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- PDB-1ij0: Coiled Coil Trimer GCN4-pVLS Ser at Buried D Position -

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Basic information

Entry
Database: PDB / ID: 1ij0
TitleCoiled Coil Trimer GCN4-pVLS Ser at Buried D Position
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsTRANSCRIPTION / COILED COIL TRIMER
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
MethodX-RAY DIFFRACTION / Resolution: 1.86 Å
AuthorsAkey, D.L. / Malashkevich, V.N. / Kim, P.S.
CitationJournal: Biochemistry / Year: 2001
Title: Buried polar residues in coiled-coil interfaces.
Authors: Akey, D.L. / Malashkevich, V.N. / Kim, P.S.
History
DepositionApr 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1686
Polymers11,9723
Non-polymers1963
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-120 kcal/mol
Surface area6230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.466, 28.616, 44.496
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homotypic coiled coil trimer

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Components

#1: Protein/peptide GENERAL CONTROL PROTEIN GCN4 / GCN4-pVLS


Mass: 3990.650 Da / Num. of mol.: 3 / Fragment: Coiled coil region / Mutation: L12S, N16V / Source method: obtained synthetically
Details: THIS PROTEIN WAS CHEMICALLY SYNTHESIZED USING Solid phase FMOC peptide synthesis. It is naturally found in Saccharomyces cerevisiae (yeast).
References: UniProt: P03069
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
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: 1.78 Å3/Da / Density % sol: 30.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Na Cacodylate, 16% PEG 8000, 0.1 M Zn Acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Method: sparse matrix method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium cacodylate11
20.2 Mzinc acetate11
316 %PEG800011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→20 Å / Num. all: 6904 / Num. obs: 6740 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.4
Reflection shellResolution: 1.86→1.94 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.036 / % possible all: 93.2
Reflection
*PLUS
% possible obs: 97.6 % / Num. measured all: 70770
Reflection shell
*PLUS
% possible obs: 93.7 % / Rmerge(I) obs: 0.0315

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
SCALEPACKdata scaling
RefinementResolution: 1.86→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 539511.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 670 9.9 %RANDOM
Rwork0.211 ---
all-7255 --
obs-6847 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.42 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å21.51 Å2
2---2.05 Å20 Å2
3---3.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 1.86→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms777 0 3 130 910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d16
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.386 67 10.7 %
Rwork0.403 557 -
obs--79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15
LS refinement shell
*PLUS
Rfactor Rfree: 0.386 / % reflection Rfree: 10.7 % / Rfactor Rwork: 0.403

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