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- PDB-3i5g: Crystal structure of rigor-like squid myosin S1 -

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Basic information

Entry
Database: PDB / ID: 3i5g
TitleCrystal structure of rigor-like squid 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 / RIGOR-LIKE / SQUID / MUSCLE MYOSIN
Function / homology
Function and homology information


myosin filament organization / myofibril assembly / A band / muscle myosin complex / myosin filament / locomotion / myosin complex / myosin II complex / structural constituent of muscle / microfilament motor activity ...myosin filament organization / myofibril assembly / A band / muscle myosin complex / myosin filament / locomotion / myosin complex / myosin II complex / structural constituent of muscle / microfilament motor activity / muscle contraction / actin filament binding / calcium ion binding / ATP binding / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #1590 / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / IQ calmodulin-binding motif / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal ...Alpha-Beta Plaits - #1590 / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / IQ calmodulin-binding motif / Myosin N-terminal SH3-like domain / 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. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / EF-hand / : / Recoverin; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, 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 / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / 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: 2.6 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 1.0Jul 28, 2009Provider: repository / Type: Initial release
SupersessionFeb 9, 2010ID: 2OVK
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 / 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 / _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)131,7405
Polymers131,5983
Non-polymers1422
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-55 kcal/mol
Surface area52890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.138, 101.751, 80.651
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABC

#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


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

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Non-polymers , 3 types, 81 molecules

#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 8% PEG 5K MME, 150MM NACL, 100MM HEPES (PH 7.6), 5% ETHYLENE GLYCOL, 5MM MGAC2, 2MM CAAC2, 2MM NAN3, 2MM BETA-MERCAPTOETHANOL, 50MM NA MALONATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDate: Aug 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→46.73 Å / Num. all: 43064 / Num. obs: 42948 / % possible obs: 94.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1S5G

1s5g


Resolution: 2.6→46.73 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2971 4327 -
Rwork0.2518 --
all-46511 -
obs-42948 92.3 %
Refinement stepCycle: LAST / Resolution: 2.6→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8898 0 8 79 8985
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00841
X-RAY DIFFRACTIONc_angle_deg1.53771

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