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- PDB-5apx: Sequence MATKDDIAN inserted between GCN4 adaptors - Structure T9(6) -

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Basic information

Entry
Database: PDB / ID: 5apx
TitleSequence MATKDDIAN inserted between GCN4 adaptors - Structure T9(6)
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 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
PHOSPHATE ION / General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / struct_ncs_dom_lim / 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 / _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 / _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)34,1994
Polymers34,1043
Non-polymers951
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-89.7 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.110, 38.250, 105.020
Angle α, β, γ (deg.)90.00, 93.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: 6

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYAA8 - 6734 - 93
2GLYGLYBB8 - 6734 - 93
3VALVALCC8 - 6634 - 92

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.314789, 0.798412, 0.51327), (-0.764241, -0.533897, 0.361787), (0.562888, -0.278375, 0.778244)-7.89187, -4.86931, 3.41776
3given(-0.219355, -0.830033, 0.512766), (0.849643, -0.420855, -0.317787), (0.479573, 0.36596, 0.797548)-7.65417, 4.783, 3.17067

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Components

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


Mass: 11368.084 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM PHOSPHATE, 0.1 M TRIS PH 8.5, 50 %(V/V) MPD

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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
ReflectionResolution: 1.8→34.9 Å / Num. obs: 18191 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.94 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.14 / % possible all: 95.4

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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: 1.8→34.95 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.314 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22597 907 5 %RANDOM
Rwork0.18702 ---
obs0.18893 17282 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.398 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.12 Å2
2--0.16 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 5 122 1577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191462
X-RAY DIFFRACTIONr_bond_other_d0.0010.021543
X-RAY DIFFRACTIONr_angle_refined_deg1.0252.0191954
X-RAY DIFFRACTIONr_angle_other_deg0.6533563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.055176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04226.34963
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09615331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.949156
X-RAY DIFFRACTIONr_chiral_restr0.0440.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
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_it2.787.946713
X-RAY DIFFRACTIONr_mcbond_other2.7797.941712
X-RAY DIFFRACTIONr_mcangle_it3.7213.254886
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.93210.779749
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: 984 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional1.115
2Bloose positional1.155
3Cloose positional15
1Aloose thermal4.7510
2Bloose thermal5.4910
3Cloose thermal5.0210
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 64 -
Rwork0.292 1232 -
obs--97.59 %
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)
112.7373-0.55414.33985.3023-2.6062.5977-0.01390.43460.262-0.03450.00580.04760.0390.15750.00810.39380.0255-0.01730.4427-0.03450.293-21.0827-2.1838-54.1116
23.8125-2.8297-1.62343.1701-0.652215.1128-0.16760.2997-0.0778-0.2523-0.088-0.00980.085-0.23520.25560.48080.0042-0.01490.3963-0.06760.17-17.5903-6.5318-38.6243
35.7711.9376.95571.95912.963312.12630.035-0.01520.17960.0133-0.08480.06490.0557-0.18350.04980.01860.00560.03130.01170.0160.0656-9.5342.88070.3023
42.1351-2.8882.66249.34122.934211.41820.07590.0474-0.2745-0.41660.03520.3811-0.70390.0912-0.11110.5582-0.0196-0.13820.58270.06440.328-29.09993.4574-51.3036
54.62482.88815.02864.7952.004615.1669-0.20080.20770.4553-0.19420.1505-0.04280.1682-0.55480.05030.39310.0271-0.03120.42320.03990.1404-19.85384.7541-38.4053
61.2002-0.0551.81090.75050.212310.84020.0566-0.0269-0.04250.0269-0.01860.02990.1212-0.067-0.0380.0062-0.00030.01520.00270.01340.1181-7.2784-4.384-0.3868
710.45940.6116-9.62561.40991.789312.8927-0.00970.1749-0.4157-0.10830.2586-0.3817-0.23150.2774-0.24890.5734-0.0406-0.00810.4658-0.03360.382-30.2526-6.1915-50.9047
84.4424-2.67442.1053.32073.200413.2645-0.2888-0.0172-0.23560.33330.16990.22970.5678-0.02140.11890.3728-0.0683-0.00110.40790.03380.1867-27.9329-2.8507-35.2943
94.7147-1.29756.18131.8397-1.767312.2029-0.0720.08950.0534-0.0610.0645-0.0255-0.24580.00570.00750.0224-0.00720.03260.0122-0.01210.0861-2.66811.3825-2.766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 14
2X-RAY DIFFRACTION2A15 - 28
3X-RAY DIFFRACTION3A29 - 67
4X-RAY DIFFRACTION4B8 - 14
5X-RAY DIFFRACTION5B15 - 28
6X-RAY DIFFRACTION6B29 - 67
7X-RAY DIFFRACTION7C8 - 14
8X-RAY DIFFRACTION8C15 - 28
9X-RAY DIFFRACTION9C29 - 66

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