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- PDB-3bas: Crystal structure of the N-terminal region of the scallop myosin ... -

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Basic information

Entry
Database: PDB / ID: 3bas
TitleCrystal structure of the N-terminal region of the scallop myosin rod, monoclinic (C2) form
ComponentsMyosin heavy chain, striated muscle/General control protein GCN4 chimera
KeywordsCONTRACTILE PROTEIN / Alpha-helical coiled coil / disorder / salt links / Actin-binding / ATP-binding / Calmodulin-binding / Cytoplasm / Motor protein / Muscle protein / Myosin / Nucleotide-binding / Thick filament
Function / homology
Function and homology information


mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / myosin filament ...mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / myosin filament / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / myosin II complex / microfilament motor activity / myofibril / sarcomere organization / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / muscle contraction / RNA polymerase II transcription regulator complex / : / actin filament binding / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Basic region leucine zipper / Myosin S1 fragment, N-terminal / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Basic region leucine zipper / Myosin S1 fragment, N-terminal / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / General control transcription factor GCN4 / Myosin heavy chain, striated muscle
Similarity search - Component
Biological speciesArgopecten irradians (bay scallop)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBrown, J.H. / Cohen, C.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: An unstable head-rod junction may promote folding into the compact off-state conformation of regulated myosins.
Authors: Brown, J.H. / Yang, Y. / Reshetnikova, L. / Gourinath, S. / Suveges, D. / Kardos, J. / Hobor, F. / Reutzel, R. / Nyitray, L. / Cohen, C.
#1: Journal: Nature / Year: 2003
Title: Visualization of an unstable coiled coil from the scallop myosin rod.
Authors: Li, Y. / Brown, J.H. / Reshetnikova, L. / Blazsek, A. / Farkas, L. / Nyitray, L. / Cohen, C.
#2: Journal: Proc Natl Acad Sci U S A / Year: 2006
Title: Crystal structures of human cardiac beta-myosin II S2-Delta provide insight into the functional role of the S2 subfragment.
Authors: Wulf Blankenfeldt / Nicolas H Thomä / John S Wray / Mathias Gautel / Ilme Schlichting /
Abstract: Myosin II is the major component of the muscle thick filament. It consists of two N-terminal S1 subfragments ("heads") connected to a long dimeric coiled-coil rod. The rod is in itself twofold ...Myosin II is the major component of the muscle thick filament. It consists of two N-terminal S1 subfragments ("heads") connected to a long dimeric coiled-coil rod. The rod is in itself twofold symmetric, but in the filament, the two heads point away from the filament surface and are therefore not equivalent. This breaking of symmetry requires the initial section of the rod, subfragment 2 (S2), to be relatively flexible. S2 is an important functional element, involved in various mechanisms by which the activity of smooth and striated muscle is regulated. We have determined crystal structures of the 126 N-terminal residues of S2 from human cardiac beta-myosin II (S2-Delta), of both WT and the disease-associated E924K mutant. S2-Delta is a straight parallel dimeric coiled coil, but the N terminus of one chain is disordered in WT-S2-Delta due to crystal contacts, indicative of unstable local structure. Bulky noncanonical side chains pack into a/d positions of S2-Delta's N terminus, leading to defined local asymmetry and axial stagger, which could induce nonequivalence of the S1 subfragments. Additionally, S2 possesses a conserved charge distribution with three prominent rings of negative potential within S2-Delta, the first of which may provide a binding interface for the "blocked head" of smooth muscle myosin in the OFF state. The observation that many disease-associated mutations affect the second negatively charged ring further suggests that charge interactions play an important role in regulation of cardiac muscle activity through myosin-binding protein C.
History
DepositionNov 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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
Remark 999 SEQUENCE THE PEPTIDE CONTAINS A GSHM TETRAPEPTIDE, FOLLOWED BY THE N-TERMINAL 51 RESIDUES OF THE ... SEQUENCE THE PEPTIDE CONTAINS A GSHM TETRAPEPTIDE, FOLLOWED BY THE N-TERMINAL 51 RESIDUES OF THE BAY SCALLOP MYOSIN ROD (RESIDUES 835-885 OF THE BAY SCALLOP MYOSIN HEAVY CHAIN, GI:5612), FOLLOWED BY A GS LINKER, FOLLOWED BY THE LEUCINE ZIPPER OF THE YEAST GCN4 TRANSCRIPTION FACTOR (RESIDUES 250-281 OF GI:171584 DENOTED AS RESIDUES 888-919 IN THE SUBMITTED COORDINATES).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin heavy chain, striated muscle/General control protein GCN4 chimera
B: Myosin heavy chain, striated muscle/General control protein GCN4 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2453
Polymers21,1182
Non-polymers1271
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.335, 44.912, 39.878
Angle α, β, γ (deg.)90.000, 95.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1-

IOD

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Components

#1: Protein Myosin heavy chain, striated muscle/General control protein GCN4 chimera / -/Amino acid biosynthesis regulatory protein


Mass: 10559.174 Da / Num. of mol.: 2
Fragment: Bay Scallop Myosin (Residues 835-885)/Yeast GCN4 Transcription Factor (Residues 250-281)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argopecten irradians (bay scallop), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Genus: Argopecten, Saccharomyces / Species: , / Strain: , / Tissue: Adductor muscle/- / Gene: -/GCN4, AAS3, ARG9, YEL009C / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P24733, UniProt: P03069
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.5 microliter of protein solution (4 mg/ml protein in 30 mM MOPS buffer pH 7.2, 40 mM NaCl, 2 mM NaN3) mixed with 3 microliters of (16.6% PEG 3350, 4.6% MPD, 13 mM NaCl, 2 mM NaN3, 10 mM ...Details: 1.5 microliter of protein solution (4 mg/ml protein in 30 mM MOPS buffer pH 7.2, 40 mM NaCl, 2 mM NaN3) mixed with 3 microliters of (16.6% PEG 3350, 4.6% MPD, 13 mM NaCl, 2 mM NaN3, 10 mM MOPS pH 7.2) and equilibrated against (15% PEG 3350, 4.2% MPD, 18 mM MOPS, 24 mM NaCl), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
Details: Bent triangular asymmetric cut Si(111) monochromator for horizontal focusing, and Rh-coated Si mirror for vertical focusing.
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 8283 / % possible obs: 84.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.082 / Χ2: 1.544 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.382.70.2455191.13453.6
2.38-2.482.80.2455891.1760.9
2.48-2.5930.1736441.19167.7
2.59-2.733.10.1947601.1777.6
2.73-2.93.20.1788581.26189.8
2.9-3.123.50.1589591.29599.2
3.12-3.443.70.119801.48399.9
3.44-3.933.70.079851.95199.9
3.93-4.953.60.0489911.74399.9
4.95-503.50.0449982.15598.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NKN

1nkn


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 878 8.9 %Random
Rwork0.246 ---
obs0.246 8272 84.2 %-
Solvent computationBsol: 34.3 Å2
Displacement parametersBiso mean: 46.066 Å2
Baniso -1Baniso -2Baniso -3
1-14.316 Å20 Å2-1.848 Å2
2---25.872 Å20 Å2
3---11.557 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 1 59 1445
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_deg0.882
X-RAY DIFFRACTIONc_dihedral_angle_d2
X-RAY DIFFRACTIONc_improper_angle_d2.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.3-2.380.4661460.3102X-RAY DIFFRACTION46747.6
2.38-2.480.285710.2586X-RAY DIFFRACTION58661
2.48-2.590.3135670.2484X-RAY DIFFRACTION64867.4
3.93-4.930.23451150.2023X-RAY DIFFRACTION99199.8
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param

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