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- PDB-6cw2: Crystal structure of a yeast SAGA transcriptional coactivator Ada... -

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Basic information

Entry
Database: PDB / ID: 6cw2
TitleCrystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 1
Components
  • Histone acetyltransferase GCN5
  • Transcriptional adapter 2
  • antibody heavy chain
  • antibody light chain
KeywordsGENE REGULATION / Ada2/Gcn5 structure
Function / homology
Function and homology information


ADA complex / SAGA-type complex / histone crotonyltransferase activity / SLIK (SAGA-like) complex / histone H3 acetyltransferase activity / replication-born double-strand break repair via sister chromatid exchange / rDNA heterochromatin formation / SAGA complex / protein-lysine-acetyltransferase activity / phosphatidylserine binding ...ADA complex / SAGA-type complex / histone crotonyltransferase activity / SLIK (SAGA-like) complex / histone H3 acetyltransferase activity / replication-born double-strand break repair via sister chromatid exchange / rDNA heterochromatin formation / SAGA complex / protein-lysine-acetyltransferase activity / phosphatidylserine binding / histone reader activity / Estrogen-dependent gene expression / histone acetyltransferase complex / chromosome, centromeric region / Ub-specific processing proteases / subtelomeric heterochromatin formation / histone acetyltransferase activity / histone acetyltransferase / : / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / chromatin organization / transcription coactivator activity / chromosome, telomeric region / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytosol
Similarity search - Function
Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / : / Transcriptional adapter 2-alpha-like domain / Histone acetyltransferase GCN5 / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain ...Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / : / Transcriptional adapter 2-alpha-like domain / Histone acetyltransferase GCN5 / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / SAGA complex subunit ADA2 / Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsSun, J. / Paduch, M. / Kim, S.A. / Kramer, R.M. / Barrios, A.F. / Lu, V. / Luke, J. / Usatyuk, S. / Kossiakoff, A.A. / Tan, S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088236 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111651 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM094588 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM072688 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54HG006436 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2.
Authors: Sun, J. / Paduch, M. / Kim, S.A. / Kramer, R.M. / Barrios, A.F. / Lu, V. / Luke, J. / Usatyuk, S. / Kossiakoff, A.A. / Tan, S.
History
DepositionMar 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Histone acetyltransferase GCN5
C: Transcriptional adapter 2
A: antibody heavy chain
B: antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9706
Polymers90,8394
Non-polymers1312
Water91951
1
A: antibody heavy chain
B: antibody light chain


Theoretical massNumber of molelcules
Total (without water)47,9522
Polymers47,9522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-36 kcal/mol
Surface area18040 Å2
MethodPISA
2
D: Histone acetyltransferase GCN5
C: Transcriptional adapter 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0174
Polymers42,8862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-26 kcal/mol
Surface area18980 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10770 Å2
ΔGint-73 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.816, 191.816, 92.674
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules DC

#1: Protein Histone acetyltransferase GCN5


Mass: 29081.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GCN5, ADA4, SWI9, YGR252W / Plasmid: PST44 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: Q03330, histone acetyltransferase
#2: Protein Transcriptional adapter 2


Mass: 13804.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ADA2, SCKG_0090 / Plasmid: PST44 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: A0A250W8G8, UniProt: Q02336*PLUS

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Antibody , 2 types, 2 molecules AB

#3: Antibody antibody heavy chain


Mass: 24548.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody antibody light chain


