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- PDB-5whg: Vms1 mitochondrial localization core -

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Basic information

Entry
Database: PDB / ID: 5whg
TitleVms1 mitochondrial localization core
ComponentsProtein VMS1
KeywordsDNA BINDING PROTEIN / ROS signalling / oxidative stress / mitochondrial quality control
Function / homology
Function and homology information


catalytic activity, acting on a tRNA / Cdc48p-Npl4p-Vms1p AAA ATPase complex / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / aminoacyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / ERAD pathway / RNA endonuclease activity / rescue of stalled ribosome / Hydrolases; Acting on ester bonds ...catalytic activity, acting on a tRNA / Cdc48p-Npl4p-Vms1p AAA ATPase complex / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / aminoacyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / ERAD pathway / RNA endonuclease activity / rescue of stalled ribosome / Hydrolases; Acting on ester bonds / endoplasmic reticulum membrane / mitochondrion / metal ion binding / cytosol / cytoplasm
Similarity search - Function
VLRF1/Vms1 / : / Bacteroidetes VLRF1 release factor / Vms1-like release factor 1 (VLRF1) domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
tRNA endonuclease VMS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsFredrickson, E.K. / Schubert, H.L. / Rutter, J. / Hill, C.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115129 United States
CitationJournal: Mol. Cell / Year: 2017
Title: Sterol Oxidation Mediates Stress-Responsive Vms1 Translocation to Mitochondria.
Authors: Nielson, J.R. / Fredrickson, E.K. / Waller, T.C. / Rendon, O.Z. / Schubert, H.L. / Lin, Z. / Hill, C.P. / Rutter, J.
History
DepositionJul 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein VMS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9092
Polymers44,8441
Non-polymers651
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.864, 62.864, 154.383
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein VMS1 / VCP/CDC48-associated mitochondrial stress-responsive protein 1


Mass: 44843.703 Da / Num. of mol.: 1 / Mutation: delta 38-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VMS1, YDR049W / Production host: Escherichia coli (E. coli) / References: UniProt: Q04311
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 286 K / Method: evaporation / pH: 8.5
Details: 22-24% PEG MME 2000, 100 mM Tris pH 8.5, and 0.2 M TMAO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2013 / Details: Rh coated flat
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 10237 / % possible obs: 96.6 % / Redundancy: 10.3 % / Biso Wilson estimate: 88.91 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Χ2: 1.031 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.99.30.7630.8160.2620.8071.00766
2.9-3.0210.50.550.9070.1780.5781.062100
3.02-3.1510.60.3750.9570.1210.3941.046100
3.15-3.32100.260.9740.0860.2741.034100
3.32-3.5310.50.1820.9860.0590.1921.025100
3.53-3.810.70.1350.9920.0430.1420.967100
3.8-4.1810.10.1050.9930.0350.111.07999.9
4.18-4.7910.80.0860.9960.0270.091.025100
4.79-6.0310.50.0710.9970.0230.0751.04899.9
6.03-4010.40.0410.9990.0130.0431.01499.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→24.062 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71 / Details: Refined against I+,SigI+, I-, SigI-
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1041 10.25 %Random selection
Rwork0.1871 ---
obs0.193 10237 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.43 Å2 / Biso mean: 106.4493 Å2 / Biso min: 51.51 Å2
Refinement stepCycle: final / Resolution: 2.7→24.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 1 29 1766
Biso mean--127.25 96.3 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081770
X-RAY DIFFRACTIONf_angle_d0.9722378
X-RAY DIFFRACTIONf_chiral_restr0.049264
X-RAY DIFFRACTIONf_plane_restr0.006294
X-RAY DIFFRACTIONf_dihedral_angle_d13.1751068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6983-2.76570.35891440.305612001344100
2.7657-2.84040.33141340.270811821316100
2.8404-2.92380.2691320.212612071339100
2.9238-3.0180.27091280.187912341362100
3.018-3.12570.22571400.177711881328100
3.1257-3.25050.26281330.201211811314100
3.2505-3.39810.28071380.207212121350100
3.3981-3.57670.26411360.184911981334100
3.5767-3.80.24391440.183712021346100
3.8-4.09210.2041440.158512001344100
4.0921-4.50140.19111400.146612381378100
4.5014-5.14730.20191340.147911911325100
5.1473-6.46410.27581400.207511881328100
6.4641-24.06290.27531330.21511198133199
Refinement TLS params.Method: refined / Origin x: 26.7007 Å / Origin y: 17.3242 Å / Origin z: 58.6358 Å
111213212223313233
T0.7968 Å20.1991 Å20.0109 Å2-0.5182 Å2-0.0998 Å2--0.7214 Å2
L2.2558 °2-1.5529 °2-0.1731 °2-5.6072 °2-0.8464 °2--6.959 °2
S-0.0352 Å °-0.2923 Å °0.1191 Å °0.6443 Å °0.3049 Å °-0.0146 Å °-0.6603 Å °-0.0663 Å °-0.2648 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA13 - 1
2X-RAY DIFFRACTION1allW1 - 38

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