[English] 日本語
Yorodumi
- PDB-5w0t: Crystal structure of monomeric Msp1 from S. cerevisiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w0t
TitleCrystal structure of monomeric Msp1 from S. cerevisiae
ComponentsProtein MSP1
KeywordsHYDROLASE / AAA ATPase
Function / homology
Function and homology information


extraction of mislocalized protein from mitochondrial outer membrane / Class I peroxisomal membrane protein import / membrane protein dislocase activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / protein targeting to mitochondrion / protein hexamerization / peroxisomal membrane / mitochondrial outer membrane / membrane => GO:0016020 / ATP hydrolysis activity ...extraction of mislocalized protein from mitochondrial outer membrane / Class I peroxisomal membrane protein import / membrane protein dislocase activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / protein targeting to mitochondrion / protein hexamerization / peroxisomal membrane / mitochondrial outer membrane / membrane => GO:0016020 / ATP hydrolysis activity / mitochondrion / ATP binding
Similarity search - Function
AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Outer mitochondrial transmembrane helix translocase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.63 Å
AuthorsKeenan, R.J. / Wohlever, M.L. / Mateja, A.M.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01 GM086487 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)2T32HL7381 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5T32CA9594 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM119194 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007183 United States
Citation
Journal: Mol. Cell / Year: 2017
Title: Msp1 Is a Membrane Protein Dislocase for Tail-Anchored Proteins.
Authors: Wohlever, M.L. / Mateja, A. / McGilvray, P.T. / Day, K.J. / Keenan, R.J.
#1: Journal: EMBO J. / Year: 2014
Title: Msp1/ATAD1 maintains mitochondrial function by facilitating the degradation of mislocalized tail-anchored proteins.
Authors: Chen, Y.C. / Umanah, G.K. / Dephoure, N. / Andrabi, S.A. / Gygi, S.P. / Dawson, T.M. / Dawson, V.L. / Rutter, J.
#2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: The conserved AAA-ATPase Msp1 confers organelle specificity to tail-anchored proteins.
Authors: Okreglak, V. / Walter, P.
#3: Journal: Cell / Year: 2011
Title: The AAA+ ATPase Thorase regulates AMPA receptor-dependent synaptic plasticity and behavior.
Authors: Zhang, J. / Wang, Y. / Chi, Z. / Keuss, M.J. / Pai, Y.M. / Kang, H.C. / Shin, J.H. / Bugayenko, A. / Wang, H. / Xiong, Y. / Pletnikov, M.V. / Mattson, M.P. / Dawson, T.M. / Dawson, V.L.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein MSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6536
Polymers34,3431
Non-polymers3105
Water19811
1
A: Protein MSP1
hetero molecules

A: Protein MSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,30712
Polymers68,6862
Non-polymers62110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+2/31
Buried area4920 Å2
ΔGint-18 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.351, 56.351, 206.707
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

-
Components

#1: Protein Protein MSP1 / Tat-binding homolog 4


Mass: 34343.125 Da / Num. of mol.: 1 / Fragment: UNP residues 51-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MSP1, YTA4, YGR028W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pRIL / References: UniProt: P28737
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: ~9 mg/ml protein in 20 mM Hepes pH 7.5, 100 mM NaCl and 1 mM DTT was mixed with reservoir solution containing 16% PEG3350 and 0.6 M Sodium Thiocyanate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.63→206.71 Å / Num. obs: 11608 / % possible obs: 100 % / Redundancy: 17.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.051 / Net I/σ(I): 9.9
Reflection shellResolution: 2.63→2.7 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.447 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 843 / CC1/2: 0.762 / Rpim(I) all: 0.491 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_2499refinement
xia2data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.63→68.902 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.02
RfactorNum. reflection% reflection
Rfree0.2596 548 4.79 %
Rwork0.2301 --
obs0.2317 11438 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 261.93 Å2 / Biso mean: 76.4023 Å2 / Biso min: 40.07 Å2
Refinement stepCycle: final / Resolution: 2.63→68.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 21 11 2367
Biso mean--63.1 57.95 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022419
X-RAY DIFFRACTIONf_angle_d0.553263
X-RAY DIFFRACTIONf_chiral_restr0.04379
X-RAY DIFFRACTIONf_plane_restr0.003415
X-RAY DIFFRACTIONf_dihedral_angle_d14.7361494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.63-2.89470.40511150.35352651276697
2.8947-3.31350.35471290.29662719284899
3.3135-4.17470.26811500.229526992849100
4.1747-68.9260.21161540.190428212975100
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)
12.6945-0.2184-0.6141.3797-0.17013.41930.21150.4177-0.33-0.5441-0.09250.31270.4361-0.0061-00.56840.0835-0.07160.8464-0.00490.6611-18.404828.277254.6267
22.90340.60461.3233.03172.10324.35950.18-0.256-0.37780.3465-0.2681-0.06020.90820.508-0.00310.48990.01640.02940.83730.0510.6289-15.037524.968968.0844
34.15330.66860.48452.15560.22792.41360.1649-0.5860.35060.3046-0.45080.0327-0.3230.1356-0.00010.5821-0.2370.06640.9454-0.09240.59320.473742.164592.0821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 138 )A50 - 138
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 270 )A139 - 270
3X-RAY DIFFRACTION3chain 'A' and (resid 271 through 353 )A271 - 353

+
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