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- EMDB-23027: Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core) -

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Basic information

Entry
Database: EMDB / ID: EMD-23027
TitleCryo-EM structure of the human SAGA coactivator complex (TRRAP, core)
Map dataLocSpiral filtered map
Sample
  • Complex: human SAGA
    • Complex: human SAGA
      • Protein or peptide: x 10 types
    • Complex: STAGA complex 65 subunit gamma
      • Protein or peptide: x 1 types
  • Ligand: x 1 types
Function / homology
Function and homology information


regulation of nucleobase-containing compound metabolic process / regulation of macromolecule metabolic process / SAGA-type complex / positive regulation of response to stimulus / : / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / regulation of cellular response to stress ...regulation of nucleobase-containing compound metabolic process / regulation of macromolecule metabolic process / SAGA-type complex / positive regulation of response to stimulus / : / regulation of somatic stem cell population maintenance / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / regulation of cellular response to stress / transcription factor TFTC complex / SLIK (SAGA-like) complex / negative regulation of microtubule depolymerization / hepatocyte differentiation / maintenance of protein location in nucleus / SAGA complex / RNA polymerase binding / limb development / transcription preinitiation complex / nucleus organization / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / regulation of RNA splicing / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / histone deacetylase complex / histone acetyltransferase complex / gastrulation / positive regulation of transcription initiation by RNA polymerase II / embryonic placenta development / regulation of DNA repair / somitogenesis / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / visual perception / male germ cell nucleus / nuclear estrogen receptor binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / transcription coregulator activity / G1/S transition of mitotic cell cycle / multicellular organism growth / mRNA transcription by RNA polymerase II / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / nuclear matrix / autophagy / transcription corepressor activity / microtubule cytoskeleton / kinase activity / HATs acetylate histones / positive regulation of cell growth / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / protein stabilization / Ub-specific processing proteases / nuclear speck / chromatin remodeling / protein heterodimerization activity / phosphorylation / focal adhesion / apoptotic process / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
STAGA complex 65 subunit gamma / Transcription-associated protein 1 / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Spt20-like, SEP domain / Spt20, SEP domain / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. ...STAGA complex 65 subunit gamma / Transcription-associated protein 1 / Transcription factor Spt20 / Transcriptional coactivator Hfi1/Transcriptional adapter 1 / Transcriptional regulator of RNA polII, SAGA, subunit / Spt20-like, SEP domain / Spt20, SEP domain / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TAF6, C-terminal HEAT repeat domain superfamily / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Armadillo-like helical / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Transformation/transcription domain-associated protein / Ataxin-7 / Transcription initiation protein SPT3 homolog / TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L / STAGA complex 65 subunit gamma / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor TFIID subunit 12 / Transcription factor SPT20 homolog / Transcriptional adapter 1 / Transcription initiation factor TFIID subunit 9B / TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human) / unclassified Rhodococcus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsHerbst DA / Esbin MN / Nogales E
Funding support United States, European Union, Switzerland, 6 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)CC30250 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127018 United States
European Molecular Biology Organization (EMBO)ALTF 1002-2018European Union
Swiss National Science FoundationP2BSP3_181878 Switzerland
Howard Hughes Medical Institute (HHMI)CC34430 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM098218 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structure of the human SAGA coactivator complex.
Authors: Dominik A Herbst / Meagan N Esbin / Robert K Louder / Claire Dugast-Darzacq / Gina M Dailey / Qianglin Fang / Xavier Darzacq / Robert Tjian / Eva Nogales /
Abstract: The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are ...The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer.
History
DepositionNov 24, 2020-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.37
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6.37
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ktr
  • Surface level: 6.37
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23027.png

Downloads & links

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Map

FileDownload / File: emd_23027.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocSpiral filtered map
Voxel sizeX=Y=Z: 1.187 Å
Density
Contour LevelBy AUTHOR: 6.37 / Movie #1: 6.37
Minimum - Maximum0.0 - 25.375307
Average (Standard dev.)0.17207587 (±0.75278217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 427.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1871.1871.187
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z427.320427.320427.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean0.00025.3750.172

