDB-1w7j: Crystal Structure Of Myosin V Motor With Essential Light Chain + ... -

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Basic information

Entry
Database: PDB / ID: 1w7j
TitleCrystal Structure Of Myosin V Motor With Essential Light Chain + ADP-BeFx - Near Rigor
Components
  • MYOSIN LIGHT CHAIN 1
  • MYOSIN VA
KeywordsMOTOR PROTEIN / UNCONVENTIONAL MYOSIN / MYOSIN V / CHICKEN / MOLECULAR MOTOR / ATPASE / ELC / IQ MOTIF / MUSCLE PROTEIN / ATP-BINDING / ACTIN- BINDING / CALMODULIN-BINDING / MYOSIN / PHOSPHORYLATION
Function / homology
Function and homology information


minus-end directed microfilament motor activity / unconventional myosin complex / insulin-responsive compartment / muscle myosin complex / muscle filament sliding / myosin complex / myosin II complex / structural constituent of muscle / microfilament motor activity / filamentous actin ...minus-end directed microfilament motor activity / unconventional myosin complex / insulin-responsive compartment / muscle myosin complex / muscle filament sliding / myosin complex / myosin II complex / structural constituent of muscle / microfilament motor activity / filamentous actin / cytoskeletal motor activity / Smooth Muscle Contraction / skeletal muscle tissue development / vesicle-mediated transport / muscle contraction / actin filament organization / protein localization to plasma membrane / cellular response to insulin stimulus / actin filament binding / actin cytoskeleton / calmodulin binding / Golgi membrane / calcium ion binding / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / 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, 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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Myosin light chain 6B / Unconventional myosin-Va
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCoureux, P.-D. / Sweeney, H.L. / Houdusse, A.
CitationJournal: Embo J. / Year: 2004
Title: Three Myosin V Structures Delineate Essential Features of Chemo-Mechanical Transduction
Authors: Coureux, P.-D. / Sweeney, H.L. / Houdusse, A.
History
DepositionSep 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOSIN VA
B: MYOSIN LIGHT CHAIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2155
Polymers108,6972
Non-polymers5183
Water9,458525
1
A: MYOSIN VA
B: MYOSIN LIGHT CHAIN 1
hetero molecules

A: MYOSIN VA
B: MYOSIN LIGHT CHAIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,43010
Polymers217,3954
Non-polymers1,0356
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)169.684, 95.988, 84.306
Angle α, β, γ (deg.)90.00, 96.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MYOSIN VA / MYOSIN 5A / DILUTE MYOSIN HEAVY CHAIN / NON-MUSCLE / MYOSIN HEAVY CHAIN P190 / MYOSIN-V / MYOSIN


Mass: 91607.172 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-792
Source method: isolated from a genetically manipulated source
Details: ADP-BEFX / Source: (gene. exp.) GALLUS GALLUS (chicken) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q02440
#2: Protein MYOSIN LIGHT CHAIN 1 / LIGHT CHAIN 1 / SLOW-TWITCH MUSCLE A ISOFORM / MLC1SA / ALKALI


Mass: 17090.277 Da / Num. of mol.: 1 / Fragment: RESIDUES 59-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P14649

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Non-polymers , 4 types, 528 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 3.3 Å3/Da / Density % sol: 61.9 %
Crystal growpH: 6.3
Details: 12% PEG 8000, 50 MM MES PH 6.3, 2 MM DTT AND 2 MM NAN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→84.51 Å / Num. obs: 86066 / % possible obs: 99.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OE9

1oe9


Resolution: 2→20 Å / SU B: 2.948 / SU ML: 0.084 / ESU R: 0.144 / ESU R Free: 0.135
RfactorNum. reflection% reflection
Rfree0.224 4530 5 %
Rwork0.194 --
obs0.196 85999 99.83 %
Displacement parametersBiso mean: 27.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.47 Å2
2---0.19 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6872 0 32 525 7429

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