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- PDB-1w5k: AN ANTI-PARALLEL FOUR HELIX BUNDLE -

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Basic information

Entry
Database: PDB / ID: 1w5k
TitleAN ANTI-PARALLEL FOUR HELIX BUNDLE
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsFOUR HELIX BUNDLE / ANTIPARALLEL FOUR HELIX BUNDLE
Function / homology
Function and homology information


protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / 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 / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / 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 / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / 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 / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA 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 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 / SIRAS / Resolution: 1.92 Å
AuthorsYadav, M.K. / Leman, L.J. / Stout, C.D. / Ghadiri, M.R.
CitationJournal: Biochemistry / Year: 2006
Title: Coiled Coils at the Edge of Configurational Heterogeneity. Structural Analyses of Parallel and Antiparallel Homotetrameric Coiled Coils Reveal Configurational Sensitivity to a Single Solvent- ...Title: Coiled Coils at the Edge of Configurational Heterogeneity. Structural Analyses of Parallel and Antiparallel Homotetrameric Coiled Coils Reveal Configurational Sensitivity to a Single Solvent-Exposed Amino Acid Substitution.
Authors: Yadav, M.K. / Leman, L.J. / Price, D.J. / Brooks, C.L. / Stout, C.D. / Ghadiri, M.R.
History
DepositionAug 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag

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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
D: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)17,0764
Polymers17,0764
Non-polymers00
Water1,67593
1
A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4

A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)17,0764
Polymers17,0764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
2
C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)17,0764
Polymers17,0764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.886, 37.311, 104.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide
GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / KHHC33


Mass: 4269.016 Da / Num. of mol.: 4 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 251 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: ...ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 251 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 256 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: CYS 268 TO GLU ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 275 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 276 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: TYR 265 TO HIS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.9 %
Description: STRUCTURE WAS ORIGINALLY SOLVED BETWEEN SIRAS PHASING BETWEEN 2SEMET PEPTIDE AND IT'S DERIVATIVE SOAKED WITH 50MM KAUCN2
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP, 1UL OF 10MG/ML PEPTIDE IN WATER, 1UL 100MM CAPS, 30% PEG 400, PH 10.5, 1UL OF 50MM TCEP IN WATER

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDate: Jan 9, 2003
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→37.31 Å / Num. obs: 19519 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 2.69 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.4
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.3 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
SOLVE/RESOLVEphasing
ARP/wARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.92→105.41 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.868 / SU B: 4.294 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.307 501 4.8 %RANDOM
Rwork0.249 ---
obs0.251 10007 98.4 %-
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: 23.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2---0.29 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.92→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 0 93 1174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211101
X-RAY DIFFRACTIONr_bond_other_d0.0060.021106
X-RAY DIFFRACTIONr_angle_refined_deg1.022.0051460
X-RAY DIFFRACTIONr_angle_other_deg0.70132531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0965132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0490.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021201
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02229
X-RAY DIFFRACTIONr_nbd_refined0.1910.2260
X-RAY DIFFRACTIONr_nbd_other0.2420.21228
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.2632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5731.5672
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90621071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6113429
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8884.5389
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: 1.92→1.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 28
Rwork0.279 733

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