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- PDB-2ec6: Placopecten Striated Muscle Myosin II -

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Basic information

Entry
Database: PDB / ID: 2ec6
TitlePlacopecten Striated Muscle Myosin II
Components
  • Myosin essential light chain
  • Myosin heavy chain
  • Myosin regulatory light chain
KeywordsCONTRACTILE PROTEIN / muscle / rigor-like / actin binding
Function / homology
Function and homology information


myosin filament organization / myofibril assembly / muscle myosin complex / myosin filament / locomotion / myosin complex / myosin II complex / structural constituent of muscle / microfilament motor activity / myofibril ...myosin filament organization / myofibril assembly / muscle myosin complex / myosin filament / locomotion / myosin complex / myosin II complex / structural constituent of muscle / microfilament motor activity / myofibril / muscle contraction / actin filament binding / calcium ion binding / ATP binding
Similarity search - Function
Alpha-Beta Plaits - #1590 / Myosin VI head, motor domain, U50 subdomain / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal ...Alpha-Beta Plaits - #1590 / Myosin VI head, motor domain, U50 subdomain / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / 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 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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
Sulfhydryl light chain / Myosin regulatory light chain / Myosin heavy chain
Similarity search - Component
Biological speciesPlacopecten magellanicus (sea scallop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsYang, Y. / Brown, J. / Samudrala, G. / Reutzel, R. / Szent-Gyorgyi, A.
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
DepositionFeb 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 8, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin heavy chain
B: Myosin regulatory light chain
C: Myosin essential light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8484
Polymers128,8083
Non-polymers401
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-74 kcal/mol
Surface area57300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.273, 50.366, 156.774
Angle α, β, γ (deg.)90.00, 101.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myosin heavy chain


Mass: 95832.875 Da / Num. of mol.: 1 / Fragment: residues 1-838
Source method: isolated from a genetically manipulated source
Details: The source was obtained from the Marine Biological Laboratory (MBL)
Source: (gene. exp.) Placopecten magellanicus (sea scallop) / References: UniProt: Q26079
#2: Protein Myosin regulatory light chain / R-LC


Mass: 15354.388 Da / Num. of mol.: 1 / Fragment: residues 23-156 / Mutation: Y84F, T151A
Source method: isolated from a genetically manipulated source
Details: The source was obtained from the Marine Biological Laboratory (MBL)
Source: (gene. exp.) Placopecten magellanicus (sea scallop) / References: UniProt: Q26069
#3: Protein Myosin essential light chain / E-LC / Sulfhydryl light chain / SHLC


Mass: 17620.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The source was obtained from the Marine Biological Laboratory (MBL)
Source: (gene. exp.) Placopecten magellanicus (sea scallop) / References: UniProt: Q26066
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 90mM CaCl2, 8.5% PEG 6K, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.25→20 Å / Num. all: 21051 / Num. obs: 18825 / % possible obs: 94.7 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.4
Reflection shellResolution: 3.25→20 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2 / Num. unique all: 1852 / Rsym value: 0.458 / % possible all: 87.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→20 Å / σ(F): 1.5 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1724 -8.2
Rwork0.279 ---
obs0.279 18825 89.4 %-
all-21051 --
Displacement parametersBiso mean: 39.7 Å2
Refinement stepCycle: LAST / Resolution: 3.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8545 0 1 31 8577

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