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- PDB-6xnm: GCN4-p1 Peptide Trimer with tyrosine residue at position 16 -

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Basic information

Entry
Database: PDB / ID: 6xnm
TitleGCN4-p1 Peptide Trimer with tyrosine residue at position 16
Components
  • GCN4-p1 peptide with A16
  • GCN4-p1 peptide with Y16
KeywordsTRANSCRIPTION / Coil-coil / tyrosine
Function / homology
Function and homology information


Activation of the AP-1 family of transcription factors / protein localization to nuclear periphery / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / response to amino acid starvation / mediator complex binding / amino acid biosynthetic process / TFIID-class transcription factor complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II ...Activation of the AP-1 family of transcription factors / protein localization to nuclear periphery / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / response to amino acid starvation / mediator complex binding / amino acid biosynthetic process / TFIID-class transcription factor complex binding / 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 / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / DNA-templated transcription / 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: 2.25 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 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN4-p1 peptide with A16
B: GCN4-p1 peptide with Y16
C: GCN4-p1 peptide with A16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,11110
Polymers10,9503
Non-polymers1617
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Differential Scanning Calorimetry (DSC)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-77 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.553, 34.482, 46.936
Angle α, β, γ (deg.)90.000, 100.650, 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
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

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Components

#1: Protein/peptide GCN4-p1 peptide with A16 / Amino acid biosynthesis regulatory protein


Mass: 3619.280 Da / Num. of mol.: 2 / Mutation: N16A / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069
#2: Protein/peptide GCN4-p1 peptide with Y16 / Amino acid biosynthesis regulatory protein


Mass: 3711.375 Da / Num. of mol.: 1 / Mutation: N16Y / 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.: 7 / Mutation: N16Y / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.13 %
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 me-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: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→13.77 Å / Num. obs: 7950 / % possible obs: 91.53 % / Redundancy: 1.9 % / Biso Wilson estimate: 22.67 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.04139 / Rpim(I) all: 0.04139 / Rrim(I) all: 0.05854 / Net I/σ(I): 20.01
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.08967 / Mean I/σ(I) obs: 9.6 / Num. unique obs: 818 / CC1/2: 0.942 / CC star: 0.985 / Rpim(I) all: 0.08967 / Rrim(I) all: 0.1268 / % possible all: 91.42

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Processing

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

1swi


Resolution: 2.25→13.77 Å / SU ML: 0.4792 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.7621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3581 756 10 %
Rwork0.2247 6806 -
obs0.2383 7562 87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.83 Å2
Refinement stepCycle: LAST / Resolution: 2.25→13.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 0 7 43 803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009801
X-RAY DIFFRACTIONf_angle_d1.29281069
X-RAY DIFFRACTIONf_chiral_restr0.0518125
X-RAY DIFFRACTIONf_plane_restr0.0049130
X-RAY DIFFRACTIONf_dihedral_angle_d2.798728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.420.39321570.27791380X-RAY DIFFRACTION87.28
2.42-2.670.40741440.2921349X-RAY DIFFRACTION85.9
2.67-3.050.40141540.25161384X-RAY DIFFRACTION89.63
3.05-3.830.39131430.19761313X-RAY DIFFRACTION82.73
3.83-13.770.27891580.18671380X-RAY DIFFRACTION89.57
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)
12.98310238444-0.81856221403-1.134623852793.7480180932-2.361679838472.839535577850.142233062332-0.328156671275-0.0347277957738-0.356127992681-0.07523055177490.0211439310750.4249540676511.16150519682-0.1253225624920.176573145372-0.0359694235847-0.0388878748870.162816690963-0.03112784232960.168462452742-9.5695206594-10.536656333419.943834277
21.032257171370.7149996407830.4841567502092.17380101096-0.3115400766821.51048118281-0.08270511179050.0926917003922-0.3430025345480.09227861741930.2393868963220.00508069533312-0.240576628678-0.486334547497-0.1440572526220.24286319495-0.001428134607410.04819761232670.2324545749940.0330094581850.241105356491-14.3357975632-2.2739415738320.5336153787
31.53243853987-0.1404320567390.9674351448761.455397543081.156393420794.87326300240.364082079561-0.0172309527424-0.125580804405-0.1887124105870.09734441998030.1705426044720.192733066554-0.731290218190.01114676226250.433697684398-0.0555486628099-0.01267893819190.324406917441-0.0287263533720.114756208906-18.8007891779-10.116504173220.3758946773
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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