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Supplemental data

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Mask #1

Fileemd_23027_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: LocSpiral filtered multibody map of the TRRAP module

Fileemd_23027_additional_1.map
AnnotationLocSpiral filtered multibody map of the TRRAP module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: LocSpiral filtered multibody map of the core module

Fileemd_23027_additional_2.map
AnnotationLocSpiral filtered multibody map of the core module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Relion postprocessed map

Fileemd_23027_additional_3.map
AnnotationRelion postprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_23027_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_23027_half_map_2.map
Annotationhalf map 1
Projections & Slices
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Sample components

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Entire : human SAGA

EntireName: human SAGA
Components
  • Complex: human SAGA
    • Complex: human SAGA
      • Protein or peptide: Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein
      • Protein or peptide: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
      • Protein or peptide: Isoform 3 of Transcription factor SPT20 homolog
      • Protein or peptide: Transcription initiation factor TFIID subunit 9B
      • Protein or peptide: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
      • Protein or peptide: Transcription initiation factor TFIID subunit 12
      • Protein or peptide: Transcription initiation factor TFIID subunit 10
      • Protein or peptide: Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homologTranscription (biology)
      • Protein or peptide: Transcriptional adapter 1
      • Protein or peptide: Ataxin-7Ataxin 7
    • Complex: STAGA complex 65 subunit gamma
      • Protein or peptide: STAGA complex 65 subunit gamma,DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma,DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma,DhaA
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid

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Supramolecule #1: human SAGA

SupramoleculeName: human SAGA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11 / Details: endogeneous human SAGA purified from HeLa cells
Molecular weightTheoretical: 1.420272 MDa

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Supramolecule #2: human SAGA

SupramoleculeName: human SAGA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #5-#11 / Details: endogeneous human SAGA purified from HeLa cells
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa / Tissue: cervix

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Supramolecule #3: STAGA complex 65 subunit gamma

SupramoleculeName: STAGA complex 65 subunit gamma / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Transformation/transcription domain-associated protein,Transforma...