Mass: 23403.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 53 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 5.52 Å3/Da / Density % sol: 77.72 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 8.5
Details: 10 mM Tris-Cl pH 8.5, 200 mM Li2SO4, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.67→166.12 Å / Num. obs: 55876 / % possible obs: 100 % / Redundancy: 20.1 % / Rpim(I) all: 0.045 / Net I/σ(I): 15.4
Reflection shellResolution: 2.67→2.75 Å / Redundancy: 19.9 % / Num. unique obs: 4546 / Rpim(I) all: 0.947 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→95.908 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2838 2712 4.87 %
Rwork0.2501 53001 -
obs0.2517 55713 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245 Å2 / Biso mean: 86.9959 Å2 / Biso min: 42.37 Å2
Refinement stepCycle: final / Resolution: 2.67→95.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5895 0 2 51 5948
Biso mean--91.51 67.45 -
Num. residues----772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096043
X-RAY DIFFRACTIONf_angle_d1.7338221
X-RAY DIFFRACTIONf_chiral_restr0.073916
X-RAY DIFFRACTIONf_plane_restr0.0111051
X-RAY DIFFRACTIONf_dihedral_angle_d15.2712130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6702-2.71870.36521510.30722688283997
2.7187-2.7710.29981160.29752785290199
2.771-2.82760.32651450.28432730287599
2.8276-2.88910.29341440.273227792923100
2.8891-2.95630.33561450.276427582903100
2.9563-3.03020.34421460.264327642910100
3.0302-3.11210.29331530.255927832936100
3.1121-3.20370.28551430.239127692912100
3.2037-3.30710.24971280.245628112939100
3.3071-3.42530.2791180.234928052923100
3.4253-3.56250.3151800.246727522932100
3.5625-3.72460.31371300.255527802910100
3.7246-3.9210.29121550.248727842939100
3.921-4.16670.27951280.236328232951100
4.1667-4.48840.23831390.21227762915100
4.4884-4.940.23551410.222728322973100
4.94-5.65480.2771090.234128452954100
5.6548-7.12410.27851570.27128433000100
7.1241-95.96990.30021840.28328943078100
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)
13.39212.97850.46455.47120.7915.3445-0.6748-0.2813-1.04190.60380.491-0.18270.8590.80570.27910.92090.2392-0.00990.7804-0.17560.844539.3594106.7664-9.4437
22.45772.1292-1.55667.7157-0.06382.75130.02280.16690.00370.87040.5199-0.6242-0.1727-0.3687-0.47650.65330.36690.05481.07-0.02060.579227.071687.6286-3.1244
33.10940.1529-0.47622.519-0.40793.62030.1316-0.10920.14790.07320.09410.623-0.2225-1.2406-0.2280.55480.25770.07971.02740.04930.685216.680283.6239-9.4367
43.11651.0586-1.02913.53472.352.87730.0117-0.0019-0.3437-0.2070.22770.507-0.4982-0.7141-0.25470.63220.34310.04970.99950.04930.608922.351190.5454-20.9035
50.2723-0.6036-1.02865.57171.40123.879-0.3176-0.033-0.0533-0.5852-0.15431.0333-0.1554-1.1780.4080.68120.2269-0.01711.1179-0.05130.750220.721986.0445-26.6315
60.2942-0.4830.25436.6151-1.26970.26450.2209-0.11790.2047-0.1739-0.6598-1.3203-0.10530.0520.37680.88630.35480.14920.7955-0.04120.872437.8414120.8705-21.2401
74.42232.42412.84325.84340.22969.3296-0.03111.4548-0.81890.95510.7885-1.72840.5599-0.3505-0.92211.11920.0284-0.04620.5827-0.09720.927834.1497138.3879-32.1168
83.46891.8996-2.99274.0743-0.16013.2920.6368-0.5543-0.9781-0.38310.01290.32130.54210.6371-0.19871.00450.21790.00940.4672-0.01950.987523.3759128.9692-27.0851
93.86523.67242.26993.85872.65442.00060.7049-0.8463-0.6590.7414-0.41340.26951.00750.2177-0.10681.16480.256-0.09310.56290.05260.858129.5303131.3966-19.2119
104.79341.5636-2.44744.65173.50456.0621-0.19890.2940.69460.4077-0.3261-0.2561-1.0541-0.12090.48971.20020.08810.05160.57260.16020.955928.4223139.9734-19.8646
110.9924-2.1142-1.11214.61532.6812.002-0.11330.35450.8289-0.8989-0.7316-0.168-0.65450.25360.85641.21960.37440.01590.77620.01621.120436.5522119.7185-31.946
126.98712.5106-3.34392.67981.69467.33450.61650.40410.02420.48310.2163-1.0988-1.9624-1.2751-0.72481.02040.38030.11170.84380.12090.744329.9768110.2617-25.8088
138.93850.6365-3.03093.99661.75852.0224-0.23811.31710.4506-0.6062-0.12620.5439-0.7087-1.32530.26160.82090.49370.01150.9622-0.03410.606527.798103.6112-31.6453
142.7332-3.3546-0.44354.9816-0.77562.53560.87820.16520.1161-1.2868-0.5447-0.2061-1.1548-0.4316-0.40590.7750.2990.10510.7429-0.12630.618343.5501102.602-27.1967
