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- PDB-3bts: Crystal structure of a ternary complex of the transcriptional rep... -

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Basic information

Entry
Database: PDB / ID: 3bts
TitleCrystal structure of a ternary complex of the transcriptional repressor Gal80p (Gal80S0 [G301R]) and the acidic activation domain of Gal4p (aa 854-874) from Saccharomyces cerevisiae with NAD
Components
  • Galactose/lactose metabolism regulatory protein GAL80
  • Regulatory protein GAL4
KeywordsTRANSCRIPTION / Eukaryotic transcription complex / NAD / Rossmann fold / Acetylation / Carbohydrate metabolism / DNA-binding / Galactose metabolism / Repressor / Transcription regulation / Activator / Metal-binding / Nucleus / Phosphoprotein / Zinc
Function / homology
Function and homology information


regulation of transcription from RNA polymerase II promoter by galactose / kinase inhibitor activity / galactose metabolic process / negative regulation of phosphorylation / 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 / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific ...regulation of transcription from RNA polymerase II promoter by galactose / kinase inhibitor activity / galactose metabolic process / negative regulation of phosphorylation / 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 / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Gal4 dimerisation domain / Gal4-like dimerisation domain / Fungal specific transcription factor domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / 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 ...Gal4 dimerisation domain / Gal4-like dimerisation domain / Fungal specific transcription factor domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / 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 / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Basic-leucine zipper domain superfamily / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Regulatory protein GAL4 / Galactose/lactose metabolism regulatory protein GAL80
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKumar, P.R. / Joshua-Tor, L.
CitationJournal: Science / Year: 2008
Title: NADP regulates the yeast GAL induction system.
Authors: Kumar, P.R. / Yu, Y. / Sternglanz, R. / Johnston, S.A. / Joshua-Tor, L.
History
DepositionDec 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 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 / 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_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: Galactose/lactose metabolism regulatory protein GAL80
B: Galactose/lactose metabolism regulatory protein GAL80
E: Regulatory protein GAL4
F: Regulatory protein GAL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8516
Polymers102,5244
Non-polymers1,3272
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-30.2 kcal/mol
Surface area32530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.071, 103.431, 106.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Galactose/lactose metabolism regulatory protein GAL80


Mass: 48754.434 Da / Num. of mol.: 2 / Mutation: G301R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GAL80 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: P04387
#2: Protein/peptide Regulatory protein GAL4


Mass: 2507.616 Da / Num. of mol.: 2 / Fragment: S. cerevisiae Gal4p peptide; UNP residues 854-874 / Source method: obtained synthetically / Details: S.cerevisiae Gal4(854-874) was made synthetically / References: UniProt: P04386
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 0.15M Sodium fluoride, followed by soaking in NAD to a final concentration of 5mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 27466 / Num. obs: 27319 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 58.854 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 19.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.87 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BTU

3btu


Resolution: 2.7→46.57 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.884 / SU B: 29.914 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.398 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1394 5.1 %RANDOM
Rwork0.175 ---
obs-27282 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
Refine analyzeLuzzati coordinate error obs: 0.468 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6217 0 88 127 6432
LS refinement shellResolution: 2.7→2.79 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3149 125 -
Rwork0.2102 2429 -
obs--95 %
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)
11.055-0.25820.39861.7287-0.11661.55120.0719-0.1142-0.1301-0.49290.16510.16590.10720.17750.03890.3953-0.0752-0.08020.12990.0440.229617.50499.244830.426
20.31350.36410.46690.47110.14571.2435-0.1099-0.1814-0.0482-0.13180.1386-0.02020.05880.1781-0.00310.11550.02540.04310.16160.0190.252427.23212.499356.4084
30.2093-0.23180.1010.4296-1.31182.4356-0.0329-0.2126-0.1934-0.27510.24080.41440.2856-0.12650.03430.12770.0065-0.05260.18320.07480.407616.35135.480350.1558
40.96080.95390.05071.3383-0.70670.51030.1993-0.5455-0.07320.7752-0.23390.0159-0.2174-0.32840.00010.71310.0690.05170.7503-0.04940.16331.589424.0428104.3504
51.22460.30792.03260.67970.4881.9802-0.0567-0.5331-0.14090.29520.0414-0.04650.0758-0.3647-00.21850.10420.09830.31470.05650.240728.927714.118978.4137
61.02181.35890.30880.6241-0.03351.3511-0.0448-0.51720.18160.1276-0.17190.107-0.2130.088300.47980.13920.01330.4682-0.06570.285936.987926.039985.0628
70.019-0.0274-0.011-0.0478-0.0518-0.0137-0.32720.25750.3791-0.56310.4618-0.2325-0.11170.03430.00030.5584-0.13650.10280.57520.17560.514825.459115.481334.7008
8-0.01390.02660.01530.00320.0046-0.06890.1688-0.4672-0.25510.2244-0.54260.84740.0607-0.21270.00180.9732-0.05020.34241.0941-0.01620.485526.204615.6055100.3703
90.765-0.16980.60673.6326-2.50032.3125-0.4419-0.00020.14550.0957-0.3065-0.9844-0.06440.4211-0.18950.6837-0.1150.09950.3922-0.3660.25436.077114.814241.9223
100.0515-0.05880.00560.1545-0.0290.0295-0.02910.01290.0159-0.0144-0.0440.09390.17280.0038-01.9302-0.9121-0.4811.84851.22451.783828.08878.792493.4042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:155A1 - 155
2X-RAY DIFFRACTION2chain A and resid 156:330A156 - 330
3X-RAY DIFFRACTION3chain A and resid 345:435A345 - 435
4X-RAY DIFFRACTION4chain B and resid 1:155B1 - 155
5X-RAY DIFFRACTION5chain B and resid 156:330B156 - 330
6X-RAY DIFFRACTION6chain B and resid 345:435B345 - 435
7X-RAY DIFFRACTION7chain CC1
8X-RAY DIFFRACTION8chain DD1
9X-RAY DIFFRACTION9chain EE501 - 509
10X-RAY DIFFRACTION10chain FF505 - 509

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