MacromoleculeName: Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription ...Name: Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein,Transformation/transcription domain-associated protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 353.170281 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)ET LRPLAYSTLA DLVHHVRQHL PLSDLSLAVQ LFAKNIDDES LPSSIQTMSC KLLLNLVDCI RSKSEQESGN GRD VLMRML EVFVLKFHTI ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)ET LRPLAYSTLA DLVHHVRQHL PLSDLSLAVQ LFAKNIDDES LPSSIQTMSC KLLLNLVDCI RSKSEQESGN GRD VLMRML EVFVLKFHTI ARYQLSAIFK KCKPQSELGA VEAALPGVPT APAAPGPAPS PAPVPAPPPP PPPPPPATPV TPAP VPPFE KQGEKDKEDK QTFQVTDCRS LVKTLVCGVK TITWGITSCK APGAQFIPNK QLQPKETQIY IKLVKYAMQA LDIYQ VQIA GNGQTYIRVA NCQTVRMKEE KEVLEHFAGV FTMMNPLTFK EIFQTTVPYM VERISKNYAL QIVANSFLAN PTTSAL FAT ILVEYLLDRL PEMGSNVELS NLYLKLFKLV FGSVSLFAAE NEQMLKPHLH KIVNSSMELA QTAKEPYNYF LLLRALF RS IGGGSHDLLY QEFLPLLPNL LQGLNMLQSG LHKQHMKDLF VELCLTVPVR LSSLLPYLPM LMDPLVSALN GSQTLVSQ G LRTLELCVDN LQPDFLYDHI QPVRAELMQA LWRTLRNPAD SISHVAYRVL GKFGGSNRKM LKESQKLHYV VTEVQGPSI TVEFSDCKAS LQLPMEKAIE TALDCLKSAN TEPYYRRQAW EVIKCFLVAM MSLEDNKHAL YQLLAHPNFT EKTIPNVIIS HRYKAQDTP ARKTFEQALT GAFMSAVIKD LRPSALPFVA SLIRHYTMVA VAQQCGPFLL PCYQVGSQPS TAMFHSEENG S KGMDPLVL IDAIAICMAY EEKELCKIGE VALAVIFDVA SIILGSKERA CQLPLFSYIV ERLCACCYEQ AWYAKLGGVV SI KFLMERL PLTWVLQNQQ TFLKALLFVM MDLTGEVSNG AVAMAKTTLE QLLMRCATPL KDEERAEEIV AAQEKSFHHV THD LVREVT SPNSTVRKQA MHSLQVLAQV TGKSVTVIME PHKEVLQDMV PPKKHLLRHQ PANAQIGLME GNTFCTTLQP RLFT MDLNV VEHKVFYTEL LNLCEAEDSA LTKLPCYKSL PSLVPLRIAA LNALAACNYL PQSREKIIAA LFKALNSTNS ELQEA GEAC MRKFLEGATI EVDQIHTHMR PLLMMLGDYR SLTLNVVNRL TSVTRLFPNS FNDKFCDQMM QHLRKWMEVV VITHKG GQR SDGNEMKICS AIINLFHLIP AAPQTLVKPL LEVVMKTERA MLIEAGSPFR EPLIKFLTRH PSQTVELFMM EATLNDP QW SRMFMSFLKH KDARPLRDVL AANPNRFITL LLPGGAQTAV RPGSPSTSTM RLDLQFQAIK IISIIVKNDD SWLASQHS L VSQLRRVWVS ENFQERHRKE NMAATNWKEP KLLAYCLLNY CKRN(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)AGTSELVM LS LELVKTR LAVMSMEMRK NFIQAILTSL IEKSPDAKIL RAVVKIVEEW VKNNSPMAAN QTPTLREKSI LLVKMMTYIE KRF PEDLEL NAQFLDLVNY VYRDETLSGS ELTAKLEPAF LSGLRCAQPL IRAKFFEVFD NSMKRRVYER LLYVTCSQNW EAMG NHFWI KQCIELLLAV CEKSTPIGTS CQGAMLPSIT NVINLADSHD RAAFAMVTHV KQEPRERENS ESKEEDVEID IELAP GDQT STPKTKELSE KDIGNQLHML TNRHDKFLDT LREVKTGALL SAFVQLCHIS TTLAEKTWVQ LFPRLWKILS DRQQHA LAG EISPFLCSGS HQVQRDCQPS ALNCFVEAMS QCVPPIPIRP CVLKYLGKTH NLWFRSTLML EHQAFEKGLS LQIKPKQ TT EFYEQESITP PQQEILDSLA ELYSLLQEED MWAGLWQKRC KYSETATAIA YEQHGFFEQA QESYEKAMDK AKKEHERS N ASPAIFPEYQ LWEDHWIRCS KELNQWEALT EYGQSKGHIN PYLVLECAWR VSNWTAMKEA LVQVEVSCPK EMAWKVNMY RGYLAICHPE EQQLSFIERL VEMASSLAIR EWRRLPHVVS HVHTPLLQAA QQIIELQEAA QINAGLQPTN LGRNNSLHDM KTVVKTWRN RLPIVSDDLS HWSSIFMWRQ HHYQAIVTAY ENSSQHDPSS NNAMLGVHAS ASAIIQYGKI ARKQGLVNVA L DILSRIHT IPTVPIVDCF QKIRQQVKCY LQLAGVMGKN ECMQGLEVIE STNLKYFTKE MTAEFYALKG MFLAQINKSE EA NKAFSAA VQMHDVLVKA WAMWGDYLEN IFVKERQLHL GVSAITCYLH ACRHQNESKS RKYLAKVLWL LSFDDDKNTL ADA VDKYCI GVPPIQWLAW IPQLLTCLVG SEGKLLLNLI SQVGRVYPQA VYFPIRTLYL TLKIEQRERY KSDSGQQQPS SVGN QSHSA SDPGPIRATA PMWRCSRIMH MQRELHPTLL SSLEGIVDQM VWFRENWHEE VLRQLQQGLA KCYSVAFEKS GAVSD AKIT PHTLNFVKKL VSTFGVGLEN VSNVSTMFSS AASESLARRA QATAQDPVFQ KLKGQFTTDF DFSVPGSMKL HNLISK LKK WIKILEAKTK QLPKFFLIEE KCRFLSNFSA QTAEVEIPGE FLMPKPTHYY IKIARFMPRV EIVQKHNTAA RRLYIRG HN GKIYPYLVMN DACLTESRRE ERVLQLLRLL NPCLEKRKET TKRHLFFTVP RVVAVSPQMR LVEDNPSSLS LVEIYKQR C AKKGIEHDNP ISRYYDRLAT VQARGTQASH QVLRDILKEV QSNMVPRSML KEWALHTFPN ATDYWTFRKM FTIQLALIG FAEFVLHLNR LNPEMLQIAQ DTGKLNVAYF RFDINDATGD LDANRPVPFR LTPNISEFLT TIGVSGPLTA SMIAVARCFA QPNFKVDGI LKTVLRDEII AWHKKTQEDT SSPLSAAGQP ENMDSQQLVS LVQKAVTAIM TRLHNLAQFE GGESKVNTLV A AANSLDNL CRMDPAWHPW L

