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- PDB-6pf2: Crystal Structure of Amino Acids 1220-1276 of Human Beta Cardiac ... -

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Basic information

Entry
Database: PDB / ID: 6pf2
TitleCrystal Structure of Amino Acids 1220-1276 of Human Beta Cardiac Myosin Fused to Gp7 and Eb1
ComponentsMyosin, heavy polypeptide 7, cardiac muscle, beta variant
KeywordsMOTOR PROTEIN / Myosin Rod / Myosin / Coiled-Coil / Gp7 / Eb1
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
EB1-like C-terminal motif / 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 ...EB1-like C-terminal motif / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsAndreas, M.P. / Korkmaz, E.N. / Kirsch, C.J. / Hargreaves, M. / Kieffer, D.J. / Ajay, G. / Cui, Q. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R21 HL111237 United States
CitationJournal: To Be Published
Title: A Complete Model of the Cardiac Myosin Rod
Authors: Andreas, M.P. / Korkmaz, E.N. / Kirsch, C.J. / Hargreaves, M. / Kieffer, D.J. / Ajay, G. / Cui, Q. / Rayment, I.
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin, heavy polypeptide 7, cardiac muscle, beta variant
B: Myosin, heavy polypeptide 7, cardiac muscle, beta variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9635
Polymers36,7772
Non-polymers1863
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-74 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.136, 44.607, 262.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myosin, heavy polypeptide 7, cardiac muscle, beta variant /


Mass: 18388.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Human Beta cardiac myosin rod amino acids 1220-1276 with an amino-terminal fusion to Gp7 (amino acids 2-48, residue numbers 5-51) and carboxy-terminal fusion to Eb1 (amino acids 207-257, ...Details: Human Beta cardiac myosin rod amino acids 1220-1276 with an amino-terminal fusion to Gp7 (amino acids 2-48, residue numbers 5-51) and carboxy-terminal fusion to Eb1 (amino acids 207-257, residue numbers 2109-2159 )
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P12883*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystals grew spontaneously at room temperature by mixing 1:1 ratio of 16 mg/ml protein in 100 mM NaCl, 10 mM HEPES pH 7.6, 0.1 mM TCEP with well solution containing 2.4 M ammonium phosphate ...Details: Crystals grew spontaneously at room temperature by mixing 1:1 ratio of 16 mg/ml protein in 100 mM NaCl, 10 mM HEPES pH 7.6, 0.1 mM TCEP with well solution containing 2.4 M ammonium phosphate pH 8.0, 100 mM HEPPS pH 8.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 22944 / % possible obs: 94 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.03 / Rrim(I) all: 0.1 / Χ2: 0.955 / Net I/σ(I): 6.9 / Num. measured all: 232416
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.17-2.215.60.5198090.8890.2010.5590.91868.8
2.21-2.256.20.4648720.9150.170.4970.95773.3
2.25-2.296.80.4329790.9410.1510.460.99683.5
2.29-2.347.30.38310350.9590.1320.4070.99384
2.34-2.398.20.37310600.960.1240.3951.03292.2
2.39-2.448.60.37211420.9480.1230.3930.98494.4
2.44-2.5190.33811570.9640.1120.3570.98595.1
2.51-2.579.50.29411540.980.0950.311.04199.5
2.57-2.6510.80.2712260.9780.0830.2831.00998.2
2.65-2.7311.70.24411520.9840.0720.2551.02299.4
2.73-2.8311.40.19712080.9880.0580.2051.07598.8
2.83-2.9511.20.16412030.9910.0490.1721.05299.4
2.95-3.0810.90.14711970.9910.0460.1541.07498
3.08-3.2411.10.1311930.9940.040.1361.07597.9
3.24-3.4411.70.10712050.9960.0320.1121.04997.9
3.44-3.7111.60.09212220.9950.0270.0961.0399.5
3.71-4.08110.07812190.9960.0240.0820.9598.7
4.08-4.6712.30.07112440.9940.0210.0740.814100
4.67-5.8912.20.06412730.9980.0210.0680.63599.8
5.89-5011.10.049139410.0160.0510.60999.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NOH

1noh


Resolution: 2.17→43.976 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.5
RfactorNum. reflection% reflection
Rfree0.2508 1078 5 %
Rwork0.2037 --
obs0.206 21561 89.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.51 Å2 / Biso mean: 42.0242 Å2 / Biso min: 4.99 Å2
Refinement stepCycle: final / Resolution: 2.17→43.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2507 0 12 195 2714
Biso mean--46.04 30.65 -
Num. residues----307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.26880.3541850.24271627171259
2.2688-2.38840.3071120.24192102221475
2.3884-2.5380.31641280.23812455258387
2.538-2.73390.28441450.22722750289597
2.7339-3.0090.24651480.21592791293998
3.009-3.44420.2541480.20192835298398
3.4442-4.33880.20731520.15992864301699
4.3388-43.98490.23731600.21043059321999
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)
18.20621.3152-1.8744.30420.887.2686-0.1979-0.5139-0.36570.649-0.0456-0.5130.96080.66320.12410.52860.0473-0.06510.1644-0.05140.245-4.291611.7598102.3101
2-0.25540.0096-0.48610.19580.15723.4191-0.0232-0.06710.01140.05620.04470.02450.1902-0.28350.00070.1128-0.0036-0.00920.4848-0.00910.2324-8.75311.686922.3023
3-0.21320.12830.21660.0812-0.27362.38680.0146-0.03530.02090.12310.03760.0415-0.14040.5372-0.0420.25150.07570.04520.4289-0.00020.2221-9.784710.073544.4459
47.08820.75793.70676.88691.06135.03620.07320.5206-0.0182-0.56430.2155-0.5344-0.36970.8009-0.15260.2787-0.17670.07050.36990.02910.25140.046313.5653-38.4443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )A3 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 2159 )A25 - 2159
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 2133 )B4 - 2133
4X-RAY DIFFRACTION4chain 'B' and (resid 2134 through 2153 )B0

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