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- PDB-6u1o: Structure of two-domain translational regulator Yih1 reveals a po... -

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Basic information

Entry
Database: PDB / ID: 6u1o
TitleStructure of two-domain translational regulator Yih1 reveals a possible mechanism of action
ComponentsProtein IMPACT homolog
KeywordsTRANSLATION / translational regulation
Function / homology
Function and homology information


GCN2-mediated signaling / regulation of translational initiation / negative regulation of kinase activity / protein kinase inhibitor activity / actin monomer binding / negative regulation of protein-containing complex assembly / cellular response to amino acid starvation / negative regulation of protein phosphorylation / ribosome binding / nucleus / cytoplasm
Similarity search - Function
Impact, N-terminal / Uncharacterised protein family UPF0029, Impact, conserved site / Impact family / Impact, N-terminal domain superfamily / Uncharacterized protein family UPF0029 / Uncharacterized protein family UPF0029 signature. / RWD domain / RWD domain / RWD domain profile. / RWD ...Impact, N-terminal / Uncharacterised protein family UPF0029, Impact, conserved site / Impact family / Impact, N-terminal domain superfamily / Uncharacterized protein family UPF0029 / Uncharacterized protein family UPF0029 signature. / RWD domain / RWD domain / RWD domain profile. / RWD / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Protein IMPACT homolog
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsHarjes, E. / Jameson, G.B. / Edwards, P.J.B. / Goroncy, A.K. / Loo, T. / Norris, G.E.
CitationJournal: Febs Lett. / Year: 2021
Title: Experimentally based structural model of Yih1 provides insight into its function in controlling the key translational regulator Gcn2.
Authors: Harjes, E. / Jameson, G.B. / Tu, Y.H. / Burr, N. / Loo, T.S. / Goroncy, A.K. / Edwards, P.J.B. / Harjes, S. / Munro, B. / Gobl, C. / Sattlegger, E. / Norris, G.E.
History
DepositionAug 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein IMPACT homolog


Theoretical massNumber of molelcules
Total (without water)29,0471
Polymers29,0471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein IMPACT homolog


Mass: 29047.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YIH1, YCR059C, YCR59C / Production host: Escherichia coli (E. coli) / References: UniProt: P25637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D (H)CCH-TOCSY
141isotropic12D 1H-15N HSQC
151isotropic13D H(CCO)NH
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] Yeast Impact homologue Ancient domain, 90% H2O/10% D2O
Label: triple labeled / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Yeast Impact homologue Ancient domain / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 30 mM / Label: condition1 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.25data extraction
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 0 Å2 / Biso mean: 0 Å2 / Biso min: 0 Å2
NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.structure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CARAKeller and Wuthrichchemical shift assignment
CANDIDHerrmann, Guntert and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2 / Details: explicit water
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 12

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