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

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Basic information

Entry
Database: PDB / ID: 3crp
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


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 / 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
DepositionApr 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5366
Polymers19,5135
Non-polymers231
Water2,342130
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)15,6335
Polymers15,6104
Non-polymers231
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-60.7 kcal/mol
Surface area7010 Å2
MethodPISA
2
E: GCN4 leucine zipper

E: GCN4 leucine zipper

E: GCN4 leucine zipper

E: GCN4 leucine zipper


Theoretical massNumber of molelcules
Total (without water)15,6104
Polymers15,6104
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
Buried area5530 Å2
ΔGint-57.4 kcal/mol
Surface area6760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.473, 79.473, 54.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assemblies are a hetero-tetramer, and a homo-tetramer generated by symmtry element.

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Components

#1: Protein/peptide GCN4 leucine zipper / Amino acid biosynthesis regulatory protein


Mass: 3902.606 Da / Num. of mol.: 2 / 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 / Amino acid biosynthesis regulatory protein


Mass: 3902.540 Da / Num. of mol.: 3 / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.8
Details: 0.1M Tris-HCl, 0.05M magnesium chloride, 13% PEG 4000, pH 9.8, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 18, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→25.1 Å / Num. all: 19756 / Num. obs: 19756 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 9 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1281 / % possible all: 99.9

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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 2NRN

2nrn


Resolution: 1.7→25.1 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.122 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Isotropic with TLS group assigned for each peptide chain
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23045 1012 5.1 %RANDOM
Rwork0.20274 ---
all0.20419 19756 --
obs0.20419 19756 99.4 %-
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: 37.345 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 1 130 1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221261
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5342.0041685
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6645153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1532655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46115272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.252156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02872
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.2640
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.2889
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2950.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4950.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8731.5783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52621242
X-RAY DIFFRACTIONr_scbond_it2.9413483
X-RAY DIFFRACTIONr_scangle_it4.9384.5443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 70 -
Rwork0.195 1288 -
obs-1358 94.8 %
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)
14.96361.1842-5.66131.4007-1.059719.26680.1958-0.19790.17890.002-0.03270.026-0.23560.1073-0.1631-0.2494-0.01940.0005-0.2189-0.0164-0.300210.61830.05717.143
22.4470.5508-0.20911.9721-1.182810.6364-0.03250.0081-0.0589-0.0606-0.0032-0.0660.3066-0.14080.0357-0.23810.0115-0.0171-0.2073-0.0242-0.268818.17227.517.077
33.0393-1.6822-1.13022.9103-1.746813.14920.06580.06760.0453-0.0647-0.2144-0.1753-0.43780.2890.1486-0.21610.0033-0.0078-0.2255-0.0093-0.268121.85934.82220.723
41.7581-1.45982.11086.1782-5.296415.81090.1055-0.0616-0.0311-0.11260.02280.14780.1344-0.0125-0.1283-0.18170.01770.004-0.2539-0.0019-0.307314.57439.68821.165
52.4699-0.26261.44694.39815.311327.38640.181-0.21980.0266-0.0569-0.00860.3068-0.1932-1.0621-0.1725-0.1469-0.11380.007-0.03990.0207-0.166933.2339.114-0.774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 321 - 32
2X-RAY DIFFRACTION2BB1 - 341 - 34
3X-RAY DIFFRACTION3CC1 - 311 - 31
4X-RAY DIFFRACTION4DD1 - 321 - 32
5X-RAY DIFFRACTION5EE3 - 313 - 31

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