153.3299-2.7799-0.00252.5431-1.11745.115-0.7213-1.3472-0.31421.04580.65960.49690.55091.2447-0.14770.70750.45870.15791.13440.0470.698656.856173.0008-11.9792
164.216-1.47040.46423.7137-0.78651.4796-0.3569-0.9573-0.14030.48970.2431-0.121-0.17-0.3960.09580.73690.44370.09041.02890.06920.600848.418579.8739-12.7619
173.1953-3.71640.27286.381-1.07371.1781-0.2362-0.4910.0005-0.14440.2144-0.14850.21320.1967-00.58570.26840.02090.83240.03040.405951.370979.5766-17.6839
183.1741-1.4868-1.22051.06670.71910.516-0.00930.0388-0.3818-0.2115-0.332-0.10370.46821.25450.31330.89630.63960.14281.60920.24610.832874.710760.059-22.2512
195.68514.62883.71035.3132.23545.72060.5355-0.0854-0.82321.23750.2935-1.06750.68610.4134-0.61260.75390.4110.0351.3652-0.06510.727374.503965.957-26.5149
207.2959-1.1072-4.55182.34370.02793.03730.14510.30420.1481-0.0074-0.2949-0.94220.62811.91340.32380.79180.47070.08271.93270.32120.846580.699963.1189-25.3459
213.5417-0.2285-2.98692.09610.97542.8389-0.2983-0.73350.1643-0.3645-0.403-0.12630.11351.83720.63290.94460.61170.08361.66860.18770.68176.219461.8373-14.8517
224.4165-0.881-1.3891.75590.23334.0902-0.13550.3947-0.27290.1209-0.00780.1497-0.05190.45720.11470.55960.20280.04170.831-0.04450.542151.987385.5893-36.0703
237.5022-1.0103-4.51032.9324-0.10194.2258-0.6821-0.2501-0.2130.01450.29360.04090.2080.49580.45390.54550.1974-0.04920.8966-0.0480.511952.169581.9102-32.8456
240.5923-0.3722-0.48271.49090.41770.3543-0.1911-0.289-0.1213-0.0759-0.0946-1.07490.86031.0024-0.08841.06311.02690.37751.79690.00920.609775.060261.6513-35.6707
250.6388-0.95811.36126.907-3.07513.02010.11250.2138-0.2516-0.42470.29880.08290.8720.1523-0.30790.97790.44590.15751.23260.08180.705372.763758.1995-40.0746
263.94520.7834-2.68762.1479-0.96824.05010.2048-0.1933-0.0194-0.3938-0.2355-0.49470.69441.2353-0.18310.80370.51760.13051.47520.02260.651570.144768.5496-36.6331
271.0297-1.4133-0.55594.12741.62150.636-0.33740.4178-1.2049-1.8153-0.26830.63191.98430.17930.64941.84570.56080.33341.1822-0.17381.020474.514652.9816-38.3577
281.7177-0.7987-0.56950.92030.74830.6017-0.2676-0.053-0.9914-0.1932-0.11910.00090.57650.2923-0.13481.73970.92640.50411.76450.17251.252980.766252.0353-43.0358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 72 through 89 )D72 - 89
2X-RAY DIFFRACTION2chain 'D' and (resid 90 through 110 )D90 - 110
3X-RAY DIFFRACTION3chain 'D' and (resid 111 through 187 )D111 - 187
4X-RAY DIFFRACTION4chain 'D' and (resid 188 through 233 )D188 - 233
5X-RAY DIFFRACTION5chain 'D' and (resid 234 through 259 )D234 - 259
6X-RAY DIFFRACTION6chain 'D' and (resid 260 through 298 )D260 - 298
7X-RAY DIFFRACTION7chain 'D' and (resid 299 through 312 )D299 - 312
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 18 )C6 - 18
9X-RAY DIFFRACTION9chain 'C' and (resid 19 through 31 )C19 - 31
10X-RAY DIFFRACTION10chain 'C' and (resid 32 through 49 )C32 - 49
11X-RAY DIFFRACTION11chain 'C' and (resid 50 through 66 )C50 - 66
12X-RAY DIFFRACTION12chain 'C' and (resid 67 through 80 )C67 - 80
13X-RAY DIFFRACTION13chain 'C' and (resid 81 through 107 )C81 - 107
14X-RAY DIFFRACTION14chain 'C' and (resid 108 through 120 )C108 - 120
15X-RAY DIFFRACTION15chain 'A' and (resid 4 through 20 )A4 - 20
16X-RAY DIFFRACTION16chain 'A' and (resid 21 through 86 )A21 - 86
17X-RAY DIFFRACTION17chain 'A' and (resid 87 through 138 )A87 - 138
18X-RAY DIFFRACTION18chain 'A' and (resid 139 through 173 )A139 - 173
19X-RAY DIFFRACTION19chain 'A' and (resid 174 through 191 )A174 - 191
20X-RAY DIFFRACTION20chain 'A' and (resid 192 through 217 )A192 - 217
21X-RAY DIFFRACTION21chain 'A' and (resid 218 through 232 )A218 - 232
22X-RAY DIFFRACTION22chain 'B' and (resid 1 through 76 )B1 - 76
23X-RAY DIFFRACTION23chain 'B' and (resid 77 through 102 )B77 - 102
24X-RAY DIFFRACTION24chain 'B' and (resid 103 through 130 )B103 - 130
25X-RAY DIFFRACTION25chain 'B' and (resid 131 through 159 )B131 - 159
26X-RAY DIFFRACTION26chain 'B' and (resid 160 through 175 )B160 - 175
27X-RAY DIFFRACTION27chain 'B' and (resid 176 through 199 )B176 - 199
28X-RAY DIFFRACTION28chain 'B' and (resid 200 through 215 )B200 - 215

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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