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- PDB-3ck4: A heterospecific leucine zipper tetramer -

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Basic information

Entry
Database: PDB / ID: 3ck4
TitleA heterospecific leucine zipper tetramer
Components(GCN4 leucine zipper) x 2
KeywordsPROTEIN BINDING / Coiled coils / anti-parallel tetramer / protein complex / heterospecific interaction / Activator / Amino-acid biosynthesis / DNA-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation
Function / homology
Function and homology information


nitrogen catabolite activation of transcription from RNA polymerase II promoter / 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 ...nitrogen catabolite activation of transcription from RNA polymerase II promoter / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, J.
CitationJournal: Chem.Biol. / Year: 2008
Title: A heterospecific leucine zipper tetramer.
Authors: Deng, Y. / Liu, J. / Zheng, Q. / Li, Q. / Kallenbach, N.R. / Lu, M.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN4 leucine zipper
B: GCN4 leucine zipper
C: GCN4 leucine zipper
D: GCN4 leucine zipper
E: GCN4 leucine zipper
F: GCN4 leucine zipper
G: GCN4 leucine zipper
H: GCN4 leucine zipper
I: GCN4 leucine zipper
J: GCN4 leucine zipper
K: GCN4 leucine zipper
L: GCN4 leucine zipper
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,93816
Polymers47,84112
Non-polymers974
Water7,296405
1
A: GCN4 leucine zipper
B: GCN4 leucine zipper
C: GCN4 leucine zipper
D: GCN4 leucine zipper
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9715
Polymers15,9474
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-69 kcal/mol
Surface area7400 Å2
MethodPISA
2
E: GCN4 leucine zipper
F: GCN4 leucine zipper
G: GCN4 leucine zipper
H: GCN4 leucine zipper
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9715
Polymers15,9474
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-70.8 kcal/mol
Surface area7390 Å2
MethodPISA
3
I: GCN4 leucine zipper
J: GCN4 leucine zipper
K: GCN4 leucine zipper
L: GCN4 leucine zipper
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9966
Polymers15,9474
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-66.7 kcal/mol
Surface area7420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.846, 49.107, 51.917
Angle α, β, γ (deg.)115.77, 94.21, 109.62
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a hetero-tetramer.

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Components

#1: Protein/peptide
GCN4 leucine zipper


Mass: 3986.765 Da / Num. of mol.: 6 / Fragment: UNP residues 251-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GCN4, AAS3, ARG9 / Plasmid: pAE4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03069
#2: Protein/peptide
GCN4 leucine zipper


Mass: 3986.699 Da / Num. of mol.: 6 / Fragment: UNP residues 251-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GCN4, AAS3, ARG9 / Plasmid: pAE4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03069
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M magnesium chloride, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9786 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 23, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→45.2 Å / Num. all: 41918 / Num. obs: 41918 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4137 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B22

2b22


Resolution: 1.7→45.18 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.327 / SU ML: 0.075
Isotropic thermal model: Isotropic with TLS group assigned for each peptide chain
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22062 2111 5 %RANDOM
Rwork0.17055 ---
all0.173 41918 --
obs0.17305 41918 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.554 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.32 Å20 Å2
2---0.19 Å20.05 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 4 405 3572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223175
X-RAY DIFFRACTIONr_angle_refined_deg1.5372.0114252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8865375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99125.797138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09315710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5421517
X-RAY DIFFRACTIONr_chiral_restr0.0980.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022161
X-RAY DIFFRACTIONr_nbd_refined0.2090.21631
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2257
X-RAY DIFFRACTIONr_metal_ion_refined0.110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.223
X-RAY DIFFRACTIONr_mcbond_it0.9771.51968
X-RAY DIFFRACTIONr_mcangle_it1.45323118
X-RAY DIFFRACTIONr_scbond_it2.66831314
X-RAY DIFFRACTIONr_scangle_it4.2274.51134
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 130 -
Rwork0.222 2736 -
obs-2866 88.5 %
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)
12.4415-1.36263.35994.6645-4.610918.92570.06680.14040.0881-0.13090.0040.0303-0.33530.0135-0.0708-0.18980.01370.0291-0.2159-0.0019-0.103544.81415.7864.123
22.155-0.81991.17524.1398-4.109213.34080.1650.30820.0524-0.208-0.0910.0049-0.18650.2768-0.0741-0.19390.0168-0.0206-0.1478-0.0234-0.130948.8099.398-0.238
31.9016-0.1846-0.56171.8807-2.20859.44770.01260.2288-0.2086-0.1731-0.04630.07140.2562-0.00050.0337-0.190.0096-0.0266-0.1818-0.0288-0.124841.0623.345-1.388
43.7852-0.7644-0.17621.9227-0.945818.9747-0.00810.3538-0.0315-0.1341-0.15370.14470.0045-0.45880.1619-0.2071-0.001-0.0146-0.1818-0.0187-0.099335.6649.2880.935
53.91242.29444.97026.59139.950720.4243-0.12990.283-0.1625-0.14090.3061-0.1731-0.07490.5978-0.1762-0.2003-0.01860.0448-0.14550-0.137724.5644.8367.199
62.75681.76892.72416.11726.147611.30740.0825-0.0491-0.15040.18220.0679-0.07830.23290.1561-0.1504-0.2145-0.00570.0136-0.19270.0517-0.173417.2191.4429.644
74.08394.27313.55829.15567.885310.26320.0358-0.04950.131-0.0531-0.23240.1989-0.0856-0.1670.1966-0.22010.0103-0.0034-0.18320.0551-0.20811.3577.8345.407
84.30185.21167.907510.185913.318521.5179-0.08680.33250.1135-0.50950.278-0.2162-0.65550.493-0.1912-0.1242-0.0480.0496-0.10650.0455-0.148216.97911.875-0.17
914.47731.10677.90572.06490.10776.7665-0.1623-0.49040.18410.1732-0.00970.186-0.061-0.16660.172-0.13470.01210.0497-0.2180.0098-0.15132.83931.17915.681
107.3558-0.4062.04382.1044-0.18922.2856-0.0666-0.18350.06310.120.02690.069-0.0281-0.01160.0397-0.1397-0.00280.0067-0.24070.002-0.192433.31338.02610.773
118.204-1.6953.0122.1919-0.98334.0030.0340.3901-0.0736-0.1503-0.09-0.01950.10360.15810.056-0.1217-0.0210.0192-0.2112-0.0286-0.183738.16732.9772.959
1210.7373-2.49447.63282.8551-1.71347.1710.1120.3779-0.2517-0.242-0.12760.27750.25770.01610.0155-0.1074-0.01740.0187-0.1634-0.0502-0.101733.23325.8323.526
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 311 - 31
2X-RAY DIFFRACTION2BB2 - 332 - 33
3X-RAY DIFFRACTION3CC1 - 341 - 34
4X-RAY DIFFRACTION4DD2 - 342 - 34
5X-RAY DIFFRACTION5EE2 - 322 - 32
6X-RAY DIFFRACTION6FF1 - 341 - 34
7X-RAY DIFFRACTION7GG1 - 331 - 33
8X-RAY DIFFRACTION8HH2 - 312 - 31
9X-RAY DIFFRACTION9II1 - 311 - 31
10X-RAY DIFFRACTION10JJ1 - 341 - 34
11X-RAY DIFFRACTION11KK2 - 342 - 34
12X-RAY DIFFRACTION12LL1 - 311 - 31

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