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- PDB-3i1g: Crystal structure of a GCN4 leucine zipper mutant at 1.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 3i1g
TitleCrystal structure of a GCN4 leucine zipper mutant at 1.6 A resolution
ComponentsGeneral control protein GCN4
KeywordsMETAL BINDING PROTEIN / LEUCINE ZIPPER / GCN4 / SYNTHETIC PEPTIDE / HELIX / DOUBLE HELIX / Activator / Amino-acid biosynthesis / DNA-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation
Function / homology
Function and homology information


FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process ...FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
: / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDiao, J.S. / Tortajada, A. / Yeh, J.I.
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal structure of a super leucine zipper, an extended two-stranded super long coiled coil.
Authors: Diao, J.
History
DepositionJun 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)3,9031
Polymers3,9031
Non-polymers00
Water41423
1
A: General control protein GCN4

A: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)7,8052
Polymers7,8052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area940 Å2
ΔGint-7.3 kcal/mol
Surface area5420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.145, 31.145, 57.324
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

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Components

#1: Protein/peptide General control protein GCN4 / Amino acid biosynthesis regulatory protein


Mass: 3902.543 Da / Num. of mol.: 1 / Fragment: Leucine zipper domain: UNP residues 249-281 / Mutation: K251A, D255A, Y265W, H266N / Source method: obtained synthetically
Details: Synthetic peptide with the sequence of yeast GCN4, UNP entry P03069 (GCN4_YEAST), residues 249-281
References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.19 %
Description: 1. ACKNOWLEDGEMENT: THIS WORK WAS SUPPORTED BY THE AFSOR GRANT F49620-03-1-0365 TO J.I.YEH. 2. DIFFRACTION DATA STATISTICS IN REMARK 200 IS PRESENTED FOR SPACE GROUP P32 ONLY. ...Description: 1. ACKNOWLEDGEMENT: THIS WORK WAS SUPPORTED BY THE AFSOR GRANT F49620-03-1-0365 TO J.I.YEH. 2. DIFFRACTION DATA STATISTICS IN REMARK 200 IS PRESENTED FOR SPACE GROUP P32 ONLY. DIFFRACTION DATA WERE PROCESSED IN P32 FIRST, AND THEN THE STRUCTURE FACTOR AMPLITUDES IN P32 WERE REDUCED TO THOSE IN P3221 (SEE THE AUTHORS' PAPER).
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Protein solution: 8 mg/mL Leucine zipper peptide, 0.1 M Sodium acetate pH 4.5. Reservoir solution: 0.2 M CaCl2, 0.1 M Sodium acetate pH 4.5, 20 % v/v Isopropanol, VAPOR DIFFUSION, HANGING ...Details: Protein solution: 8 mg/mL Leucine zipper peptide, 0.1 M Sodium acetate pH 4.5. Reservoir solution: 0.2 M CaCl2, 0.1 M Sodium acetate pH 4.5, 20 % v/v Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2005
Details: Pt-coated toroidal Si mirror for horizontal and vertical focusing followed by double flat Si crystal monochromator
RadiationMonochromator: Double flat Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→19.64 Å / Num. all: 7098 / Num. obs: 7098 / % possible obs: 85.9 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 20.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 194 / Rsym value: 0.24 / % possible all: 23.6

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A STANDARD HELIX OF 28 POLYALANINE RESIDUES

Resolution: 1.6→19.64 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 478704.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.287 389 9.5 %RANDOM
Rwork0.257 ---
obs0.257 4104 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.407 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2--1.73 Å20 Å2
3----3.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms283 0 0 23 306
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.59
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.492
X-RAY DIFFRACTIONc_scangle_it3.862.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.07 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.172 6 3.1 %
Rwork0.421 176 -
obs--37.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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