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- PDB-2wq2: GCN4 leucine zipper mutant with three IxxNTxx motifs coordinating... -

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Basic information

Entry
Database: PDB / ID: 2wq2
TitleGCN4 leucine zipper mutant with three IxxNTxx motifs coordinating iodide
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsTRANSCRIPTION / TAA / NUCLEUS / COILED COIL / DNA-BINDING / PROTEIN EXPORT / ION COORDINATION / POLAR CORE RESIDUES / TRIMERIC AUTOTRANSPORTER ADHESIN / TRANSCRIPTION REGULATION / ACTIVATOR
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
IODIDE ION / General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å
AuthorsHartmann, M.D. / Hernandez Alvarez, B. / Lupas, A.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A Coiled-Coil Motif that Sequesters Ions to the Hydrophobic Core.
Authors: Hartmann, M.D. / Ridderbusch, O. / Zeth, K. / Albrecht, R. / Testa, O. / Woolfson, D.N. / Sauer, G. / Dunin-Horkawicz, S. / Lupas, A.N. / Alvarez, B.H.
History
DepositionAug 12, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3484
Polymers3,9671
Non-polymers3813
Water1,04558
1
A: GENERAL CONTROL PROTEIN GCN4
hetero molecules

A: GENERAL CONTROL PROTEIN GCN4
hetero molecules

A: GENERAL CONTROL PROTEIN GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,04512
Polymers11,9023
Non-polymers1,1429
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area2790 Å2
ΔGint-23.42 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.340, 56.340, 56.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-1001-

IOD

21A-1002-

IOD

31A-1003-

IOD

41A-2020-

HOH

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Components

#1: Protein/peptide GENERAL CONTROL PROTEIN GCN4 / GCN4 LEUCINE ZIPPER MUTANT / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN


Mass: 3967.468 Da / Num. of mol.: 1 / Fragment: COILED-COIL DOMAIN, RESIDUES 249-281 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 257 TO ILE ENGINEERED RESIDUE IN CHAIN A, LEU 260 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, VAL 257 TO ILE ENGINEERED RESIDUE IN CHAIN A, LEU 260 TO ASN ENGINEERED RESIDUE IN CHAIN A, LEU 261 TO THR ENGINEERED RESIDUE IN CHAIN A, ASN 264 TO ILE ENGINEERED RESIDUE IN CHAIN A, LEU 267 TO ASN ENGINEERED RESIDUE IN CHAIN A, GLU 268 TO THR ENGINEERED RESIDUE IN CHAIN A, VAL 271 TO ILE ENGINEERED RESIDUE IN CHAIN A, LEU 274 TO ASN ENGINEERED RESIDUE IN CHAIN A, LYS 275 TO THR

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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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growDetails: 2.4 M (NH4)2HPO4, 100 MM TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→18 Å / Num. obs: 6605 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.83 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 16.3
Reflection shellResolution: 1.35→1.44 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.08 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.36→17.85 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.187 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18378 331 5 %RANDOM
Rwork0.14154 ---
obs0.14359 6254 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.774 Å2
Refinement stepCycle: LAST / Resolution: 1.36→17.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms241 0 3 58 302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022249
X-RAY DIFFRACTIONr_bond_other_d0.0020.02168
X-RAY DIFFRACTIONr_angle_refined_deg0.8761.948334
X-RAY DIFFRACTIONr_angle_other_deg0.8593419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.426529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84227.14314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0911553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.869151
X-RAY DIFFRACTIONr_chiral_restr0.0450.240
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02266
X-RAY DIFFRACTIONr_gen_planes_other00.0239
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.15524150
X-RAY DIFFRACTIONr_mcbond_other1.7512460
X-RAY DIFFRACTIONr_mcangle_it4.54132245
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2154899
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.6927289
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.0673417
X-RAY DIFFRACTIONr_sphericity_free2.768361
X-RAY DIFFRACTIONr_sphericity_bonded2.5523416
LS refinement shellResolution: 1.355→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 24 -
Rwork0.202 439 -
obs--100 %

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