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- EMDB-9664: Tra1 subunit from Saccharomyces cerevisiae SAGA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9664
TitleTra1 subunit from Saccharomyces cerevisiae SAGA complex
Map data
Sample
  • Complex: Tra1 / ScTra1
    • Protein or peptide: Transcription-associated protein 1
KeywordsEpigenetics / Acetyltransferase / Transcription / Co-activator
Function / homology
Function and homology information


: / SLIK (SAGA-like) complex / SAGA complex / NuA4 histone acetyltransferase complex / 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. / FATC 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 (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsZheng XD / Liu GC
CitationJournal: Cell Discov / Year: 2019
Title: Architecture of SAGA complex.
Authors: Gaochao Liu / Xiangdong Zheng / Haipeng Guan / Yong Cao / Hongyuan Qu / Junqing Kang / Xiangle Ren / Jianlin Lei / Meng-Qiu Dong / Xueming Li / Haitao Li /
History
DepositionSep 25, 2018-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ig9
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9664.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.401 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.052679177 - 0.122503795
Average (Standard dev.)0.00017765604 (±0.0025359453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 504.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4011.4011.401
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z504.360504.360504.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0530.1230.000

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Supplemental data

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Mask #1

Fileemd_9664_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_9664_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_9664_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_9664_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Tra1 / ScTra1

EntireName: Tra1 / ScTra1
Components
  • Complex: Tra1 / ScTra1
    • Protein or peptide: Transcription-associated protein 1

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Supramolecule #1: Tra1 / ScTra1

SupramoleculeName: Tra1 / ScTra1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: One of the major part from SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Organelle: Nucleus / Location in cell: nucleus
Molecular weightTheoretical: 1.8 MDa

