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- PDB-2o7h: Crystal structure of trimeric coiled coil GCN4 leucine zipper -

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Basic information

Entry
Database: PDB / ID: 2o7h
TitleCrystal structure of trimeric coiled coil GCN4 leucine zipper
ComponentsGeneral control protein GCN4
KeywordsTRANSCRIPTION / Transcription regulation / Nuclear protein / DNA-binding / Amino-acid biosynthesis / Activator / Trimeric Coiled coil
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / 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 superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsJawhari, H. / Honnappa, S. / Steinmetz, M.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Molecular basis of coiled-coil oligomerization-state specificity
Authors: Ciani, B. / Bjelic, S. / Honnappa, S. / Jawhari, H. / Jaussi, R. / Payapilly, A. / Jowitt, T. / Steinmetz, M.O. / Kammerer, R.A.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 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 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
B: General control protein GCN4
C: General control protein GCN4
D: General control protein GCN4
E: General control protein GCN4
F: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)25,0676
Polymers25,0676
Non-polymers00
Water3,315184
1
A: General control protein GCN4
B: General control protein GCN4
C: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)12,5333
Polymers12,5333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-36 kcal/mol
Surface area6230 Å2
MethodPISA, PQS
2
D: General control protein GCN4
E: General control protein GCN4
F: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)12,5333
Polymers12,5333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-32 kcal/mol
Surface area6290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.051, 56.256, 54.863
Angle α, β, γ (deg.)90.00, 129.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-59-

HOH

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Components

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


Mass: 4177.807 Da / Num. of mol.: 6 / Fragment: LEUCINE ZIPPER / Mutation: E22R, K27E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GCN4 / Plasmid: pET 15b-His-Theoredoxin / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03069
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.82 Å3/Da / Density % sol: 32.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% 2-Proponal, 0.2M Sodium Citrate, 0.1M Sodium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 2006 / Details: Osmic mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 15146 / Num. obs: 15146 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.86→1.91 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 7.59 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZIJ

1zij


Resolution: 1.86→42.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.47 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23097 759 5 %RANDOM
Rwork0.17855 ---
all0.18128 ---
obs0.18128 14384 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20.71 Å2
2---0.72 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.86→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 0 184 1780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221602
X-RAY DIFFRACTIONr_angle_refined_deg1.1022.0092122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2745184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02224.41986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3615372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2131518
X-RAY DIFFRACTIONr_chiral_restr0.070.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021134
X-RAY DIFFRACTIONr_nbd_refined0.1910.2845
X-RAY DIFFRACTIONr_nbtor_refined0.290.21099
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2198
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4350.228
X-RAY DIFFRACTIONr_mcbond_it2.162956
X-RAY DIFFRACTIONr_mcangle_it3.1431496
X-RAY DIFFRACTIONr_scbond_it5.4294.5686
X-RAY DIFFRACTIONr_scangle_it7.696626
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 43 -
Rwork0.172 1039 -
obs--97.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23960.106-0.14590.92791.673.6002-0.03590.0079-0.01180.04620.0287-0.02510.04140.0530.00720.00040.0016-0.0047-0.01280.0057-0.010714.6255-23.33463.5827
20.6855-0.2586-0.84540.661.01511.9044-0.0159-0.0431-0.0443-0.02110.01330.0363-0.0015-0.01130.0026-0.00570.0077-0.0034-0.0011-0.001-0.00935.7346-25.52414.2104
30.4291.00230.68752.39421.83852.13510.02620.05950.04540.00740.02860.0035-0.020.0163-0.0548-0.0207-0.0066-0.0091-0.0008-0.0012-0.0028.4893-18.6156-1.542
43.49682.0108-0.35391.6566-0.49210.4708-0.1607-0.1731-0.01090.24350.117-0.0316-0.063-0.03430.04370.04420.05790.0309-0.01550.0125-0.03114.3228-36.754913.7752
52.1331.33180.65512.19280.08110.2802-0.0884-0.0126-0.09940.21770.15310.0641-0.04680.0292-0.06470.01230.0330.01960.00050.0046-0.02118.7925-44.283810.5061
62.47570.7153-0.22061.1002-0.32640.0969-0.1407-0.0746-0.07770.02380.09640.0304-0.06870.01610.04430.00190.01660.0103-0.01090.00180.006415.4838-37.80934.4732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 322 - 34
2X-RAY DIFFRACTION2BB2 - 314 - 33
3X-RAY DIFFRACTION3CC1 - 333 - 35
4X-RAY DIFFRACTION4DD0 - 312 - 33
5X-RAY DIFFRACTION5EE1 - 313 - 33
6X-RAY DIFFRACTION6FF1 - 313 - 33

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