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- PDB-3coq: Structural Basis for Dimerization in DNA Recognition by Gal4 -

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Basic information

Entry
Database: PDB / ID: 3coq
TitleStructural Basis for Dimerization in DNA Recognition by Gal4
Components
  • DNA (5'-D(*DAP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DAP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')
  • DNA (5'-D(*DTP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DTP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')
  • Regulatory protein GAL4
KeywordsTranscription/DNA / helix bundle / Protein-DNA complex / zinc binuclear cluster / Activator / Carbohydrate metabolism / DNA-binding / Galactose metabolism / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Transcription-DNA COMPLEX
Function / homology
Function and homology information


regulation of transcription from RNA polymerase II promoter by galactose / galactose metabolic process / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / zinc ion binding ...regulation of transcription from RNA polymerase II promoter by galactose / galactose metabolic process / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
Gal4 dimerisation domain / Gal4-like dimerisation domain / Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / CD2-Gal4 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily ...Gal4 dimerisation domain / Gal4-like dimerisation domain / Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / CD2-Gal4 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Basic-leucine zipper domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Regulatory protein GAL4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 2.4 Å
AuthorsHong, M. / Fitzgerald, M.X. / Harper, S. / Luo, C. / Speicher, D.W.
CitationJournal: Structure / Year: 2008
Title: Structural basis for dimerization in DNA recognition by gal4.
Authors: Hong, M. / Fitzgerald, M.X. / Harper, S. / Luo, C. / Speicher, D.W. / Marmorstein, R.
History
DepositionMar 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: diffrn / diffrn_radiation_wavelength ...diffrn / diffrn_radiation_wavelength / diffrn_source / entity_src_gen / ndb_struct_na_base_pair / pdbx_entity_src_syn / software
Item: _diffrn_source.pdbx_wavelength_list / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._diffrn_source.pdbx_wavelength_list / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
D: DNA (5'-D(*DAP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DAP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')
E: DNA (5'-D(*DTP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DTP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')
A: Regulatory protein GAL4
B: Regulatory protein GAL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6219
Polymers33,2414
Non-polymers3805
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-70.8 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.495, 40.829, 90.418
Angle α, β, γ (deg.)90.000, 95.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

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DNA chain , 2 types, 2 molecules DE

#1: DNA chain DNA (5'-D(*DAP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DAP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')


Mass: 6144.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*DTP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DTP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3')


Mass: 6126.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules AB

#3: Protein Regulatory protein GAL4


Mass: 10484.505 Da / Num. of mol.: 2
Fragment: DNA binding domain with complete dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GAL4 / Production host: Escherichia coli (E. coli) / References: UniProt: P04386

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Non-polymers , 3 types, 38 molecules

#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 40mM Mg(OAc)2, 25mM sodium phosphate, 5% PEG400, 5% MPD, pH 5.5, VAPOR DIFFUSION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Mg(OAc)211
2sodium phosphate11
3PEG40011
4MPD11
5Mg(OAc)212
6sodium phosphate12
7PEG40012
8MPD12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.2823,1.2830,1.2448
SYNCHROTRONCHESS F12
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.28231
21.2831
31.24481
ReflectionResolution: 2.4→50 Å / Num. obs: 18311 / % possible obs: 98.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.066 / Χ2: 1.079 / Net I/σ(I): 16.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.417 / Num. unique all: 1758 / Χ2: 0.963 / % possible all: 97

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALEPACKdata scaling
CNSrefinement
SOLVEphasing
DENZOdata reduction
PDB_EXTRACT3.005data extraction
HKL-2000data collection
CNSphasing
RefinementResolution: 2.4→28.94 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 21.794 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.457 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1304 9.3 %RANDOM
Rwork0.207 ---
obs0.213 14040 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.172 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.23 Å2
2---0.17 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 814 12 33 2313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222391
X-RAY DIFFRACTIONr_angle_refined_deg3.3372.4323380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3185176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99523.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.66615330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7431514
X-RAY DIFFRACTIONr_chiral_restr0.1740.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021440
X-RAY DIFFRACTIONr_nbd_refined0.2970.21047
X-RAY DIFFRACTIONr_nbtor_refined0.3410.21527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.27
X-RAY DIFFRACTIONr_mcbond_it1.6041.5933
X-RAY DIFFRACTIONr_mcangle_it2.63221446
X-RAY DIFFRACTIONr_scbond_it3.05331933
X-RAY DIFFRACTIONr_scangle_it4.4564.51934
LS refinement shellResolution: 2.4→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 96 -
Rwork0.386 889 -
all-985 -
obs--92.23 %
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)
13.9151-1.2409-1.63910.8944-0.18133.66020.00840.3831-0.47620.3413-0.3943-0.14640.2909-0.26950.38590.0046-0.018-0.0243-0.40230.01190.088626.554711.482119.8274
22.6633-1.131.56991.8362-1.16334.13810.01390.25030.42750.3904-0.45590.08-0.3453-0.01350.4420.00990.0420.0188-0.272-0.03880.02529.431529.8245119.8894
38.347-2.9739-0.12012.970.16230.94130.26891.2570.1994-0.0638-0.4235-0.11650.0590.11430.1545-0.16070.2189-0.0140.28170.1032-0.234919.86921.5164100.909
46.9143-3.29030.88843.31320.19240.84880.26751.11530.1416-0.1083-0.36820.05240.02350.02110.1008-0.16760.18640.03110.29450.0468-0.252916.153122.3954100.8826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 96
2X-RAY DIFFRACTION2B8 - 96
3X-RAY DIFFRACTION3D1 - 20
4X-RAY DIFFRACTION4E21 - 40

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