[English] 日本語
Yorodumi
- PDB-5cj1: Crystal structure of the coiled coil of MYH7 residues 1526 to 157... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cj1
TitleCrystal structure of the coiled coil of MYH7 residues 1526 to 1571 fused to Gp7
ComponentsGp7-MYH7-(1526-1571) chimera protein
KeywordsMOTOR PROTEIN / myosin / coiled coil / fusion
Function / homology
Function and homology information


viral scaffold / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / muscle filament sliding ...viral scaffold / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / muscle filament sliding / myosin complex / myosin II complex / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / virion assembly / myofibril / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / stress fiber / cardiac muscle contraction / muscle contraction / regulation of heart rate / sarcomere / Z disc / actin filament binding / calmodulin binding / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / 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. ...Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / 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
Myosin-7 / Capsid assembly scaffolding protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTaylor, K.C. / Korkmaz, E.N. / Andreas, M.P. / Ajay, G. / Heinz, N.T. / 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: Proteins / Year: 2016
Title: A composite approach towards a complete model of the myosin rod.
Authors: Korkmaz, E.N. / Taylor, K.C. / Andreas, M.P. / Ajay, G. / Heinze, N.T. / Cui, Q. / Rayment, I.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gp7-MYH7-(1526-1571) chimera protein
B: Gp7-MYH7-(1526-1571) chimera protein
C: Gp7-MYH7-(1526-1571) chimera protein
D: Gp7-MYH7-(1526-1571) chimera protein
E: Gp7-MYH7-(1526-1571) chimera protein
F: Gp7-MYH7-(1526-1571) chimera protein
G: Gp7-MYH7-(1526-1571) chimera protein
H: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)92,3828
Polymers92,3828
Non-polymers00
Water3,027168
1
A: Gp7-MYH7-(1526-1571) chimera protein
B: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)23,0962
Polymers23,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-43 kcal/mol
Surface area13690 Å2
MethodPISA
2
C: Gp7-MYH7-(1526-1571) chimera protein
D: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)23,0962
Polymers23,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-42 kcal/mol
Surface area13470 Å2
MethodPISA
3
E: Gp7-MYH7-(1526-1571) chimera protein
F: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)23,0962
Polymers23,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-43 kcal/mol
Surface area13400 Å2
MethodPISA
4
G: Gp7-MYH7-(1526-1571) chimera protein
H: Gp7-MYH7-(1526-1571) chimera protein


Theoretical massNumber of molelcules
Total (without water)23,0962
Polymers23,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-40 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.085, 64.466, 93.594
Angle α, β, γ (deg.)70.53, 77.51, 74.15
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Gp7-MYH7-(1526-1571) chimera protein / Gene product 7 / Gp7 / Head morphogenesis protein / Scaffold protein / Myosin heavy chain 7 / ...Gene product 7 / Gp7 / Head morphogenesis protein / Scaffold protein / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 11547.798 Da / Num. of mol.: 8
Fragment: UNP P13848 residues 2-52, UNP P12833 residues 1526-1571
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human)
Plasmid: pET31b / Gene: MYH7, MYHCB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13848, UniProt: P12883
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% (w/v) PEG 8000, 400 mM malonate pH 7.2, and 100 mM triethanolamine pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2014
Details: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 67161 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 30.26 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/av σ(I): 23.15 / Net I/σ(I): 15.57
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
PHENIXdev_1819refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NO4

