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- PDB-2fxo: Structure of the human beta-myosin S2 fragment -

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Basic information

Entry
Database: PDB / ID: 2fxo
TitleStructure of the human beta-myosin S2 fragment
ComponentsMyosin heavy chain, cardiac muscle beta isoformMyosin
KeywordsCONTRACTILE PROTEIN / COILED COIL (DIMERIC / PARALLEL) / FAMILIAL HYPERTROPHIC CARDIOMYOPATHY / FHC-ASSOCIATED MUTANT E924K / THICK FILAMENT
Function / homology
Function and homology information


regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / myosin II complex / adult heart development / cardiac muscle hypertrophy in response to stress ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / myosin II complex / adult heart development / cardiac muscle hypertrophy in response to stress / myosin complex / sarcomere organization / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myofibril / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / stress fiber / cardiac muscle contraction / regulation of heart rate / sarcomere / muscle contraction / Z disc / actin filament binding / calmodulin binding / ATP binding / cytoplasm
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 / 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 ...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 / 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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD WITH SEMI-BRUTE- FORCE MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBlankenfeldt, W. / Thoma, N.H. / Wray, J.S. / Gautel, M. / Schlichting, I.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Mutations in Beta-Myosin S2 that Cause Familial Hypertrophic Cardiomyopathy (Fhc) Abolish the Interaction with the Regulatory Domain of Myosin-Binding Protein-C
Authors: Gruen, M. / Gautel, M.
#2: 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.
History
DepositionFeb 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.4Nov 10, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin heavy chain, cardiac muscle beta isoform
B: Myosin heavy chain, cardiac muscle beta isoform
C: Myosin heavy chain, cardiac muscle beta isoform
D: Myosin heavy chain, cardiac muscle beta isoform


Theoretical massNumber of molelcules
Total (without water)60,4254
Polymers60,4254
Non-polymers00
Water0
1
A: Myosin heavy chain, cardiac muscle beta isoform
B: Myosin heavy chain, cardiac muscle beta isoform


Theoretical massNumber of molelcules
Total (without water)30,2122
Polymers30,2122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-72 kcal/mol
Surface area18880 Å2
MethodPISA
2
C: Myosin heavy chain, cardiac muscle beta isoform
D: Myosin heavy chain, cardiac muscle beta isoform


Theoretical massNumber of molelcules
Total (without water)30,2122
Polymers30,2122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-72 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.157, 41.867, 97.795
Angle α, β, γ (deg.)91.11, 92.73, 107.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Myosin heavy chain, cardiac muscle beta isoform / Myosin / BETA-MYOSIN / MyHC-beta


Mass: 15106.145 Da / Num. of mol.: 4 / Fragment: DELTA-S2 FRAGMENT (838-963) / Mutation: E924K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: HEART MUSCLE / Gene: HSBMHC / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12883

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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: 52.3 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, SODIUM ACETATE, TRIS-HCL, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 16, 2001
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 20190 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 61 Å2 / Rsym value: 0.08 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.388 / % possible all: 96.6

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
SHELXDphasing
MOLEMAN2model building
REFMACrefinement
MOLEMAN2phasing
RefinementMethod to determine structure: SAD WITH SEMI-BRUTE- FORCE MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XNM

1xnm
PDB Unreleased entry


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 20.647 / SU ML: 0.458 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.891 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions. Target sigma values for restrained B-factor refinement have been relaxed to 10 A*A to reflect the special shape of the molecule. Atoms that ...Details: Hydrogens have been added in the riding positions. Target sigma values for restrained B-factor refinement have been relaxed to 10 A*A to reflect the special shape of the molecule. Atoms that could not be located have been assigned a temperature factor of 500 A*A and occupancy value of 0 for better discernability.
RfactorNum. reflection% reflectionSelection details
Rfree0.349 1040 5.1 %RANDOM
Rwork0.273 ---
obs0.277 19157 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å21.34 Å2-5.88 Å2
2--0.74 Å2-0.69 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 0 0 0 4145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214151
X-RAY DIFFRACTIONr_bond_other_d00.023874
X-RAY DIFFRACTIONr_angle_refined_deg1.5262.0195508
X-RAY DIFFRACTIONr_angle_other_deg3.6539178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045504
X-RAY DIFFRACTIONr_chiral_restr0.0710.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024472
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02648
X-RAY DIFFRACTIONr_nbd_refined0.2330.2914
X-RAY DIFFRACTIONr_nbd_other0.2590.23836
X-RAY DIFFRACTIONr_nbtor_other0.1040.22490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.27
X-RAY DIFFRACTIONr_mcbond_it6.269102539
X-RAY DIFFRACTIONr_mcangle_it8.38104054
X-RAY DIFFRACTIONr_scbond_it6.774101612
X-RAY DIFFRACTIONr_scangle_it9.684101454
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.511 73
Rwork0.378 1396
Refinement TLS params.

T33: 0.1116 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.03651.22563.75890.28890.83882.36260.0751-0.0033-0.1861-0.0104-0.0372-0.03090.0352-0.0052-0.03790.1368-0.00540.10980.01960.017-4.811-1.159-2.575
25.90351.38514.25850.32861.00372.9717-0.02650.21580.21850.0059-0.0620.0235-0.00430.10170.08850.1523-0.00380.07840.06940.0438-43.72310.025-25.626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-3 - 9631 - 129
2X-RAY DIFFRACTION1BB-1 - 9613 - 127
3X-RAY DIFFRACTION2CC-2 - 9622 - 128
4X-RAY DIFFRACTION2DD-1 - 9633 - 129

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