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- EMDB-3824: Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 -

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Basic information

Entry
Database: EMDB / ID: EMD-3824
TitleCryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1
Map data
Sample
  • Complex: Tra1 - Transcription-associated protein 1
    • Protein or peptide: Transcription-associated protein 1
KeywordsCoactivator / PIKK / SAGA / NuA4 / TRANSCRIPTION
Function / homology
Function and homology information


SLIK (SAGA-like) complex / SAGA complex / NuA4 histone acetyltransferase complex / Ub-specific processing proteases / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / : / PIK-related kinase, FAT / FAT domain / FATC domain / PIK-related kinase / FAT domain profile. ...Tra1, HEAT repeat ring region / Tra1, HEAT repeat central region / Tra1 HEAT repeat central region / Tra1 HEAT repeat ring region / : / PIK-related kinase, FAT / FAT domain / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Transcription-associated protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDiaz-Santin LM / Lukoyanova N
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust102535/Z/13/Z United Kingdom
Royal SocietyRG140138 United Kingdom
CitationJournal: Elife / Year: 2017
Title: Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution.
Authors: Luis Miguel Díaz-Santín / Natasha Lukoyanova / Emir Aciyan / Alan Cm Cheung /
Abstract: Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the ...Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the Phosphoinositide 3-Kinase-related kinase (PIKK) family and a direct target for multiple sequence-specific activators. We present the Cryo-EM structure of Tra1 to 3.7 Å resolution, revealing an extensive network of alpha-helical solenoids organized into a diamond ring conformation and is strikingly reminiscent of DNA-PKcs, suggesting a direct role for Tra1 in DNA repair. The structure was fitted into an existing SAGA EM reconstruction and reveals limited contact surfaces to Tra1, hence it does not act as a molecular scaffold within SAGA. Mutations that affect activator targeting are distributed across the Tra1 structure, but also cluster within the N-terminal Finger region, indicating the presence of an activator interaction site. The structure of Tra1 is a key milestone in deciphering the mechanism of multiple coactivator complexes.
History
DepositionJul 24, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseAug 9, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ojs
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3824.png

Downloads & links

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Map

FileDownload / File: emd_3824.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 290 pix.
= 307.4 Å		1.06 Å/pix.
x 290 pix.
= 307.4 Å		1.06 Å/pix.
x 290 pix.
= 307.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.122903876 - 0.20766993
Average (Standard dev.)0.0005694987 (±0.005844923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 307.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z290290290
origin x/y/z0.0000.0000.000
length x/y/z307.400307.400307.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS290290290
D min/max/mean-0.1230.2080.001

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Supplemental data

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Sample components

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Entire : Tra1 - Transcription-associated protein 1

EntireName: Tra1 - Transcription-associated protein 1
Components
  • Complex: Tra1 - Transcription-associated protein 1
    • Protein or peptide: Transcription-associated protein 1

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Supramolecule #1: Tra1 - Transcription-associated protein 1

SupramoleculeName: Tra1 - Transcription-associated protein 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 433 KDa

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Macromolecule #1: Transcription-associated protein 1

