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- PDB-4hu6: Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: ... -

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Basic information

Entry
Database: PDB / ID: 4hu6
TitleOxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Cyclic product
ComponentsGeneral control protein GCN4
KeywordsTRANSCRIPTION / side-chain staple / side-chain cross-link
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 / 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 / Oxidative Stress Induced Senescence / 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 / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / 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
ACETATE ION / General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHaney, C.M. / Horne, W.S.
CitationJournal: Chemistry / Year: 2013
Title: Oxime Side-Chain Cross-Links in an alpha-Helical Coiled-Coil Protein: Structure, Thermodynamics, and Folding-Templated Synthesis of Bicyclic Species.
Authors: Haney, C.M. / Horne, W.S.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Category: pdbx_entity_src_syn / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num ..._pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6099
Polymers16,2154
Non-polymers3945
Water1,18966
1
A: General control protein GCN4
B: General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3185
Polymers8,1082
Non-polymers2103
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-20 kcal/mol
Surface area4880 Å2
MethodPISA
2
C: General control protein GCN4
D: General control protein GCN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2924
Polymers8,1082
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-19 kcal/mol
Surface area5170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.945, 33.102, 41.075
Angle α, β, γ (deg.)93.91, 111.95, 98.74
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


Mass: 4053.754 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P03069
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 1.6 M sodium chloride, 5% w/v PEG 1500; crystal was treated with 1 equiv. sodium periodate relative to protein and allowed to incubate for 2 days prior to ...Details: 0.1 M sodium acetate pH 4.6, 1.6 M sodium chloride, 5% w/v PEG 1500; crystal was treated with 1 equiv. sodium periodate relative to protein and allowed to incubate for 2 days prior to harvesting, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 22, 2012 / Details: Rigaku VariMax Optics
RadiationMonochromator: Rigaku VariMax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28.52 Å / Num. obs: 6255 / % possible obs: 95.2 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2ZTA

2zta


Resolution: 2.3→28.52 Å / SU ML: 0.42 / σ(F): 2 / Phase error: 34.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.292 319 5.12 %RANDOM; THIN RESOLUTION SHELLS
Rwork0.2586 ---
obs0.2603 6225 94.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.064 Å2 / ksol: 0.411 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.4926 Å2-1.2921 Å20.0257 Å2
2--0.1576 Å25.1161 Å2
3---7.335 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 26 66 1165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091135
X-RAY DIFFRACTIONf_angle_d1.4791503
X-RAY DIFFRACTIONf_dihedral_angle_d19.984488
X-RAY DIFFRACTIONf_chiral_restr0.094164
X-RAY DIFFRACTIONf_plane_restr0.003192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.89750.38841610.30392904X-RAY DIFFRACTION94
2.8975-28.52250.26111580.24343002X-RAY DIFFRACTION96

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