[English] 日本語
Yorodumi
- PDB-5wlz: Crystal Structure of Amino Acids 1677-1758 of Human Beta Cardiac ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wlz
TitleCrystal Structure of Amino Acids 1677-1758 of Human Beta Cardiac Myosin Fused to Xrcc4
ComponentsDNA repair protein XRCC4,Myosin-7
KeywordsMOTOR PROTEIN / Myosin / Xrcc4 / Coiled-Coil
Function / homology
Function and homology information


FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination ...FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of the force of heart contraction / protein localization to site of double-strand break / 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 / cellular response to lithium ion / 2-LTR circle formation / skeletal muscle contraction / response to X-ray / striated muscle contraction / SUMOylation of DNA damage response and repair proteins / ATP metabolic process / stress fiber / cardiac muscle contraction / regulation of heart rate / sarcomere / muscle contraction / Nonhomologous End-Joining (NHEJ) / Z disc / double-strand break repair via nonhomologous end joining / double-strand break repair / actin filament binding / site of double-strand break / calmodulin binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / XRCC4-like, N-terminal domain superfamily / 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 / Beta Complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Myosin-7 / DNA repair protein XRCC4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsAndreas, M.P. / Ajay, G. / Gellings, J. / 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: J. Struct. Biol. / Year: 2017
Title: Design considerations in coiled-coil fusion constructs for the structural determination of a problematic region of the human cardiac myosin rod.
Authors: Andreas, M.P. / Ajay, G. / Gellings, J.A. / Rayment, I.
History
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
C: DNA repair protein XRCC4,Myosin-7
D: DNA repair protein XRCC4,Myosin-7
A: DNA repair protein XRCC4,Myosin-7
B: DNA repair protein XRCC4,Myosin-7


Theoretical massNumber of molelcules
Total (without water)98,0194
Polymers98,0194
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-100 kcal/mol
Surface area42310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.290, 102.940, 136.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
DNA repair protein XRCC4,Myosin-7 / / X-ray repair cross-complementing protein 4 / Myosin heavy chain 7 / Myosin heavy chain slow isoform ...X-ray repair cross-complementing protein 4 / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 24504.676 Da / Num. of mol.: 4
Fragment: UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758
Mutation: E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4, MYH7, MYHCB / Production host: Escherichia coli (E. coli) / References: UniProt: Q13426, UniProt: P12883

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8-10% methyl-ether polyethylene glycol (MEPEG) 5K, 300 mM glycine, bis-tris propane pH 7.0, 1.5-3.0% (w/v) jeffamine M-600

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 16299 / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 17.1
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 808 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IK9

1ik9


Resolution: 3.5→44.068 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9
RfactorNum. reflection% reflection
Rfree0.2495 785 5.01 %
Rwork0.2135 --
obs0.2154 15666 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→44.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6360 0 0 0 6360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026448
X-RAY DIFFRACTIONf_angle_d0.4238663
X-RAY DIFFRACTIONf_dihedral_angle_d13.0553965
X-RAY DIFFRACTIONf_chiral_restr0.034987
X-RAY DIFFRACTIONf_plane_restr0.0021108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5002-3.71940.30881280.26542421X-RAY DIFFRACTION99
3.7194-4.00640.29281290.23722434X-RAY DIFFRACTION100
4.0064-4.40920.2211280.20662448X-RAY DIFFRACTION100
4.4092-5.04650.2511310.18232481X-RAY DIFFRACTION100
5.0465-6.3550.26151310.23522490X-RAY DIFFRACTION100
6.355-44.0710.20251380.18672607X-RAY DIFFRACTION100
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)
11.82140.88380.26453.51221.34143.46950.0368-0.4162-0.49160.7877-0.09890.06060.4554-0.07790.0510.6449-0.0066-0.03730.16590.19560.31081.315114.0921-12.4891
20.26080.34350.30030.86830.97433.0671-0.43390.3745-0.1026-0.4110.0055-0.0995-1.28310.33990.23220.4324-0.1164-0.040.27580.01040.3406-1.948530.074-64.5758
31.9874-0.96730.95594.4461-1.53433.34960.1066-0.19990.47320.39070.0142-0.2095-0.09980.2431-0.08060.4178-0.05780.0550.1448-0.15090.20724.749752.1553-12.9772
4-0.04040.18720.3520.3881.14974.5555-0.25330.2215-0.0974-0.0754-0.13230.30430.69070.1896-0.5890.4163-0.16260.00560.60390.00720.2126-1.63228.9568-62.1535
54.13640.5980.37364.58390.49433.8526-0.0679-0.05550.4678-0.1514-0.1580.0051-0.45030.08690.12930.03010.06280.00420.10790.03260.2857-19.554525.4912-31.6425
69.17294.84982.65318.16643.08313.89310.176-0.61370.30960.3368-0.0165-0.0368-0.3791-0.2728-0.1430.46770.13880.14960.1303-0.02360.2155-23.209727.3535-24.6098
70.15810.3117-0.37340.662-0.27951.4461-0.1374-0.1933-0.4237-0.1956-0.2408-0.41940.07240.7873-0.09210.25630.0650.05580.2762-0.06410.569223.18796.7303-44.73
83.0289-2.0047-0.19134.9213-0.62071.9687-0.02490.0347-0.3189-0.24670.10780.37770.5807-0.1927-0.0240.2399-0.13890.13390.0373-0.01470.2211-19.1865-10.7243-31.895
96.4208-3.5838-4.70055.72973.44524.02640.20030.8904-0.9649-0.4187-1.02971.0704-0.0472-1.04050.45010.4356-0.1692-0.2550.3964-0.00620.6575-26.7021-14.1447-36.0248
103.5481-0.1883-2.54020.40180.13662.20470.365-0.12850.7778-0.2443-0.1607-0.273-0.31480.7127-0.35380.23730.19570.17890.43970.02120.442921.65689.4722-43.8868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid -1 through 118 )
2X-RAY DIFFRACTION2chain 'C' and (resid 119 through 1748 )
3X-RAY DIFFRACTION3chain 'D' and (resid 1 through 118 )
4X-RAY DIFFRACTION4chain 'D' and (resid 119 through 1745 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2 through 73 )
6X-RAY DIFFRACTION6chain 'A' and (resid 74 through 118 )
7X-RAY DIFFRACTION7chain 'A' and (resid 119 through 1739 )
8X-RAY DIFFRACTION8chain 'B' and (resid -1 through 86 )
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 118 )
10X-RAY DIFFRACTION10chain 'B' and (resid 119 through 1739 )

+
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