MacromoleculeName: Transcription-associated protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 436.527281 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKMSLTEQI EQFASRFRDD DATLQSRYST LSELYDIMEL LNSPEDYHFF LQAVIPLLLN QLKEVPISY DAHSPEQKLR NSMLDIFNRC LMNQTFQPYA MEVLEFLLSV LPKENEENGI LCMKVLTTLF KSFKSILQDK L DSFIRIII ...String:
MDYKDHDGDY KDHDIDYKDD DDKMSLTEQI EQFASRFRDD DATLQSRYST LSELYDIMEL LNSPEDYHFF LQAVIPLLLN QLKEVPISY DAHSPEQKLR NSMLDIFNRC LMNQTFQPYA MEVLEFLLSV LPKENEENGI LCMKVLTTLF KSFKSILQDK L DSFIRIII QIYKNTPNLI NQTFYEAGKA EQGDLDSPKE PQADELLDEF SKNDEEKDFP SKQSSTEPRF ENSTSSNGLR SS MFSFKIL SECPITMVTL YSSYKQLTST SLPEFTPLIM NLLNIQIKQQ QEAREQAESR GEHFTSISTE IINRPAYCDF ILA QIKATS FLAYVFIRGY APEFLQDYVN FVPDLIIRLL QDCPSELSSA RKELLHATRH ILSTNYKKLF LPKLDYLFDE RILI GNGFT MHETLRPLAY STVADFIHNI RSELQLSEIE KTIKIYTGYL LDESLALTVQ IMSAKLLLNL VERILKLGKE NPQEA PRAK KLLMIIIDSY MNRFKTLNRQ YDTIMKYYGR YETHKKEKAE KLKNSIQDND KESEEFMRKV LEPSDDDHLM PQPKKE DIN DSPDVEMTES DKVVKNDVEM FDIKNYAPIL LLPTPTNDPI KDAFYLYRTL MSFLKTIIHD LKVFNPPPNE YTVANPK LW ASVSRVFSYE EVIVFKDLFH ECIIGLKFFK DHNEKLSPET TKKHFDISMP SLPVSATKDA RELMDYLAFM FMQMDNAT F NEIIEQELPF VYERMLEDSG LLHVAQSFLT SEITSPNFAG ILLRFLKGKL KDLGNVDFNT SNVLIRLFKL SFMSVNLFP NINEVVLLPH LNDLILNSLK YSTTAEEPLV YFYLIRTLFR SIGGGRFENL YRSIKPILQV LLQSLNQMIL TARLPHEREL YVELCITVP VRLSVLAPYL PFLMKPLVFA LQQYPDLVSQ GLRTLELCID NLTAEYFDPI IEPVIDDVSK ALFNLLQPQP F NHAISHNV VRILGKLGGR NRQFLKPPTD LTEKTELDID AIADFKINGM PEDVPLSVTP GIQSALNILQ SYKSDIHYRK SA YKYLTCV LLLMTKSSAE FPTNYTELLK TAVNSIKLER IGIEKNFDLE PTVNKRDYSN QENLFLRLLE SVFYATSIKE LKD DAMDLL NNLLDHFCLL QVNTTLLNKR NYNGTFNIDL KNPNFMLDSS LILDAIPFAL SYYIPEVREV GVLAYKRIYE KSCL IYGEE LALSHSFIPE LAKQFIHLCY DETYYNKRGG VLGIKVLIDN VKSSSVFLKK YQYNLANGLL FVLKDTQSEA PSAIT DSAE KLLIDLLSIT FADVKEEDLG NKVLENTLTD IVCELSNANP KVRNACQKSL HTISNLTGIP IVKLMDHSKQ FLLSPI FAK PLRALPFTMQ IGNVDAITFC LSLPNTFLTF NEELFRLLQE SIVLADAEDE SLSTNIQKTT EYSTSEQLVQ LRIACIK LL AIALKNEEFA TAQQGNIRIR ILAVFFKTML KTSPEIINTT YEALKGSLAE NSKLPKELLQ NGLKPLLMNL SDHQKLTV P GLDALSKLLE LLIAYFKVEI GRKLLDHLTA WCRVEVLDTL FGQDLAEQMP TKIIVSIINI FHLLPPQADM FLNDLLLKV MLLERKLRLQ LDSPFRTPLA RYLNRFHNPV TEYFKKNMTL RQLVLFMCNI VQRPEAKELA EDFEKELDNF YDFYISNIPK NQVRVVSFF TNMVDLFNTM VITNGDEWLK KKGNMILKLK DMLNLTLKTI KENSFYIDHL QLNQSIAKFQ ALYLRFTELS E RDQNPLLL DFIDFSFSNG IKASYSLKKF IFHNIIASSN KEKQNNFIND ATLFVLSDKC LDARIFVLKN VINSTLIYEV AT SGSLKSY LVEDKKPKWL ELLHNKIWKN SNAILAYDVL DHHDLFRFEL LQLSAIFIKA DPEIIAEIKK DIIKFCWNFI KLE DTLIKQ SAYLVTSYFI SKFDFPIKVV TQVFVALLRS SHVEARYLVK QSLDVLTPVL HERMNAAGTP DTWINWVKRV MVEN SSSQN NILYQFLISH PDLFFNSRDL FISNIIHHMN KITFMSNSNS DSHTLAIDLA SLILYWENKT LEITNVNNTK TDSDG DVVM SDSKSDINPV EADTTAIIVD ANNNSPISLH LREACTAFLI RYVCASNHRA IETELGLRAI NILSELISDK HWTNVN VKL VYFEKFLIFQ DLDSENILYY CMNALDVLYV FFKNKTKEWI MENLPTIQNL LEKCIKSDHH DVQEALQKVL QVIMKAI KA