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- PDB-2wpz: GCN4 leucine zipper mutant with two VxxNxxx motifs coordinating c... -

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Basic information

Entry
Database: PDB / ID: 2wpz
TitleGCN4 leucine zipper mutant with two VxxNxxx motifs coordinating chloride
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsTRANSCRIPTION / AMINO-ACID BIOSYNTHESIS / TRANSCRIPTION REGULATION / ION COORDINATION / POLAR CORE RESIDUES / PROTEIN EXPORT / PHOSPHOPROTEIN / TAA / NUCLEUS / ACTIVATOR / COILED COIL / DNA-BINDING / TRIMERIC AUTOTRANSPORTER ADHESIN
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
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsZeth, K. / Hartmann, M.D. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B.
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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4
C: GENERAL CONTROL PROTEIN GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1275
Polymers12,0563
Non-polymers712
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-44.87 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.380, 25.440, 33.700
Angle α, β, γ (deg.)83.98, 84.86, 78.55
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 4018.619 Da / Num. of mol.: 3 / Fragment: COILED-COIL DOMAIN, RESIDUES 249-281 / Mutation: YES / Source method: obtained synthetically / Details: N-TERMINAL ACETYL GROUP / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 260 TO ASN ENGINEERED RESIDUE IN CHAIN A, ASN 264 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, LEU 260 TO ASN ENGINEERED RESIDUE IN CHAIN A, ASN 264 TO VAL ENGINEERED RESIDUE IN CHAIN A, LEU 267 TO ASN ENGINEERED RESIDUE IN CHAIN B, LEU 260 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASN 264 TO VAL ENGINEERED RESIDUE IN CHAIN B, LEU 267 TO ASN ENGINEERED RESIDUE IN CHAIN C, LEU 260 TO ASN ENGINEERED RESIDUE IN CHAIN C, ASN 264 TO VAL ENGINEERED RESIDUE IN CHAIN C, LEU 267 TO ASN
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growDetails: 30% PEG 4000, 200 MM NA-ACETATE, 0.1 M TRIS, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.25→40 Å / Num. obs: 20616 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.8
Reflection shellResolution: 1.25→1.33 Å / Redundancy: 1.98 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.85 / % possible all: 87.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 1.25→19.51 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.472 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22339 1453 7 %RANDOM
Rwork0.17807 ---
obs0.18126 19310 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.911 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20.37 Å2
2---0.06 Å2-0.3 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.25→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 2 102 918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022856
X-RAY DIFFRACTIONr_bond_other_d0.0020.02627
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9951136
X-RAY DIFFRACTIONr_angle_other_deg1.32531548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.215593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24325.83348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69915205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.903157
X-RAY DIFFRACTIONr_chiral_restr0.090.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02143
X-RAY DIFFRACTIONr_nbd_refined0.220.2216
X-RAY DIFFRACTIONr_nbd_other0.1850.2569
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2399
X-RAY DIFFRACTIONr_nbtor_other0.0770.2491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.41412515
X-RAY DIFFRACTIONr_mcbond_other1.82812195
X-RAY DIFFRACTIONr_mcangle_it5.17518804
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.18424374
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.06136332
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.7763889
X-RAY DIFFRACTIONr_sphericity_free2.48832
X-RAY DIFFRACTIONr_sphericity_bonded5.3833854
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 104 -
Rwork0.316 1383 -
obs--100 %

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