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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 (brewer's yeast) / Strain: BYL4741
Molecular weightTheoretical: 433.677281 KDa
SequenceString: MSLTEQIEQF ASRFRDDDAT LQSRYSTLSE LYDIMELLNS PEDYHFFLQA VIPLLLNQLK EVPISYDAHS PEQKLRNSML DIFNRCLMN QTFQPYAMEV LEFLLSVLPK ENEENGILCM KVLTTLFKSF KSILQDKLDS FIRIIIQIYK NTPNLINQTF Y EAGKAEQG ...String:
MSLTEQIEQF ASRFRDDDAT LQSRYSTLSE LYDIMELLNS PEDYHFFLQA VIPLLLNQLK EVPISYDAHS PEQKLRNSML DIFNRCLMN QTFQPYAMEV LEFLLSVLPK ENEENGILCM KVLTTLFKSF KSILQDKLDS FIRIIIQIYK NTPNLINQTF Y EAGKAEQG DLDSPKEPQA DELLDEFSKN DEEKDFPSKQ SSTEPRFENS TSSNGLRSSM FSFKILSECP ITMVTLYSSY KQ LTSTSLP EFTPLIMNLL NIQIKQQQEA REQAESRGEH FTSISTEIIN RPAYCDFILA QIKATSFLAY VFIRGYAPEF LQD YVNFVP DLIIRLLQDC PSELSSARKE LLHATRHILS TNYKKLFLPK LDYLFDERIL IGNGFTMHET LRPLAYSTVA DFIH NIRSE LQLSEIEKTI KIYTGYLLDE SLALTVQIMS AKLLLNLVER ILKLGKENPQ EAPRAKKLLM IIIDSYMNRF KTLNR QYDT IMKYYGRYET HKKEKAEKLK NSIQDNDKES EEFMRKVLEP SDDDHLMPQP KKEDINDSPD VEMTESDKVV KNDVEM FDI KNYAPILLLP TPTNDPIKDA FYLYRTLMSF LKTIIHDLKV FNPPPNEYTV ANPKLWASVS RVFSYEEVIV FKDLFHE CI IGLKFFKDHN EKLSPETTKK HFDISMPSLP VSATKDAREL MDYLAFMFMQ MDNATFNEII EQELPFVYER MLEDSGLL H VAQSFLTSEI TSPNFAGILL RFLKGKLKDL GNVDFNTSNV LIRLFKLSFM SVNLFPNINE VVLLPHLNDL ILNSLKYST TAEEPLVYFY LIRTLFRSIG GGRFENLYRS IKPILQVLLQ SLNQMILTAR LPHERELYVE LCITVPVRLS VLAPYLPFLM KPLVFALQQ YPDLVSQGLR TLELCIDNLT AEYFDPIIEP VIDDVSKALF NLLQPQPFNH AISHNVVRIL GKLGGRNRQF L KPPTDLTE KTELDIDAIA DFKINGMPED VPLSVTPGIQ SALNILQSYK SDIHYRKSAY KYLTCVLLLM TKSSAEFPTN YT ELLKTAV NSIKLERIGI EKNFDLEPTV NKRDYSNQEN LFLRLLESVF YATSIKELKD DAMDLLNNLL DHFCLLQVNT TLL NKRNYN GTFNIDLKNP NFMLDSSLIL DAIPFALSYY IPEVREVGVL AYKRIYEKSC LIYGEELALS HSFIPELAKQ FIHL CYDET YYNKRGGVLG IKVLIDNVKS SSVFLKKYQY NLANGLLFVL KDTQSEAPSA ITDSAEKLLI DLLSITFADV KEEDL GNKV LENTLTDIVC ELSNANPKVR NACQKSLHTI SNLTGIPIVK LMDHSKQFLL SPIFAKPLRA LPFTMQIGNV DAITFC LSL PNTFLTFNEE LFRLLQESIV LADAEDESLS TNIQKTTEYS TSEQLVQLRI ACIKLLAIAL KNEEFATAQQ GNIRIRI LA VFFKTMLKTS PEIINTTYEA LKGSLAENSK LPKELLQNGL KPLLMNLSDH QKLTVPGLDA LSKLLELLIA YFKVEIGR K LLDHLTAWCR VEVLDTLFGQ DLAEQMPTKI IVSIINIFHL LPPQADMFLN DLLLKVMLLE RKLRLQLDSP FRTPLARYL NRFHNPVTEY FKKNMTLRQL VLFMCNIVQR PEAKELAEDF EKELDNFYDF YISNIPKNQV RVVSFFTNMV DLFNTMVITN GDEWLKKKG NMILKLKDML NLTLKTIKEN SFYIDHLQLN QSIAKFQALY LRFTELSERD QNPLLLDFID FSFSNGIKAS Y SLKKFIFH NIIASSNKEK QNNFINDATL FVLSDKCLDA RIFVLKNVIN STLIYEVATS GSLKSYLVED KKPKWLELLH NK IWKNSNA ILAYDVLDHH DLFRFELLQL SAIFIKADPE IIAEIKKDII KFCWNFIKLE DTLIKQSAYL VTSYFISKFD FPI KVVTQV FVALLRSSHV EARYLVKQSL DVLTPVLHER MNAAGTPDTW INWVKRVMVE NSSSQNNILY QFLISHPDLF FNSR DLFIS NIIHHMNKIT FMSNSNSDSH TLAIDLASLI LYWENKTLEI TNVNNTKTDS DGDVVMSDSK SDINPVEADT TAIIV DANN NSPISLHLRE ACTAFLIRYV CASNHRAIET ELGLRAINIL SELISDKHWT NVNVKLVYFE KFLIFQDLDS ENILYY CMN ALDVLYVFFK NKTKEWIMEN LPTIQNLLEK CIKSDHHDVQ EALQKVLQVI MKAIKAQGVS VIIEEESPGK TFIQMLT SV ITQDLQETSS VTAGVTLAWV LFMNFPDNIV PLLTPLMKTF SKLCKDHLSI SQPKDAMALE EARITTKLLE KVLYILSL K VSLLGDSRRP FLSTVALLID HSMDQNFLRK IVNMSRSWIF NTEIFPTVKE KAAILTKMLA FEIRGEPSLS KLFYEIVLK LFDQEHFNNT EITVRMEQPF LVGTRVEDIG IRKRFMTILD