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- PDB-5apq: Sequence IENKAD inserted between GCN4 adaptors - Structure A6 -

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Basic information

Entry
Database: PDB / ID: 5apq
TitleSequence IENKAD inserted between GCN4 adaptors - Structure A6
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsSTRUCTURAL 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 transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / 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 / regulation of cell cycle / 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
General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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


Theoretical massNumber of molelcules
Total (without water)33,2363
Polymers33,2363
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-82.5 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.370, 34.810, 104.160
Angle α, β, γ (deg.)90.00, 101.09, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 3 - 63 / Label seq-ID: 29 - 89

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.491022, 0.87113, 0.005498), (-0.871135, -0.491038, 0.002196), (0.004613, -0.003711, 0.999982)-14.89676, -8.69944, 0.03639
3given(-0.502919, -0.86432, 0.004741), (0.864333, -0.502917, 0.001675), (0.000936, 0.00494, 0.999987)-15.08488, 8.76671, 0.01717

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Components

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


Mass: 11078.732 Da / Num. of mol.: 3 / 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.: 46 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 95 MM TRI-SODIUM CITRATE PH 5.6, 19 %(V/V) ISOPROPANOL, 19 %(W/V) PEG 4000, 5 %(V/V) GLYCEROL

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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 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.422
111/2H-3/2K, -1/2H-1/2K, -1/2H+1/2K-L20.31
111/2H+3/2K, 1/2H-1/2K, -1/2H-1/2K-L30.269
ReflectionResolution: 2.1→30 Å / Num. obs: 12389 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.71 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.28 / % possible all: 96.2

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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: 2.1→30.04 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.491 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25143 634 5.1 %RANDOM
Rwork0.20773 ---
obs0.20996 11754 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.214 Å2
Baniso -1Baniso -2Baniso -3
1-32.37 Å20 Å2-0.34 Å2
2--8.56 Å20 Å2
3----40.94 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 0 46 1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191476
X-RAY DIFFRACTIONr_bond_other_d0.0010.021495
X-RAY DIFFRACTIONr_angle_refined_deg0.8092.0111980
X-RAY DIFFRACTIONr_angle_other_deg0.67333454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4155180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70727.39169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94415318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.933153
X-RAY DIFFRACTIONr_chiral_restr0.0430.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
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_it5.50913.405729
X-RAY DIFFRACTIONr_mcbond_other5.513.391728
X-RAY DIFFRACTIONr_mcangle_it7.0722.537906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.29619.11747
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 958 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A5.93
1A6.15
1A5.61
2B5.93
2B6.15
2B5.61
3C5.93
3C6.15
3C5.61
LS refinement shellResolution: 2.098→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 28 -
Rwork0.23 832 -
obs--92.18 %
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)
117.1474-4.18718.83891.2633-3.432111.3001-0.17570.25140.31660.00720.0323-0.07660.0816-0.39070.14340.23390.0161-0.01460.1609-0.00390.1831-13.306-6.1205-60.7469
24.60971.3528-0.29531.79532.005412.4894-0.20040.2434-0.29320.1263-0.17010.07770.4318-0.04510.37050.2318-0.0029-0.00870.0764-0.0220.2106-15.604-1.72-40.767
36.95995.0007-0.145.99545.221711.8243-0.0413-0.0884-0.0575-0.0508-0.1930.0546-0.0704-0.34010.23430.27740.0914-0.02160.0971-0.06410.3467-11.4683.8838-18.652
43.5064-0.34563.44690.3161-1.836111.63150.0232-0.2462-0.0220.10550.0128-0.0006-0.3199-0.1531-0.0360.22910.0140.00910.0219-0.01490.1527-5.22553.04616.5041
53.5477-5.0061-5.31617.14476.936811.99880.01840.0625-0.0498-0.0325-0.10880.05560.08530.12120.09040.2047-0.0322-0.02070.3148-0.00410.1837-3.25390.3299-60.7693
61.94870.1618-0.91340.9089-1.74588.4025-0.00380.097-0.0180.0331-0.0784-0.0488-0.12370.09550.08210.15580.01430.00280.0193-0.02150.1652-5.9212-3.8866-40.7848
76.5357-3.2239-4.36011.72961.37617.2572-0.09490.14930.12980.0219-0.0417-0.10490.281-0.30170.13660.1938-0.01760.00450.0799-0.01580.2489-13.6245-2.8433-18.1818
81.50660.22110.45920.61231.823511.9398-0.065-0.1654-0.01010.0445-0.0388-0.0230.0744-0.1980.10370.15660.00760.00370.02040.00340.1357-14.95282.78966.9097
92.75711.6529-5.66476.5264-3.291411.64660.2174-0.0156-0.03810.0233-0.2647-0.2971-0.45610.04360.04730.17110.0005-0.01660.32450.01590.167-13.81945.7175-60.7969
102.1365-0.23972.62860.81750.0228.9068-0.035-0.04060.0701-0.0108-0.00250.08760.099-0.3370.03750.1605-0.00820.00040.01910.00570.149-8.9515.4272-40.9762
110.3347-0.50461.32584.7643-2.10095.2812-0.00980.06620.02470.0797-0.1032-0.1513-0.0940.28940.1130.1384-0.00820.01720.17060.00520.25-5.7425-1.5966-18.254
121.51150.0286-1.0110.4676-0.2310.26490.0275-0.15350.04180.0369-0.0085-0.0133-0.06140.3023-0.0190.1659-0.0064-0.00970.0198-0.00360.1618-9.665-5.40656.0189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 7
2X-RAY DIFFRACTION2A8 - 29
3X-RAY DIFFRACTION3A30 - 37
4X-RAY DIFFRACTION4A38 - 80
5X-RAY DIFFRACTION5B-6 - 7
6X-RAY DIFFRACTION6B8 - 29
7X-RAY DIFFRACTION7B30 - 37
8X-RAY DIFFRACTION8B38 - 80
9X-RAY DIFFRACTION9C-6 - 7
10X-RAY DIFFRACTION10C8 - 29
11X-RAY DIFFRACTION11C30 - 37
12X-RAY DIFFRACTION12C38 - 80

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