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- PDB-5aps: Sequence IENKKAD inserted between GCN4 adaptors - Structure A7 -

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Basic information

Entry
Database: PDB / ID: 5aps
TitleSequence IENKKAD inserted between GCN4 adaptors - Structure A7
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsSTRUCTURAL PROTEIN / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsHartmann, M.D. / Mendler, C.T. / Lupas, A.N. / Hernandez Alvarez, B.
CitationJournal: Elife / Year: 2016
Title: alpha / beta coiled coils.
Authors: Hartmann, M.D. / Mendler, C.T. / Bassler, J. / Karamichali, I. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B.
History
DepositionSep 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)11,2081
Polymers11,2081
Non-polymers00
Water1,51384
1
A: GENERAL CONTROL PROTEIN GCN4

A: GENERAL CONTROL PROTEIN GCN4

A: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)33,6243
Polymers33,6243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area6890 Å2
ΔGint-79.4 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.240, 38.240, 87.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 11207.912 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 0.1 M CITRIC ACID PH 3.5, 3 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→18.2 Å / Num. obs: 16040 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.35 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.2
Reflection shellResolution: 1.37→1.45 Å / Redundancy: 6.33 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.52 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPQ

2wpq


Resolution: 1.37→17.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.199 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23823 809 5 %RANDOM
Rwork0.19546 ---
obs0.19749 15218 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.032 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.37→17.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms510 0 0 84 594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019552
X-RAY DIFFRACTIONr_bond_other_d0.0010.02575
X-RAY DIFFRACTIONr_angle_refined_deg1.9422.024743
X-RAY DIFFRACTIONr_angle_other_deg0.73831338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.383572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56826.15426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30815130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.732153
X-RAY DIFFRACTIONr_chiral_restr0.0830.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02605
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02102
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0941.278264
X-RAY DIFFRACTIONr_mcbond_other1.071.272263
X-RAY DIFFRACTIONr_mcangle_it1.5171.91332
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3221.68288
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.37→1.405 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 57 -
Rwork0.297 1072 -
obs--96.99 %
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)
110.3554.6332-1.52899.398-0.31518.3273-0.16110.082-0.6742-0.30730.0043-0.68220.50510.5580.15680.12170.04230.04720.1030.00920.10424.13184.842252.0835
21.92050.1238-1.70632.451-0.486913.0882-0.0031-0.3283-0.02450.32910.00440.06210.05530.1775-0.00140.07040.01250.01110.06390.00540.002418.26175.313870.4827
31.36110.04520.77112.19412.526613.945-0.01710.1356-0.05-0.1459-0.04170.05920.2679-0.26370.05870.03570.0041-0.00640.0513-0.01390.007113.773712.0116109.8196
47.13591.113-0.60056.2752-0.21192.3550.06060.05230.03980.0925-0.1155-0.0838-0.1705-0.01240.05490.11470.0071-0.01350.0949-0.01170.057117.687418.4398131.5305
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9
2X-RAY DIFFRACTION2A10 - 32
3X-RAY DIFFRACTION3A33 - 61
4X-RAY DIFFRACTION4A62 - 9999

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