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- PDB-6xnf: GCN4-p1 Peptide Trimer with Tetrafluoroiodophenylalanine residue ... -

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Basic information

Entry
Database: PDB / ID: 6xnf
TitleGCN4-p1 Peptide Trimer with Tetrafluoroiodophenylalanine residue at position 16 (TFI-F16)
Components
  • GCN4-p1 peptide with A16
  • GCN4-p1 peptide with TFI-F16
KeywordsTRANSCRIPTION / Coil-coil / tetrafluoroiodo-modified phenylalanine
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRowe Hartje, R.K. / Czarny, R.S. / Ho, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1608146 United States
National Science Foundation (NSF, United States)1905328 United States
CitationJournal: To Be Published
Title: Engineering Specific Protein-Protein Interactions Through Halogen and Hydrogen Bonds
Authors: Rowe Hartje, R.K. / Ferrero, M. / Cavallo, G. / Metrangolo, P. / Ho, A. / Czarny, R. / Ho, P.S.
History
DepositionJul 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 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: GCN4-p1 peptide with TFI-F16
B: GCN4-p1 peptide with A16
C: GCN4-p1 peptide with A16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2247
Polymers11,1323
Non-polymers924
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-74 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.650, 35.190, 47.020
Angle α, β, γ (deg.)90.000, 100.647, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein/peptide GCN4-p1 peptide with TFI-F16 / Amino acid biosynthesis regulatory protein


Mass: 3893.234 Da / Num. of mol.: 1 / Mutation: TFI-F16 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069
#2: Protein/peptide GCN4-p1 peptide with A16 / Amino acid biosynthesis regulatory protein


Mass: 3619.280 Da / Num. of mol.: 2 / Mutation: TFI-F16 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Mutation: N16A / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystallization drops were prepared by mixing 2 uL of stock peptide solution with 2 uL of mother liquor and allowed to equilibrate at 298 K over a well containing 500 uL of mother liquor. ...Details: Crystallization drops were prepared by mixing 2 uL of stock peptide solution with 2 uL of mother liquor and allowed to equilibrate at 298 K over a well containing 500 uL of mother liquor. The stock peptide solution (total concentration 1.5 mM) was prepared by mixing 2:1 ratios of the A16 peptide with TFI-F16 in 10 mM potassium phosphate, 100 mM potassium chloride pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→46.21 Å / Num. obs: 43081 / % possible obs: 99.47 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.09809 / Rpim(I) all: 0.04159 / Rrim(I) all: 0.1068 / Net I/σ(I): 11.38
Reflection shellResolution: 2→2.072 Å / Redundancy: 6 % / Rmerge(I) obs: 0.7578 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 3998 / CC1/2: 0.766 / CC star: 0.931 / Rpim(I) all: 0.8326 / Rrim(I) all: 0.3375 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SWI

1swi


Resolution: 2→46.21 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4397
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2537 609 5.02 %
Rwork0.1973 11515 -
obs0.2002 12124 95.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.45 Å2
Refinement stepCycle: LAST / Resolution: 2→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms767 0 4 70 841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083829
X-RAY DIFFRACTIONf_angle_d1.071111
X-RAY DIFFRACTIONf_chiral_restr0.0579128
X-RAY DIFFRACTIONf_plane_restr0.0046133
X-RAY DIFFRACTIONf_dihedral_angle_d2.9085884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.31831400.25142679X-RAY DIFFRACTION88.68
2.2-2.520.2711560.22322952X-RAY DIFFRACTION97
2.52-3.170.29011590.21412996X-RAY DIFFRACTION99.12
3.17-46.210.22051540.17042888X-RAY DIFFRACTION96.17
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9613178468940.892011961599-1.036525275123.09326687118-3.563401760664.082884049830.196360227373-0.138188279995-0.083315510312-0.177072986649-0.1553715230880.04584498118950.5151829453710.114152437086-0.05245801850650.16494773803-0.0146130728728-0.01651810331230.1916548457730.009803355033420.20097163352319.39595161475.9381453572218.8869714342
20.5760015613570.330778658909-0.7459239256061.988601948671.544971008533.14195294740.00390395032235-0.0106314599653-0.1060454383030.0921020419918-0.109158358214-0.0009531600032060.594885815588-0.6734537210280.1184909163580.1805096607950.02026765395490.007201774942280.215870527310.01471725949570.2224377871511.00431510215.458401643718.7748944831
32.593956973430.3555406774222.488745879632.71411720632-1.753797429064.00331434453-0.0106094732815-0.0878575655453-0.2343478903310.267937788174-0.0390192226006-0.145660772989-0.83695555545-0.161796473140.07003792239580.2009252733820.00344172588617-0.01518115387750.213345446058-0.01444898980990.22912662987215.713731750613.860762444620.6637341413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 30 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 30 )

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