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BMRB: 30028

5IIR

GCN4p pH 4.4

Authors

Brady, M.R., Kaplan, A.R., Alexandrescu, A.T.

Assembly

General control protein GCN4

Entity

1. General control protein GCN4 (polymer, Thiol state: not present), 33 monomers, 3828.347 × 2 Da Detail

GSMKQLEDKV EELLSKNYHL ENEVARLKKL VGE

Total weight

7656.694 Da

Max. entity weight

3828.347 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.1 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.1 % (371 of 403)	93.9 % (201 of 214)	88.2 % (135 of 153)	97.2 % (35 of 36)
Backbone	95.5 % (189 of 198)	94.1 % (64 of 68)	95.9 % (93 of 97)	97.0 % (32 of 33)
Sidechain	90.3 % (213 of 236)	93.8 % (137 of 146)	83.9 % (73 of 87)	100.0 % (3 of 3)
Aromatic	66.7 % (8 of 12)	100.0 % (6 of 6)	33.3 % (2 of 6)
Methyl	92.1 % (35 of 38)	94.7 % (18 of 19)	89.5 % (17 of 19)

1. entity 1

GSMKQLEDKV EELLSKNYHL ENEVARLKKL VGE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.4, Details 1.5 mM [U-99% 13C; U-99% 15N] GCN4p, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GCN4p	[U-99% 13C; U-99% 15N]		1.5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4.4, Details 1.5 mM [U-99% 13C; U-99% 15N] GCN4p, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	GCN4p	[U-99% 13C; U-99% 15N]		1.5 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5IIR, Strand ID: A, B Detail

Release date

2016-03-02

Citation

Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix
Kaplan, A.R., Brady, M.R., Maciejewski, M.W., Kammerer, R.A., Alexandrescu, A.T.
Biochemistry (2017), 56, 1604-1619, PubMed 28230348 , DOI 10.1021/acs.biochem.6b00634 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 30029 released on 2016-03-02
    Title GCN4p pH 1.5
  BMRB: 30027 released on 2016-03-01
    Title GCN4p pH 6.6

Related entities 1. General control protein GCN4, : 1 : 5 : 58 : 76 entities Detail

Interaction partners 1. General control protein GCN4, : 13 interactors Detail

More details for 13 interactors identified by 9 citations

Experiments performed 7 experiments Detail

1 3D HNCACB

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.4, Details 1.5 mM [U-99% 13C; U-99% 15N] GCN4p, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GCN4p	[U-99% 13C; U-99% 15N]		1.5 mM

2 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.4, Details 1.5 mM [U-99% 13C; U-99% 15N] GCN4p, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GCN4p	[U-99% 13C; U-99% 15N]		1.5 mM

3 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.4, Details 1.5 mM [U-99% 13C; U-99% 15N] GCN4p, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GCN4p	[U-99% 13C; U-99% 15N]		1.5 mM

4 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.4, Details 1.5 mM [U-99% 13C; U-99% 15N] GCN4p, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GCN4p	[U-99% 13C; U-99% 15N]		1.5 mM

5 3D HNCO

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.4, Details 1.5 mM [U-99% 13C; U-99% 15N] GCN4p, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GCN4p	[U-99% 13C; U-99% 15N]		1.5 mM

6 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 4.6, Details 1.5 mM [U-99% 13C; U-99% 15N] GCN4p, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	GCN4p	[U-99% 13C; U-99% 15N]		1.5 mM

7 2D 15N NOESY

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.4, Details 1.5 mM [U-99% 13C; U-99% 15N] GCN4p, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GCN4p	[U-99% 13C; U-99% 15N]		1.5 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30028_5iir.nef
Input source #2: Coordindates	5iir.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---
GSMKQLEDKVEELLSKNYHLENEVARLKKLVGE
|||||||||||||||||||||||||||||||||
GSMKQLEDKVEELLSKNYHLENEVARLKKLVGE

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

--------10--------20--------30---
GSMKQLEDKVEELLSKNYHLENEVARLKKLVGE
|||||||||||||||||||||||||||||||||
GSMKQLEDKVEELLSKNYHLENEVARLKKLVGE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	33	0	0	100.0
B	B	33	0	0	100.0

Content subtype: combined_30028_5iir.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	372		100.0 (chain: A, length: 33)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	696 (1)	noe	97.0 (chain: A, length: 33), 97.0 (chain: B, length: 33)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	112 (1)	hbond	93.9 (chain: A, length: 33), 93.9 (chain: B, length: 33)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	136 (136)	.	93.9 (chain: A, length: 33), 93.9 (chain: B, length: 33)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 135
  - ¹H chemical shifts: 202
  - ¹⁵N chemical shifts: 35
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 97.0%
  - Entity_assembly_ID: B, Chain length: 33, Sequence coverage: 97.0%
- Total number of restraints: 696
- Weight of restraints: 1.0 (696)
- Potential type of restraints: square-well-parabolic (696)
- Range of distance target values: 2.61, 5.62 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 93.9%
    - Entity_assembly_ID: B, Chain length: 33, Sequence coverage: 93.9%
  - Total number of restraints: 112
  - Weight of restraints: 1.0 (112)
  - Potential type of restraints: square-well-parabolic (112)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - 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: 33, Sequence coverage: 93.9%
  - Entity_assembly_ID: B, Chain length: 33, Sequence coverage: 93.9%
- Total number of restraints: 136
- Total number of restraints per polymer type: 136
- Weight of restraints: 1.0 (136)
- Potential type of restraints: square-well-parabolic (136)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords Supercoil parameters, TRANSCRIPTION, canonical alpha helix, closely related NMR structures, conformational transition, electrostatics, knobs-into-holes, leucine zipper, salt bridge