[English] 日本語
Yorodumi
- PDB-8brh: Co-crystal structure of She4 with Myo4 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8brh
TitleCo-crystal structure of She4 with Myo4 peptide
Components
  • KLLA0E16699p
  • Myo4 peptide (LYS-PHE-ILE-VAL-SER-HIS-TYR)
KeywordsCHAPERONE / UNC-45 / UCS / myosin
Function / homologyUNC-45/Cro1/She4, central domain / Myosin-binding striated muscle assembly central / chaperone-mediated protein folding / Hsp90 protein binding / Armadillo-like helical / Armadillo-type fold / cytoplasm / KLLA0E16699p
Function and homology information
Biological speciesKluyveromyces lactis (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsArnese, R. / Gudino, R. / Meinhart, A. / Clausen, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
Citation
Journal: To be published
Title: Co-crystal structure of She4 with Myo4 peptide
Authors: Arnese, R. / Gudino, R. / Meinhart, A. / Clausen, T.
#1: Journal: bioRxiv / Year: 2022
Title: UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome
Authors: Vogel, A. / Arnese, R. / Gudino, R. / Sehr, D. / Bylicki, A. / Meinhart, A. / Clausen, T.
History
DepositionNov 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KLLA0E16699p
B: Myo4 peptide (LYS-PHE-ILE-VAL-SER-HIS-TYR)


Theoretical massNumber of molelcules
Total (without water)76,7522
Polymers76,7522
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.480, 128.480, 77.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein KLLA0E16699p


Mass: 75856.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: She4 / Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0_E16699g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CMY7
#2: Protein/peptide Myo4 peptide (LYS-PHE-ILE-VAL-SER-HIS-TYR)


Mass: 895.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM bicine/Trizma base pH 8.5 10% P20K, 20% PEG MME 550 20mM carboxylic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.1512 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1512 Å / Relative weight: 1
ReflectionResolution: 2.4→49.47 Å / Num. obs: 29225 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.1406 / Rrim(I) all: 0.1502 / Net I/σ(I): 10.05
Reflection shellResolution: 2.4→2.54 Å / Num. unique obs: 4655 / CC1/2: 0.465 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BRG

8brg


Resolution: 2.4→49.47 Å / SU ML: 0.3596 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 1483 5.09 %
Rwork0.2118 27668 -
obs0.2137 29151 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5083 0 0 132 5215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075158
X-RAY DIFFRACTIONf_angle_d0.92766983
X-RAY DIFFRACTIONf_chiral_restr0.0565839
X-RAY DIFFRACTIONf_plane_restr0.0052882
X-RAY DIFFRACTIONf_dihedral_angle_d13.941930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.391210.38112496X-RAY DIFFRACTION99.85
2.48-2.570.33321310.2992494X-RAY DIFFRACTION99.96
2.57-2.670.31821360.26082488X-RAY DIFFRACTION99.96
2.67-2.790.32691240.27612507X-RAY DIFFRACTION100
2.79-2.940.2471450.2342466X-RAY DIFFRACTION99.96
2.94-3.120.30771370.23132508X-RAY DIFFRACTION99.96
3.12-3.360.26011480.22712487X-RAY DIFFRACTION99.96
3.36-3.70.26691440.21852507X-RAY DIFFRACTION100
3.7-4.240.22241270.18332522X-RAY DIFFRACTION99.92
4.24-5.340.20771340.1792564X-RAY DIFFRACTION99.96
5.34-49.470.21211360.1852629X-RAY DIFFRACTION99.68
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)
13.068316634530.520306447078-0.336234123181.56356497881-0.2839087197482.253023804940.2283903420810.259884233065-0.291434861154-0.355193779555-0.152215195888-0.2816716273970.182738817560.120256698779-0.07575228083690.4553913038690.1203934004050.05248718148210.5672530325230.004646578537260.539181849952-68.7727197377-6.6905047891510.8806182747
23.526680290351.55197489325-1.624368013571.68624590277-0.7484371197571.129869158590.0741592416007-0.1768421427130.04732058862940.204676980007-0.008353419323380.101954553521-0.02650601115350.0710932786522-0.04868356278120.3624466736670.0461457998346-0.01122325963270.392994887440.02263173005920.268104856098-19.574828951420.9731927759-3.46068052377
33.543782220642.31277240506-3.283887548822.53543088546-1.658978485513.324526516310.252989846446-0.6267008970820.08799613630920.0999882256696-0.05346368172030.352677390566-0.1189364976010.720459503473-0.1472636926440.4933116944280.0423656024605-0.090278476740.770167070095-0.009433687868060.474177233877-10.646093219226.4568069737-0.730648153153
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 246 )AA1 - 2461 - 241
22chain 'A' and (resid 247 through 665 )AA247 - 665242 - 632
33chain 'B' and (resid 74 through 80 )BB74 - 801 - 7

+
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://pdbjlvh1.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