BMRBj - BMREntryMaster

Found 1 Document (0.771 seconds)

BMRB: 30375

6BQI

Structure of two-domain translational regulator Yih1 reveals a possible mechanism of action

Authors

Harjes, E., Jameson, G.B., Edwards, P.J.B., Goroncy, A.K., Loo, T., Norris, G.E.

Assembly

Protein IMPACT homolog

Entity

1. Protein IMPACT homolog (polymer), 258 monomers, 29017.12 Da Detail

MDDDHEQLVE ELEAVEAIYP DLLSKKQEDG SIIVVKVPQH EYMTLQISFP THYPSEEAPN VIEVGVCTSL AKRDLYDTKY LQHLFQEVMD SVFHRGSVCL FDFLTELDGV LYVEPEEETE PVQQSDIPTD PFEGWTASDP ITDRGSTFMA FAAHVTSEEQ AFAMLDLLKT DSKMRKANHV MSAWRIKQDG SAATYQDSDD DGETAAGSRM LHLITIMDVW NVIVVVARWF GGAHIGPDRF KHINSTAREA VVRAGFDS

Formula weight

29017.12 Da

Source organism

Saccharomyces cerevisiae S288C

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 85.3 %, Completeness (bb): 92.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.3 % (2511 of 2945)	85.3 % (1290 of 1512)	83.4 % (973 of 1167)	93.2 % (248 of 266)
Backbone	92.3 % (1408 of 1526)	95.9 % (497 of 518)	88.3 % (672 of 761)	96.8 % (239 of 247)
Sidechain	80.6 % (1342 of 1664)	79.9 % (794 of 994)	82.8 % (539 of 651)	47.4 % (9 of 19)
Aromatic	49.6 % (131 of 264)	55.3 % (73 of 132)	43.0 % (55 of 128)	75.0 % (3 of 4)
Methyl	95.5 % (277 of 290)	94.5 % (137 of 145)	96.6 % (140 of 145)

1. entity 1

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] Yih1 (Yeast Impact Homologue), 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Yih1 (Yeast Impact Homologue)	[U-13C; U-15N]		1 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 2.8 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 2.8 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 2.99 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 3 models in PDB: 6BQI, Strand ID: A Detail

Release date

2018-01-09

Citation

Experimentally based structural model of Yih1 provides insight into its function in controlling the key translational regulator Gcn2
Harjes, E., Jameson, G.B., Tu, Y.H., Burr, N., Loo, T.S., Goroncy, A.K., Edwards, P., Harjes, S., Munro, B., Gobl, C., Sattlegger, E., Norris, G.E.
FEBS Lett. (2021), 595, 324-340, PubMed 33156522 , DOI 10.1002/1873-3468.13990 , Abstract

Related entities 1. Protein IMPACT homolog, : 2 : 17 entities Detail

Interaction partners 1. Protein IMPACT homolog, : 11 interactors Detail

More details for 11 interactors identified by 5 citations

Experiments performed 7 experiments Detail

1 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] Yih1 (Yeast Impact Homologue), 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Yih1 (Yeast Impact Homologue)	[U-13C; U-15N]		1 mM

2 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] Yih1 (Yeast Impact Homologue), 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Yih1 (Yeast Impact Homologue)	[U-13C; U-15N]		1 mM

3 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] Yih1 (Yeast Impact Homologue), 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Yih1 (Yeast Impact Homologue)	[U-13C; U-15N]		1 mM

4 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] Yih1 (Yeast Impact Homologue), 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Yih1 (Yeast Impact Homologue)	[U-13C; U-15N]		1 mM

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] Yih1 (Yeast Impact Homologue), 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Yih1 (Yeast Impact Homologue)	[U-13C; U-15N]		1 mM

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] Yih1 (Yeast Impact Homologue), 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Yih1 (Yeast Impact Homologue)	[U-13C; U-15N]		1 mM

7 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details 1 mM [U-13C; U-15N] Yih1 (Yeast Impact Homologue), 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Yih1 (Yeast Impact Homologue)	[U-13C; U-15N]		1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_30375_6bqi.nef
Input source #2: Coordindates	6bqi.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MDDDHEQLVEELEAVEAIYPDLLSKKQEDGSIIVVKVPQHEYMTLQISFPTHYPSEEAPNVIEVGVCTSLAKRDLYDTKYLQHLFQEVMDSVFHRGSVCL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDDDHEQLVEELEAVEAIYPDLLSKKQEDGSIIVVKVPQHEYMTLQISFPTHYPSEEAPNVIEVGVCTSLAKRDLYDTKYLQHLFQEVMDSVFHRGSVCL

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
FDFLTELDGVLYVEPEEETEPVQQSDIPTDPFEGWTASDPITDRGSTFMAFAAHVTSEEQAFAMLDLLKTDSKMRKANHVMSAWRIKQDGSAATYQDSDD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FDFLTELDGVLYVEPEEETEPVQQSDIPTDPFEGWTASDPITDRGSTFMAFAAHVTSEEQAFAMLDLLKTDSKMRKANHVMSAWRIKQDGSAATYQDSDD

-------210-------220-------230-------240-------250--------
DGETAAGSRMLHLITIMDVWNVIVVVARWFGGAHIGPDRFKHINSTAREAVVRAGFDS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DGETAAGSRMLHLITIMDVWNVIVVVARWFGGAHIGPDRFKHINSTAREAVVRAGFDS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	258	0	0	100.0

Content subtype: combined_30375_6bqi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	2400		97.3 (chain: A, length: 258)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2973 (1)	noe	95.0 (chain: A, length: 258)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	388 (388)	.	92.2 (chain: A, length: 258)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	131 (131)	.	49.6 (chain: A, length: 258)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 258, Sequence coverage: 97.3%
- Total number of assignments
  - ¹H chemical shifts: 1235
  - ¹³C chemical shifts: 921
  - ¹⁵N chemical shifts: 244
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
119	THR	HG1	2.017

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1512	1233	81.5
¹³C chemical shifts	1167	921	78.9
¹⁵N chemical shifts	276	244	88.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	518	494	95.4
¹³C chemical shifts	516	413	80.0
¹⁵N chemical shifts	247	238	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	994	739	74.3
¹³C chemical shifts	651	508	78.0
¹⁵N chemical shifts	29	6	20.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	154	141	91.6
¹³C chemical shifts	154	144	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	132	57	43.2
¹³C chemical shifts	128	37	28.9
¹⁵N chemical shifts	4	2	50.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 258, Sequence coverage: 95.0%
- Total number of restraints: 2973
- Weight of restraints: 1.0 (2973)
- Potential type of restraints: square-well-parabolic (2973)
- Range of distance target values: 2.1, 4.15 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 258, Sequence coverage: 92.2%
- Total number of restraints: 388
- Total number of restraints per polymer type: 388
- Weight of restraints: 1.0 (388)
- Potential type of restraints: square-well-parabolic (388)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 258, Sequence coverage: 49.6%
- Total number of restraints: 131
- Potential type of restraints: undefined (131)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords SAXS, TRANSLATION, translational regulation

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Found 1 Document (0.771 seconds)

BMRB: 30375

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Protein IMPACT homolog, : 2 : 17 entities Detail

Interaction partners 1. Protein IMPACT homolog, : 11 interactors Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 5 contents Detail