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

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Basic information

Entry
Database: PDB / ID: 3bat
TitleCrystal structure of the N-terminal region of the scallop myosin rod, monoclinic (P21) form
ComponentsMyosin heavy chain, striated muscle/General control protein GCN4Myosin
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


protein localization to nuclear periphery / 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 / myosin filament / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / myosin complex / myofibril ...protein localization to nuclear periphery / 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 / myosin filament / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / myosin complex / myofibril / TFIID-class transcription factor complex binding / cytoskeletal motor activity / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / actin filament binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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
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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: Myosin heavy chain, striated muscle/General control protein GCN4
B: Myosin heavy chain, striated muscle/General control protein GCN4
C: Myosin heavy chain, striated muscle/General control protein GCN4
D: Myosin heavy chain, striated muscle/General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)42,2374
Polymers42,2374
Non-polymers00
Water1,78399
1
A: Myosin heavy chain, striated muscle/General control protein GCN4
B: Myosin heavy chain, striated muscle/General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)21,1182
Polymers21,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
MethodPISA
2
C: Myosin heavy chain, striated muscle/General control protein GCN4
D: Myosin heavy chain, striated muscle/General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)21,1182
Polymers21,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.782, 40.217, 77.404
Angle α, β, γ (deg.)90.000, 111.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10559.174 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2 microliters of protein solution (4 mg/ml protein in 30 mM MOPS buffer pH 7.2, 40 mM NaCl, 2 mM NaN3) mixed with 2 microliters of (25% PEG 3350, 50 mM NH4I) and equilibrated against 1 ml of ...Details: 2 microliters of protein solution (4 mg/ml protein in 30 mM MOPS buffer pH 7.2, 40 mM NaCl, 2 mM NaN3) mixed with 2 microliters of (25% PEG 3350, 50 mM NH4I) and equilibrated against 1 ml of (17.5% PEG 3350, 35 mM NH4I, 28 mM NaCl, 2 mM NaN3, 20 mM MOPS pH 6.2). Harvested crystals were cryoprotected in 25.5% PEG 3350 and 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
Details: channel-cut Si(111) crystal monochromator followed by a doubly focusing toroidal mirror
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 27340 / % possible obs: 98.5 % / Rmerge(I) obs: 0.052 / Χ2: 1.085 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.020.2926320.89795.5
2.02-2.10.24127150.98798.7
2.1-2.20.17627580.98399.9
2.2-2.310.14227321.07100
2.31-2.460.10327361.062100
2.46-2.650.07727901.048100
2.65-2.910.05827551.096100
2.91-3.330.04727841.33499.9
3.33-4.20.03627311.21298.4
4.2-300.03727071.10993.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NKN

1nkn


Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1704 10 %Random
Rwork0.253 ---
obs0.253 16835 98.4 %-
Solvent computationBsol: 38.499 Å2
Displacement parametersBiso mean: 53.827 Å2
Baniso -1Baniso -2Baniso -3
1-9.384 Å20 Å2-5.532 Å2
2---23.634 Å20 Å2
3---14.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 0 99 2793
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0071.5
X-RAY DIFFRACTIONc_angle_d0.8642
X-RAY DIFFRACTIONc_dihedral_angle_d17.42
X-RAY DIFFRACTIONc_improper_angle_d1.142.5
LS refinement shellResolution: 2.3→2.44 Å
RfactorNum. reflection% reflection
Rfree0.315 302 -
Rwork0.262 --
obs-2819 99.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION4CNS_TOPPAR:water.param

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