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- PDB-4db1: Cardiac human myosin S1dC, beta isoform complexed with Mn-AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4db1
TitleCardiac human myosin S1dC, beta isoform complexed with Mn-AMPPNP
ComponentsMyosin-7
KeywordsCONTRACTILE PROTEIN / S1DC / myosin / cardiac / beta isoform / MYH7 / MYHCB / MyHC-beta
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 / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / myosin II complex ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / myosin II complex / myosin complex / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / microfilament motor activity / myofibril / skeletal muscle contraction / cardiac muscle contraction / stress fiber / striated muscle contraction / ATP metabolic process / muscle contraction / regulation of heart rate / sarcomere / Z disc / actin filament binding / calmodulin binding / ATP binding / cytoplasm
Similarity search - Function
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 ...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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Myosin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKlenchin, V.A. / Deacon, J.C. / Combs, A.C. / Leinwand, L.A. / Rayment, I.
CitationJournal: To be Published
Title: Cardiac human myosin S1dC, beta isoform complexed with Mn-AMPPNP
Authors: Klenchin, V.A. / Deacon, J.C. / Combs, A.C. / Leinwand, L.A. / Rayment, I.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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-7
B: Myosin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,3266
Polymers178,2042
Non-polymers1,1224
Water3,639202
1
A: Myosin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6633
Polymers89,1021
Non-polymers5612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6633
Polymers89,1021
Non-polymers5612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-32 kcal/mol
Surface area59560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.206, 94.310, 110.894
Angle α, β, γ (deg.)90.000, 112.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myosin-7 / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac ...Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 89101.852 Da / Num. of mol.: 2 / Fragment: UNP residues 2-783
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYH7, MYHCB / Production host: Mus musculus (house mouse) / Strain (production host): C2C12 cells / References: UniProt: P12883
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: precipitant: 7.5% PEG 8000, 0.05M MES, 0.05M acetate, 0.25M sodium chloride, 0.01M manganese chloride, 0.1% sodium cholate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 58495 / Num. obs: 58495 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Χ2: 1.049 / Net I/σ(I): 9.24
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.644.92.19729191.0821100
2.64-2.6952.429211.0661100
2.69-2.7452.59128701.0391100
2.74-2.852.90729281.0541100
2.8-2.8653.14129071.0321100
2.86-2.9353.78928821.0471100
2.93-354.15429220.9961100
3-3.0854.66429131.0681100
3.08-3.1755.94829141.0291100
3.17-3.2756.6129041.0171100
3.27-3.3958.1829121.0451100
3.39-3.5359.76329251.0121100
3.53-3.69511.14329461.0471100
3.69-3.88512.96929151.0511100
3.88-4.12514.65329131.0171100
4.12-4.44516.83329461.11100
4.44-4.884.917.85329191.112199.9
4.88-5.584.916.2529711.1861100
5.58-7.014.715.32429371.0941100
7.01-254.823.45330310.8911100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREP10.2.31phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MYS

2mys


Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.2364 / WRfactor Rwork: 0.1924 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8105 / SU B: 20.348 / SU ML: 0.219 / SU R Cruickshank DPI: 0.5907 / SU Rfree: 0.3086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.591 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 2959 5.1 %RANDOM
Rwork0.21 ---
all0.2124 55769 --
obs0.2124 55440 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 148.95 Å2 / Biso mean: 40.421 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.22 Å2
2--1.39 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11052 0 64 202 11318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211381
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.95715420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18951427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26524.549510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.999151858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.51547
X-RAY DIFFRACTIONr_chiral_restr0.0790.21703
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218623
X-RAY DIFFRACTIONr_mcbond_it1.40137126
X-RAY DIFFRACTIONr_mcangle_it2.7463011370
X-RAY DIFFRACTIONr_scbond_it3.44854255
X-RAY DIFFRACTIONr_scangle_it5.616504048
LS refinement shellResolution: 2.6→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 199 -
Rwork0.279 3804 -
all-4003 -
obs-4003 93.73 %
Refinement TLS params.

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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8481-0.0297-0.35260.4218-0.07081.9180.02450.0047-0.08860.00380.01630.10060.2112-0.1227-0.04080.2262-0.0290.02540.17840.01020.27760.04343.44475.818
21.5988-0.02340.67730.79830.132.03540.00110.15290.026-0.1671-0.00480.1704-0.1931-0.63920.00370.2685-0.00260.05450.420.06470.3642-15.63251.70269.365
30.8211-0.0875-0.22150.66690.26821.30720.0164-0.1129-0.04260.0540.0366-0.12330.09310.1568-0.0530.16250.00950.01080.19390.00810.246240.63744.23257.182
42.12270.29310.51071.1118-0.11150.36020.0329-0.22120.16710.334-0.0934-0.2307-0.10170.26690.06050.3185-0.03690.00810.5124-0.02480.349555.8553.23962.227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 496
2X-RAY DIFFRACTION2A497 - 777
3X-RAY DIFFRACTION3B1 - 495
4X-RAY DIFFRACTION4B496 - 775

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