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Macromolecule #2: TAF5-like RNA polymerase II p300/CBP-associated factor-associated...

MacromoleculeName: TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 66.223047 KDa
SequenceString: MKRVRTEQIQ MAVSCYLKRR QYVDSDGPLK QGLRLSQTAE EMAANLTVQS ESGCANIVSA APCQAEPQQY EVQFGRLRNF LTDSDSQHS HEVMPLLYPL FVYLHLNLVQ NSPKSTVESF YSRFHGMFLQ NASQKDVIEQ LQTTQTIQDI LSNFKLRAFL D NKYVVRLQ ...String:
MKRVRTEQIQ MAVSCYLKRR QYVDSDGPLK QGLRLSQTAE EMAANLTVQS ESGCANIVSA APCQAEPQQY EVQFGRLRNF LTDSDSQHS HEVMPLLYPL FVYLHLNLVQ NSPKSTVESF YSRFHGMFLQ NASQKDVIEQ LQTTQTIQDI LSNFKLRAFL D NKYVVRLQ EDSYNYLIRY LQSDNNTALC KVLTLHIHLD VQPAKRTDYQ LYASGSSSRS ENNGLEPPDM PSPILQNEAA LE VLQESIK RVKDGPPSLT TICFYAFYNT EQLLNTAEIS PDSKLLAAGF DNSCIKLWSL RSKKLKSEPH QVDVSRIHLA CDI LEEEDD EDDNAGTEMK ILRGHCGPVY STRFLADSSG LLSCSEDMSI RYWDLGSFTN TVLYQGHAYP VWDLDISPYS LYFA SGSHD RTARLWSFDR TYPLRIYAGH LADVDCVKFH PNSNYLATGS TDKTVRLWSA QQGNSVRLFT GHRGPVLSLA FSPNG KYLA SAGEDQRLKL WDLASGTLYK ELRGHTDNIT SLTFSPDSGL IASASMDNSV RVWDIRNTYC SAPADGSSSE LVGVYT GQM SNVLSVQFMA CNLLLVTGIT QENQEH

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Macromolecule #3: Isoform 3 of Transcription factor SPT20 homolog