QGVSVIIEEE SPGKTFIQML TSVITQDLQE TSSVTAGVTL AWVLFMNFPD NIVPLLTPLM KTFSKLCKDH LSISQPKD A MALEEARITT KLLEKVLYIL SLKVSLLGDS RRPFLSTVAL LIDHSMDQNF LRKIVNMSRS WIFNTEIFPT VKEKAAILT KMLAFEIRGE PSLSKLFYEI VLKLFDQEHF NNTEITVRME QPFLVGTRVE DIGIRKRFMT ILDNSLERDI KERLYYVIRD QNWEFIADY PWLNQALQLL YGSFNREKEL SLKNIYCLSP PSILQEYLPE NAEMVTEVND LELSNFVKGH IASMQGLCRI I SSDFIDSL IEIFYQDPKA IHRAWVTLFP QVYKSIPKNE KYGFVRSIIT LLSKPYHTRQ ISSRTNVINM LLDSISKIES LE LPPHLVK YLAISYNAWY QSINILESIQ SNTSIDNTKI IEANEDALLE LYVNLQEEDM FYGLWRRRAK YTETNIGLSY EQI GLWDKA QQLYEVAQVK ARSGALPYSQ SEYALWEDNW IQCAEKLQHW DVLTELAKHE GFTDLLLECG WRVADWNSDR DALE QSVKS VMDVPTPRRQ MFKTFLALQN FAESRKGDQE VRKLCDEGIQ LSLIKWVSLP IRYTPAHKWL LHGFQQYMEF LEATQ IYAN LHTTTVQNLD SKAQEIKRIL QAWRDRLPNT WDDVNMWNDL VTWRQHAFQV INNAYLPLIP ALQQSNSNSN INTHAY RGY HEIAWVINRF AHVARKHNMP DVCISQLARI YTLPNIEIQE AFLKLREQAK CHYQNMNELT TGLDVISNTN LVYFGTV QK AEFFTLKGMF LSKLRAYEEA NQAFATAVQI DLNLAKAWAQ WGFFNDRRLS EEPNNISFAS NAISCYLQAA GLYKNSKI R ELLCRILWLI SIDDASGMLT NAFDSFRGEI PVWYWITFIP QLLTSLSHKE ANMVRHILIR IAKSYPQALH FQLRTTKED FAVIQRQTMA VMGDKPDTND RNGRRQPWEY LQELNNILKT AYPLLALSLE SLVAQINDRF KSTTDEDLFR LINVLLIDGT LNYNRLPFP RKNPKLPENT EKNLVKFSTT LLAPYIRPKF NADFIDNKPD YETYIKRLRY WRRRLENKLD RASKKENLEV L CPHLSNFH HQKFEDIEIP GQYLLNKDNN VHFIKIARFL PTVDFVRGTH SSYRRLMIRG HDGSVHSFAV QYPAVRHSRR EE RMFQLYR LFNKSLSKNV ETRRRSIQFN LPIAIPLSPQ VRIMNDSVSF TTLHEIHNEF CKKKGFDPDD IQDFMADKLN AAH DDALPA PDMTILKVEI FNSIQTMFVP SNVLKDHFTS LFTQFEDFWL FRKQFASQYS SFVFMSYMMM INNRTPHKIH VDKT SGNVF TLEMLPSRFP YERVKPLLKN HDLSLPPDSP IFHNNEPVPF RLTPNIQSLI GDSALEGIFA VNLFTISRAL IEPDN ELNT YLALFIRDEI ISWFSNLHRP IIENPQLREM VQTNVDLIIR KVAQLGHLNS TPTVTTQFIL DCIGSAVSPR NLARTD VNF MPWF

UniProtKB: Transcription-associated protein 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.05 MC8H18N2O4SHepes
0.15 MNaClSodium Chloride
0.0005 MC4H10O2S2DTT
0.0015 MMgCl2Magnesium Chloride
GridModel: Agar Scientific / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 94 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Two subsequent applications of protein were required to achieve the desired particle density on grids. Each application was followed by 20 sec waiting time, with a short 0.5 sec blotting ...Details: Two subsequent applications of protein were required to achieve the desired particle density on grids. Each application was followed by 20 sec waiting time, with a short 0.5 sec blotting after first application and 5 sec blotting after the second..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

1102


Details: DNA-dependent protein kinase catalytic subunit (DNA-PKcs).
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 182285
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-5ojs:
Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1

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