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- PDB-3i5f: Crystal structure of squid MG.ADP myosin S1 -

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Basic information

Entry
Database: PDB / ID: 3i5f
TitleCrystal structure of squid MG.ADP myosin S1
Components
  • Myosin catalytic light chain LC-1, mantle muscle
  • Myosin heavy chain isoform A
  • Myosin regulatory light chain LC-2, mantle muscle
KeywordsCONTRACTILE PROTEIN / SQUID / POST-RIGOR STATE / MG.ADP / MYOSIN II S1 / ATP-binding / Actin-binding / Coiled coil / Motor protein / Muscle protein / Myosin / Nucleotide-binding / Thick filament / Calcium
Function / homology
Function and homology information


myosin complex / myofibril / cytoskeletal motor activity / actin filament binding / calcium ion binding / ATP binding
Similarity search - Function
EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / IQ calmodulin-binding motif / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / IQ calmodulin-binding motif / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / 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 / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Myosin heavy chain isoform A / Myosin catalytic light chain LC-1, mantle muscle / Myosin regulatory light chain LC-2, mantle muscle
Similarity search - Component
Biological speciesLoligo pealei (longfin inshore squid)
Todarodes pacificus (Japanese flying squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYang, Y. / Gourinath, S. / Kovacs, M. / Nyitray, L. / Reutzel, R. / Himmel, D.M. / O'Neall-Hennessey, E. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Brown, J.H. / Cohen, C.
CitationJournal: Structure / Year: 2007
Title: Rigor-like structures from muscle myosins reveal key mechanical elements in the transduction pathways of this allosteric motor.
Authors: Yang, Y. / Gourinath, S. / Kovacs, M. / Nyitray, L. / Reutzel, R. / Himmel, D.M. / O'Neall-Hennessey, E. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Brown, J.H. / Cohen, C.
History
DepositionJul 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
SupersessionFeb 9, 2010ID: 2OY6
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin heavy chain isoform A
B: Myosin regulatory light chain LC-2, mantle muscle
C: Myosin catalytic light chain LC-1, mantle muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,0505
Polymers131,5983
Non-polymers4522
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-81 kcal/mol
Surface area54700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.415, 101.687, 94.751
Angle α, β, γ (deg.)90.00, 119.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Myosin heavy chain isoform A


Mass: 95939.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Loligo pealei (longfin inshore squid) / References: UniProt: O44934
#2: Protein Myosin regulatory light chain LC-2, mantle muscle / RLC


Mass: 17577.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)
References: UniProt: P08052
#3: Protein Myosin catalytic light chain LC-1, mantle muscle


Mass: 18081.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)
References: UniProt: P05945
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDate: Nov 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→43.23 Å / Num. obs: 25326 / % possible obs: 88.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 10.2
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.1 / % possible all: 41.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OVK

2ovk
PDB Unreleased entry


Resolution: 3.1→43.23 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3171 2489 -
Rwork0.2438 --
all-28192 -
obs-25254 89.6 %
Refinement stepCycle: LAST / Resolution: 3.1→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8943 0 28 0 8971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014495
X-RAY DIFFRACTIONc_angle_deg2.44299

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