MacromoleculeName: Isoform 3 of Transcription factor SPT20 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 88.12907 KDa
SequenceString: MQQALELALD RAEYVIESAR QRPPKRKYLS SGRKSVFQKL YDLYIEECEK EPEVKKLRRN VNLLEKLVMQ ETLSCLVVNL YPGNEGYSL MLRGKNGSDS ETIRLPYEEG ELLEYLDAEE LPPILVDLLE KSQVNIFHCG CVIAEIRDYR QSSNMKSPGY Q SRHILLRP ...String:
MQQALELALD RAEYVIESAR QRPPKRKYLS SGRKSVFQKL YDLYIEECEK EPEVKKLRRN VNLLEKLVMQ ETLSCLVVNL YPGNEGYSL MLRGKNGSDS ETIRLPYEEG ELLEYLDAEE LPPILVDLLE KSQVNIFHCG CVIAEIRDYR QSSNMKSPGY Q SRHILLRP TMQTLICDVH SITSDNHKWT QEDKLLLESQ LILATAEPLC LDPSIAVTCT ANRLLYNKQK MNTRPMKRCF KR YSRSSLN RQQDLSHCPP PPQLRLLDFL QKRKERKAGQ HYDLKISKAG NCVDMWKRSP CNLAIPSEVD VEKYAKVEKS IKS DDSQPT VWPAHDVKDD YVFECEAGTQ YQKTKLTILQ SLGDPLYYGK IQPCKADEES DSQMSPSHSS TDDHSNWFII GSKT DAERV VNQYQELVQN EAKCPVKMSH SSSGSASLSQ VSPGKETDQT ETVSVQSSVL GKGVKHRPPP IKLPSSSGNS SSGNY FTPQ QTSSFLKSPT PPPSSKPSSI PRKSSVDLNQ VSMLSPAALS PASSSQRSGT PKPSTPTPTP SSTPHPPDAQ SSTPST PSA TPTPQDSGFT PQPTLLTQFA QQQRSLSQAM PVTTIPLSTM VTSITPGTTA TQVMANSAGL NFINVVGSVC GAQALMS GS NPMLGCNTGA ITPAGINLSG LLPSGGLLPN ALPSAMQAAS QAGVPFGLKN TSSLRPLNLL QLPGGSLIFN TLQQQQQQ L SQFTPQQPQQ PTTCSPQQPG EQGSEQGSTS QEQALSAQQA AVINLTGVGS FMQSQAAAVA ILAASNGYGS SSSTNSSAT SSSAYRQPVK K

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Macromolecule #4: STAGA complex 65 subunit gamma,DhaA,STAGA complex 65 subunit gamm...

MacromoleculeName: STAGA complex 65 subunit gamma,DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma,DhaA,STAGA complex 65 subunit gamma,STAGA complex 65 subunit gamma,DhaA
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unclassified Rhodococcus (bacteria)
Molecular weightTheoretical: 78.079922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)MLDIP SEPCSLTIH TIQLIQHNRR LRNLIATAQA QN(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)MLDIP SEPCSLTIH TIQLIQHNRR LRNLIATAQA QN(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)DCKNP NAPFQIRHSD PESDFYRGK GEPVTELSWH SCRQLLYQAV ATILAHAGFD CANESVLETL TDVAHEYCLK FTKLLRFAVD REARLGQTPF P DVMEQVFH EVGIGSVLSL QKFWQHRIKD YHSYMLQISK QLSEEYERIV NPEKATEDAK PVKIKEEPVS DITFPVSEEL EA DLASGDQ SLPMGVLGAQ SERFPSNLEV EASPQASSAE VNASPLWNLA HVKMEPQESE EGNVSGHGVL GSDVFEEPMS GMS EAGIPQ SPDDSDSSYG SHSTDSLMGS SPVFNQRCKK RMRKIGTSGE DLYFQSGGSM AEIGTGFPFD PHYVEVLGER MHYV DVGPR DGTPVLFLHG NPTSSYVWRN IIPHVAPTHR CIAPDLIGMG KSDKPDLGYF FDDHVRFMDA FIEALGLEEV VLVIH DWGS ALGFHWAKRN PERVKGIAFM EFIRPIPTWD EWPEFARETF QAFRTTDVGR KLIIDQNVFI EGTLPMGVVR PLTEVE MDH YREPFLNPVD REPLWRFPNE LPIAGEPANI VALVEEYMDW LHQSPVPKLL FWGTPGVLIP PAEAARLAKS LPNCKAV DI GPGLNLLQED NPDLIGSEIA RWLSTLEISG DYKDHDGDYK DHDIDYKDDD DKGS

