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

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Basic information

Entry
Database: PDB / ID: 6bqi
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


negative regulation of kinase activity / GCN2-mediated signaling / regulation of translational initiation / protein kinase inhibitor activity / negative regulation of protein phosphorylation / actin monomer binding / negative regulation of protein-containing complex assembly / cellular response to amino acid starvation / 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 profile. / RWD / RWD domain ...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 profile. / RWD / RWD domain / 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 / SOLUTION SCATTERING / simulated annealing
AuthorsHarjes, E. / Jameson, G.B. / Edwards, P.J.B. / Goroncy, A.K. / Loo, T. / Norris, G.E.
CitationJournal: Febs Lett. / Year: 2020
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
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 2.0Feb 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Refinement description / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_nmr_details / pdbx_nmr_ensemble / pdbx_nmr_refine / pdbx_nmr_representative / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_keywords / struct_sheet_range
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_ensemble.conformers_calculated_total_number / _pdbx_nmr_ensemble.conformers_submitted_total_number / _pdbx_nmr_refine.details / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.text / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness
Details: Now all low energy models are present. Not: only 3 first structures are consistent with validation by chemical cross-linking and solvent paramagnetic relaxation enhancement data. Therefore ...Details: Now all low energy models are present. Not: only 3 first structures are consistent with validation by chemical cross-linking and solvent paramagnetic relaxation enhancement data. Therefore those are chosen to represent structural model of full-length Yih1
Provider: author / Type: Coordinate replacement
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15390 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 250structures 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

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121anisotropic13D HN(CA)CB
131isotropic13D 1H-15N NOESY
141isotropic13D H(CCO)NH
151isotropic13D (H)CCH-TOCSY
161isotropic13D 1H-13C NOESY aliphatic
171isotropic12D 1H-15N HSQC
NMR detailsText: The authors state that cluster 2 (as in validation report, 3 structures) is consistent with sPRE and Mass spectrometry data.

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] Yih1 (Yeast Impact Homologue), 95% H2O/5% D2O
Label: triple labeled / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: Yih1 (Yeast Impact Homologue) / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 30 mM / Label: triple labeled / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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Data collection

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

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CARAKeller and Wuthrichchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
ATNOSHermannpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 10

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