NSLERDIKER LYYVIRDQNW EFIADYPWLN QALQLLYGSF NREKELSLK NIYCLSPPSI LQEYLPENAE MVTEVNDLEL SNFVKGHIAS MQGLCRIISS DFIDSLIEIF YQDPKAIHRA W VTLFPQVY KSIPKNEKYG FVRSIITLLS KPYHTRQISS RTNVINMLLD SISKIESLEL PPHLVKYLAI SYNAWYQSIN IL ESIQSNT SIDNTKIIEA NEDALLELYV NLQEEDMFYG LWRRRAKYTE TNIGLSYEQI GLWDKAQQLY EVAQVKARSG ALP YSQSEY ALWEDNWIQC AEKLQHWDVL TELAKHEGFT DLLLECGWRV ADWNSDRDAL EQSVKSVMDV PTPRRQMFKT FLAL QNFAE SRKGDQEVRK LCDEGIQLSL IKWVSLPIRY TPAHKWLLHG FQQYMEFLEA TQIYANLHTT TVQNLDSKAQ EIKRI LQAW RDRLPNTWDD VNMWNDLVTW RQHAFQVINN AYLPLIPALQ QSNSNSNINT HAYRGYHEIA WVINRFAHVA RKHNMP DVC ISQLARIYTL PNIEIQEAFL KLREQAKCHY QNMNELTTGL DVISNTNLVY FGTVQKAEFF TLKGMFLSKL RAYEEAN QA FATAVQIDLN LAKAWAQWGF FNDRRLSEEP NNISFASNAI SCYLQAAGLY KNSKIRELLC RILWLISIDD ASGMLTNA F DSFRGEIPVW YWITFIPQLL TSLSHKEANM VRHILIRIAK SYPQALHFQL RTTKEDFAVI QRQTMAVMGD KPDTNDRNG RRQPWEYLQE LNNILKTAYP LLALSLESLV AQINDRFKST TDEDLFRLIN VLLIDGTLNY NRLPFPRKNP KLPENTEKNL VKFSTTLLA PYIRPKFNAD FIDNKPDYET YIKRLRYWRR RLENKLDRAS KKENLEVLCP HLSNFHHQKF EDIEIPGQYL L NKDNNVHF IKIARFLPTV DFVRGTHSSY RRLMIRGHDG SVHSFAVQYP AVRHSRREER MFQLYRLFNK SLSKNVETRR RS IQFNLPI AIPLSPQVRI MNDSVSFTTL HEIHNEFCKK KGFDPDDIQD FMADKLNAAH DDALPAPDMT ILKVEIFNSI QTM FVPSNV LKDHFTSLFT QFEDFWLFRK QFASQYSSFV FMSYMMMINN RTPHKIHVDK TSGNVFTLEM LPSRFPYERV KPLL KNHDL SLPPDSPIFH NNEPVPFRLT PNIQSLIGDS ALEGIFAVNL FTISRALIEP DNELNTYLAL FIRDEIISWF SNLHR PIIE NPQLREMVQT NVDLIIRKVA QLGHLNSTPT VTTQFILDCI GSAVSPRNLA RTDVNFMPWF

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

Concentration0.2 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormula
20.0 mMHEPES
150.0 mMNaClSodium chloride

Details: 20mM HEPES pH 8.5 150mM Nacl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
Details: The grid was coated with a home-made thin continuous carbon film.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: Blot for 4 seconds and wait for 30 seconds before plunging.
DetailsWe extracted it from the overall SAGA complex structure.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Specialist opticsSpherical aberration corrector: With a Cs-corrector
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 3-30 / Number real images: 8526 / Average exposure time: 0.25 sec. / Average electron dose: 5.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1350000 / Details: GPU accelerated
Startup modelType of model: INSILICO MODEL
In silico model: We use cryoSPARC software to generate in silicon automatically.
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 1.6) / Software - details: GPU accelerated
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 2.0) / Software - details: GPU accelerated / Details: GPU accelerated
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0) / Software - details: GPU accelerated / Details: GPU accelerated
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Software - details: GPU accelerated / Details: GPU accelerated / Number images used: 176464
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6ig9:
Tra1 subunit from Saccharomyces cerevisiae SAGA complex

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