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Macromolecule #5: Transcription initiation factor TFIID subunit 9B

MacromoleculeName: Transcription initiation factor TFIID subunit 9B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 27.654861 KDa
SequenceString: MESGKMAPPK NAPRDALVMA QILKDMGITE YEPRVINQML EFAFRYVTTI LDDAKIYSSH AKKPNVDADD VRLAIQCRAD QSFTSPPPR DFLLDIARQK NQTPLPLIKP YAGPRLPPDR YCLTAPNYRL KSLIKKGPNQ GRLVPRLSVG AVSSKPTTPT I ATPQTVSV ...String:
MESGKMAPPK NAPRDALVMA QILKDMGITE YEPRVINQML EFAFRYVTTI LDDAKIYSSH AKKPNVDADD VRLAIQCRAD QSFTSPPPR DFLLDIARQK NQTPLPLIKP YAGPRLPPDR YCLTAPNYRL KSLIKKGPNQ GRLVPRLSVG AVSSKPTTPT I ATPQTVSV PNKVATPMSV TSQRFTVQIP PSQSTPVKPV PATTAVQNVL INPSMIGPKN ILITTNMVSS QNTANEANPL KR KHEDDDD NDIM

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Macromolecule #6: TAF6-like RNA polymerase II p300/CBP-associated factor-associated...

MacromoleculeName: TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 67.903289 KDa
SequenceString: MSEREERRFV EIPRESVRLM AESTGLELSD EVAALLAEDV CYRLREATQN SSQFMKHTKR RKLTVEDFNR ALRWSSVEAV CGYGSQEAL PMRPAREGEL YFPEDREVNL VELALATNIP KGCAETAVRV HVSYLDGKGN LAPQGSVPSA VSSLTDDLLK Y YHQVTRAV ...String:
MSEREERRFV EIPRESVRLM AESTGLELSD EVAALLAEDV CYRLREATQN SSQFMKHTKR RKLTVEDFNR ALRWSSVEAV CGYGSQEAL PMRPAREGEL YFPEDREVNL VELALATNIP KGCAETAVRV HVSYLDGKGN LAPQGSVPSA VSSLTDDLLK Y YHQVTRAV LGDDPQLMKV ALQDLQTNSK IGALLPYFVY VVSGVKSVSH DLEQLHRLLQ VARSLFRNPH LCLGPYVRCL VG SVLYCVL EPLAASINPL NDHWTLRDGA ALLLSHIFWT HGDLVSGLYQ HILLSLQKIL ADPVRPLCCH YGAVVGLHAL GWK AVERVL YPHLSTYWTN LQAVLDDYSV SNAQVKADGH KVYGAILVAV ERLLKMKAQA AEPNRGGPGG RGCRRLDDLP WDSL LFQES SSGGGAEPSF GSGLPLPPGG AGPEDPSLSV TLADIYRELY AFFGDSLATR FGTGQPAPTA PRPPGDKKEP AAAPD SVRK MPQLTASAIV SPHGDESPRG SGGGGPASAS GPAASESRPL PRVHRARGAP RQQGPGTGTR DVFQKSRFAP RGAPHF RFI IAGRQAGRRC RGRLFQTAFP APYGPSPASR YVQKLPMIGR TSRPARRWAL SDYSLYLPL

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Macromolecule #7: Transcription initiation factor TFIID subunit 12

