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- PDB-5apw: Sequence MATKDD inserted between GCN4 adaptors - Structure T6 -

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Basic information

Entry
Database: PDB / ID: 5apw
TitleSequence MATKDD inserted between GCN4 adaptors - Structure T6
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsDNA BINDING PROTEIN / ALPHA/BETA COILED COIL / BETA LAYER / TRIMER
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 RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / 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 / 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 / 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 superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
UREA / General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)33,3456
Polymers33,2093
Non-polymers1363
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-109.3 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.200, 27.020, 101.040
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11069.746 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 250-277,250-281 / 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: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growDetails: 0.2 M CACL, 0.1 M HEPES PH 7.5, 30 %(W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→34.1 Å / Num. obs: 24470 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.04 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.6
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.33 / % possible all: 96.1

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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: 1.6→34.12 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.694 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20468 1215 5 %RANDOM
Rwork0.17337 ---
obs0.17498 23253 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.11 Å2
2--0.97 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 6 190 1785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191696
X-RAY DIFFRACTIONr_bond_other_d0.0010.021759
X-RAY DIFFRACTIONr_angle_refined_deg1.8972.0152282
X-RAY DIFFRACTIONr_angle_other_deg0.88534091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0295220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75626.36477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78115395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.02156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021839
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
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_it3.3084.239809
X-RAY DIFFRACTIONr_mcbond_other3.2514.229807
X-RAY DIFFRACTIONr_mcangle_it4.1077.0431013
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.5415.973887
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: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 77 -
Rwork0.268 1611 -
obs--93.52 %
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)
13.4894-0.2477-2.20242.69493.386713.0317-0.01870.1324-0.0692-0.10580.0583-0.14190.12840.1942-0.03960.0224-0.0015-0.01020.01350.00430.04775.9819-6.4972-20.5842
21.4833-0.24082.38691.2461-1.461311.39250.043-0.11260.01520.13470.0034-0.0204-0.03520.1967-0.04650.0182-0.0049-0.0060.0462-0.0040.07110.93075.658328.2627
31.8845-0.2323-1.54311.8906-1.093313.834-0.02130.0780.0991-0.0863-0.0318-0.0844-0.09670.19980.05310.0086-0.0047-0.00450.022-0.01050.068713.8288-2.1032-19.9019
40.70450.10820.0251.16171.67167.416-0.0113-0.0756-0.02090.08540.0010.00570.08370.00680.01030.03530.0068-0.01350.0440.0080.07892.72210.840327.195
51.66960.3471.19951.1461.87598.6724-0.00390.06150.0267-0.0956-0.05030.0482-0.0219-0.0490.05410.05120.00440.00230.0110.01920.09026.22352.5425-20.6408
60.66380.2315-1.09260.54-0.61967.17570.0006-0.0523-0.02770.0592-0.01940.00110.11230.09780.01890.0660.0211-0.0130.06860.00560.092310.992-3.371827.0403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 30
2X-RAY DIFFRACTION2A31 - 65
3X-RAY DIFFRACTION3B0 - 30
4X-RAY DIFFRACTION4B31 - 63
5X-RAY DIFFRACTION5C0 - 30
6X-RAY DIFFRACTION6C31 - 63

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