1no4


Resolution: 2.1→48.679 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3282 4.89 %Random selection
Rwork0.2075 ---
obs0.2096 67072 97.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 0 168 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086415
X-RAY DIFFRACTIONf_angle_d0.8918597
X-RAY DIFFRACTIONf_dihedral_angle_d17.1792574
X-RAY DIFFRACTIONf_chiral_restr0.035942
X-RAY DIFFRACTIONf_plane_restr0.0041153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0969-2.12820.40541200.28572511X-RAY DIFFRACTION88
2.1282-2.16150.3031680.27232733X-RAY DIFFRACTION97
2.1615-2.19690.26481340.25582758X-RAY DIFFRACTION97
2.1969-2.23480.30461510.23542789X-RAY DIFFRACTION96
2.2348-2.27550.27861300.22762744X-RAY DIFFRACTION97
2.2755-2.31920.29351400.22652769X-RAY DIFFRACTION97
2.3192-2.36660.2871570.22352755X-RAY DIFFRACTION97
2.3666-2.4180.29621460.22312753X-RAY DIFFRACTION97
2.418-2.47430.28811510.22382798X-RAY DIFFRACTION97
2.4743-2.53610.30251350.22582802X-RAY DIFFRACTION98
2.5361-2.60470.30231340.22882782X-RAY DIFFRACTION98
2.6047-2.68130.29271440.24172822X-RAY DIFFRACTION98
2.6813-2.76790.28941510.24272762X-RAY DIFFRACTION98
2.7679-2.86680.28131280.26292806X-RAY DIFFRACTION98
2.8668-2.98160.3391410.25382785X-RAY DIFFRACTION98
2.9816-3.11720.29351610.25542809X-RAY DIFFRACTION98
3.1172-3.28160.26311370.24842814X-RAY DIFFRACTION98
3.2816-3.48710.26811450.21932818X-RAY DIFFRACTION98
3.4871-3.75620.21711610.19992798X-RAY DIFFRACTION98
3.7562-4.13410.23021410.17432790X-RAY DIFFRACTION98
4.1341-4.73180.171260.1532832X-RAY DIFFRACTION98
4.7318-5.95990.19411320.1572825X-RAY DIFFRACTION98
5.9599-48.69230.1711490.1442735X-RAY DIFFRACTION96
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)
15.2412-3.0708-0.46545.99580.91014.87250.0235-0.18170.65930.01820.0868-0.6559-0.3230.1215-0.09810.2691-0.03670.03460.1930.00990.2717-27.7314-5.157821.6882
27.7754-3.6014.49661.4426-2.12162.1454-0.1393-0.6618-0.23580.05640.28410.1061-0.019-0.2787-0.23890.3550.1093-0.02470.41380.01920.26047.119-30.68535.9379
38.00050.6081-1.20967.41740.09395.7410.3398-0.46260.3110.4388-0.0492-0.6334-0.29720.6819-0.24080.25170.0195-0.06980.33270.00860.2571-8.79283.8559-14.4107
42.48452.6901-4.09410.4902-1.29992.0203-0.0020.2115-0.1227-0.05210.0445-0.00310.0215-0.12430.06240.3421-0.03360.0450.48180.10650.4362-52.1805-11.0798-7.5786
58.2560.7723-0.78364.9112.21427.2060.5454-0.2026-0.0173-0.4439-0.37090.19020.4278-0.4522-0.12580.196-0.0515-0.00050.17570.02660.1652-33.6604-18.542520.4374
67.7821-4.03062.27591.6016-1.06490.3965-0.1624-0.08150.58120.06750.0075-0.2556-0.00760.02030.11980.28890.0542-0.04850.3143-0.0070.33778.5723-27.23535.5726
78.54430.72420.58196.8257-0.38735.28370.4167-1.2410.95310.6387-0.3306-0.45620.05950.3125-0.03870.3676-0.0451-0.09690.4993-0.1310.4142-22.403624.7519-5.3695
86.9291-4.66053.02552.2017-1.70190.92770.1590.56960.3149-0.005-0.282-0.19630.02670.20420.12970.39020.0879-0.11270.46410.08370.598-63.561836.5756-24.5192
97.3261-1.16592.93775.93033.67165.13940.14370.0278-0.0884-0.0179-0.62470.3453-0.3344-0.72410.36180.34040.05450.05760.3566-0.05120.2213-43.32826.443338.9863
108.63774.9682-2.56732.1744-1.28010.5613-0.13350.089-0.5825-0.04120.0053-0.2999-0.0063-0.02050.11310.3053-0.05040.05930.2697-0.00740.4365-1.453815.620823.4076
116.56720.7098-2.51143.0829-1.5326.82030.0891-0.0766-0.53170.80540.03920.24870.9017-0.333-0.06730.4681-0.04120.09050.19540.00880.3779-36.5441-6.352139.3138
127.55093.7194-4.5261.6142-2.25662.4468-0.18450.5910.1325-0.05690.30570.06840.0941-0.2631-0.14740.3453-0.09770.03970.3363-0.0360.2481-2.969519.700522.9086
136.4-2.6843-1.08468.8784-0.11833.75340.41370.4571-0.1579-0.8886-0.3619-0.31440.01410.1079-0.08570.35270.0415-0.0290.2517-0.02060.4616-23.497319.5042-18.988
147.3983-3.53953.38270.7594-1.16381.0277-0.5171-1.0305-0.20150.17830.4977-0.0449-0.1773-0.3590.15820.36130.0791-0.07550.47360.050.5278-63.747736.7993-21.9257
158.2441-0.3382-1.25293.40411.06753.81550.15240.5170.0432-0.5572-0.03160.0811-0.031-0.0626-0.19280.51150.0636-0.04360.34320.0470.2229-14.43041.5108-27.5234
168.35925.2538-3.75372.7705-2.12071.05520.1015-0.5189-0.3709-0.0213-0.3043-0.1909-0.01880.20830.19760.3545-0.10660.07320.51940.0730.489-50.4712-11.0442-4.2857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 23 )
2X-RAY DIFFRACTION2chain 'B' and (resid 24 through 1571 )
3X-RAY DIFFRACTION3chain 'F' and (resid 4 through 23 )
4X-RAY DIFFRACTION4chain 'F' and (resid 24 through 1571 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 23 )
6X-RAY DIFFRACTION6chain 'A' and (resid 24 through 1571 )
7X-RAY DIFFRACTION7chain 'H' and (resid 5 through 23 )
8X-RAY DIFFRACTION8chain 'H' and (resid 24 through 1571 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 23 )
10X-RAY DIFFRACTION10chain 'C' and (resid 24 through 1571 )
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 23 )
12X-RAY DIFFRACTION12chain 'D' and (resid 24 through 1571 )
13X-RAY DIFFRACTION13chain 'G' and (resid 3 through 23 )
14X-RAY DIFFRACTION14chain 'G' and (resid 24 through 1570 )
15X-RAY DIFFRACTION15chain 'E' and (resid 3 through 23 )
16X-RAY DIFFRACTION16chain 'E' and (resid 24 through 1571 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more