MacromoleculeName: Transcription initiation factor TFIID subunit 12 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 17.948467 KDa
SequenceString:
MNQFGPSALI NLSNFSSIKP EPASTPPQGS MANSTAVVKI PGTPGAGGRL SPENNQVLTK KKLQDLVREV DPNEQLDEDV EEMLLQIAD DFIESVVTAA CQLARHRKSS TLEVKDVQLH LERQWNMWIP GFGSEEIRPY KKACTTEAHK QRMALIRKTT K K

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Macromolecule #8: Transcription initiation factor TFIID subunit 10

MacromoleculeName: Transcription initiation factor TFIID subunit 10 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 21.731248 KDa
SequenceString: MSCSGSGADP EAAPASAASA PGPAPPVSAP AALPSSTAAE NKASPAGTAG GPGAGAAAGG TGPLAARAGE PAERRGAAPV SAGGAAPPE GAISNGVYVL PSAANGDVKP VVSSTPLVDF LMQLEDYTPT IPDAVTGYYL NRAGFEASDP RIIRLISLAA Q KFISDIAN ...String:
MSCSGSGADP EAAPASAASA PGPAPPVSAP AALPSSTAAE NKASPAGTAG GPGAGAAAGG TGPLAARAGE PAERRGAAPV SAGGAAPPE GAISNGVYVL PSAANGDVKP VVSSTPLVDF LMQLEDYTPT IPDAVTGYYL NRAGFEASDP RIIRLISLAA Q KFISDIAN DALQHCKMKG TASGSSRSKS KDRKYTLTME DLTPALSEYG INVKKPHYFT

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Macromolecule #9: Transcription initiation protein SPT3 homolog,Transcription initi...

MacromoleculeName: Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog,Transcription initiation protein SPT3 homolog
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 33.197047 KDa
SequenceString: MNNTAASPMS TATSSSGRST GKSISFATEL QSMMYSLGDA RRPLHETAVL VEDVVHTQLI NLLQQAAEVS QLRGARVITP EDLLFLMRK DKKKLRRLLK YMFIRDYKSK IVKGIDEDDL LEDKLSGSNN ANKRQKIAQD FLNSIDQTGE LLAMFED (UNK)(UNK) (UNK) ...String:
MNNTAASPMS TATSSSGRST GKSISFATEL QSMMYSLGDA RRPLHETAVL VEDVVHTQLI NLLQQAAEVS QLRGARVITP EDLLFLMRK DKKKLRRLLK YMFIRDYKSK IVKGIDEDDL LEDKLSGSNN ANKRQKIAQD FLNSIDQTGE LLAMFED (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) ESRQLSFSKK ASKFRDWLDC SSMEIKPNV VAMEILAYLA YETVAQLVDL ALLVRQDMVT KAGDPFSHAI SATFIQYHNS AESTAACGVE AHSDAIQPCH I REAIRRYS HRIGPLSPFT NAYRRNGMAF LAC

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Macromolecule #10: Transcriptional adapter 1

MacromoleculeName: Transcriptional adapter 1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 37.432531 KDa
SequenceString: MATFVSELEA AKKNLSEALG DNVKQYWANL KLWFKQKISK EEFDLEAHRL LTQDNVHSHN DFLLAILTRC QILVSTPDGA GSLPWPGGS AAKPGKPKGK KKLSSVRQKF DHRFQPQNPL SGAQQFVAKD PQDDDDLKLC SHTMMLPTRG QLEGRMIVTA Y EHGLDNVT ...String:
MATFVSELEA AKKNLSEALG DNVKQYWANL KLWFKQKISK EEFDLEAHRL LTQDNVHSHN DFLLAILTRC QILVSTPDGA GSLPWPGGS AAKPGKPKGK KKLSSVRQKF DHRFQPQNPL SGAQQFVAKD PQDDDDLKLC SHTMMLPTRG QLEGRMIVTA Y EHGLDNVT EEAVSAVVYA VENHLKDILT SVVSRRKAYR LRDGHFKYAF GSNVTPQPYL KNSVVAYNNL IESPPAFTAP CA GQNPASH PPPDDAEQQA ALLLACSGDT LPASLPPVNM YDLFEALQVH REVIPTHTVY ALNIERIITK LWHPNHEELQ QDK VHRQRL AAKEGLLLC

