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- PDB-2wpy: GCN4 leucine zipper mutant with one VxxNxxx motif coordinating ch... -

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Basic information

Entry
Database: PDB / ID: 2wpy
TitleGCN4 leucine zipper mutant with one VxxNxxx motif coordinating chloride
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsTRANSCRIPTION / AMINO-ACID BIOSYNTHESIS / TRANSCRIPTION REGULATION / ION COORDINATION / POLAR CORE RESIDUES / PROTEIN EXPORT / PHOSPHOPROTEIN / TAA / NUCLEUS / ACTIVATOR / 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: 1.75 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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 1.3Nov 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

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Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0893
Polymers4,0181
Non-polymers712
Water34219
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)12,2669
Polymers12,0533
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4590 Å2
ΔGint-59.37 kcal/mol
Surface area6100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.330, 33.330, 50.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1033-

CL

21A-1034-

CL

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Components

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


Mass: 4017.674 Da / Num. of mol.: 1 / 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.: 19 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 264 TO VAL ENGINEERED RESIDUE IN CHAIN A, 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growDetails: 3.2 M NACL, 100 MM NA-ACETATE, PH 4.6

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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: 1.75→40 Å / Num. obs: 3548 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.37 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 1.75→14.61 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.288 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25239 248 7 %RANDOM
Rwork0.21398 ---
obs0.21679 3292 100 %-
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: 44.815 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.77 Å20 Å2
2--1.55 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 1.75→14.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms267 0 2 19 288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022270
X-RAY DIFFRACTIONr_bond_other_d0.0370.02196
X-RAY DIFFRACTIONr_angle_refined_deg1.6032.013358
X-RAY DIFFRACTIONr_angle_other_deg1.4143483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.362531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10725.38513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5091563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.929152
X-RAY DIFFRACTIONr_chiral_restr0.0850.241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0245
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_it3.3646162
X-RAY DIFFRACTIONr_mcbond_other2.967665
X-RAY DIFFRACTIONr_mcangle_it5.6619260
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.65612108
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.6391898
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 18 -
Rwork0.328 231 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -11.571 Å / Origin y: 9.881 Å / Origin z: -4.482 Å
111213212223313233
T0.0249 Å2-0.01 Å20.0064 Å2-0.0532 Å2-0.0142 Å2--0.0385 Å2
L0.1005 °20.234 °2-0.1576 °2-0.7316 °2-1.1794 °2--6.2636 °2
S0.0077 Å °0.0405 Å °-0.0375 Å °0.0333 Å °0.0397 Å °-0.0466 Å °-0.0736 Å °0.1782 Å °-0.0474 Å °

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