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Macromolecule #11: Ataxin-7

MacromoleculeName: Ataxin-7 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 95.597742 KDa
SequenceString: MSERAADDVR GEPRRAAAAA GGAAAAAARQ QQQQQQQQQP PPPQPQRQQH PPPPPRRTRP EDGGPGAAST SAAAMATVGE RRPLPSPEV MLGQSWNLWV EASKLPGKDG TELDESFKEF GKNREVMGLC REDMPIFGFC PAHDDFYLVV CNDCNQVVKP Q AFQSHYER ...String:
MSERAADDVR GEPRRAAAAA GGAAAAAARQ QQQQQQQQQP PPPQPQRQQH PPPPPRRTRP EDGGPGAAST SAAAMATVGE RRPLPSPEV MLGQSWNLWV EASKLPGKDG TELDESFKEF GKNREVMGLC REDMPIFGFC PAHDDFYLVV CNDCNQVVKP Q AFQSHYER RHSSSSKPPL AVPPTSVFSF FPSLSKSKGG SASGSNRSSS GGVLSASSSS SKLLKSPKEK LQLRGNTRPM HP IQQSRVP HGRIMTPSVK VEKIHPKMDG TLLKSAVGPT CPATVSSLVK PGLNCPSIPK PTLPSPGQIL NGKGLPAPPT LEK KPEDNS NNRKFLNKRL SEREFDPDIH CGVIDLDTKK PCTRSLTCKT HSLTQRRAVQ GRRKRFDVLL AEHKNKTREK ELIR HPDSQ QPPQPLRDPH PAPPRTSQEP HQNPHGVIPS ESKPFVASKP KPHTPSLPRP PGCPAQQGGS APIDPPPVHE SPHPP LPAT EPASRLSSEE GEGDDKEESV EKLDCHYSGH HPQPASFCTF GSRQIGRGYY VFDSRWNRLR CALNLMVEKH LNAQLW KKI PPVPSTTSPI STRIPHRTNS VPTSQCGVSY LAAATVSTSP VLLSSTCISP NSKSVPAHGT TLNAQPAASG AMDPVCS MQ SRQVSSSSSS PSTPSGLSSV PSSPMSRKPQ KLKSSKSLRP KESSGNSTNC QNASSSTSGG SGKKRKNSSP LLVHSSSS S SSSSSSSHSM ESFRKNCVAH SGPPYPSTVT SSHSIGLNCV TNKANAVNVR HDQSGRGPPT GSPAESIKRM SVMVNSSDS TLSLGPFIHQ SNELPVNSHG SFSHSHTPLD KLIGKKRKCS PSSSSINNSS SKPTKVAKVP AVNNVHMKHT GTIPGAQGLM NSSLLHQPK ARP

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Macromolecule #12: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 12 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

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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

BufferpH: 7.8
Component:
ConcentrationNameFormula
25.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
200.0 mMsodium chlorideNaClSodium chloride
0.2 mMEthylenediaminetetraacetic acid
0.5 mMtris(2-carboxyethyl)phosphine
0.01 % (v/v)nonyl phenoxypolyethoxylethanol
2.5 % (v/v)Glycerol

Details: Buffers were freshly prepared and 0.22 um filtered.
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 0, blot time 3 sec.
DetailsThe sample was crosslinked with 1 mM bis(sulfosuccinimidyl)suberate (BS3) prior to freezing

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 64000
Specialist opticsEnergy filter - Name: GIF Bioquantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10224 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2438694
CTF correctionSoftware - Name: CTFFIND (ver. 4.7.0)
Startup modelType of model: OTHER
Details: negative stain reconstruction, see related entry EMD-23028 (7KTS)
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 71488 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 2 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 209435
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7ktr:
Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core)

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