[English] 日本語
Yorodumi
- EMDB-15009: Structure of SNAPc containing Pol II pre-initiation complex bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15009
TitleStructure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC)
Map data
Sample
  • Complex: General transcription factors and SNAPc bound to U1 promoter
    • Complex: SNAPc
      • DNA: x 1 types
      • Protein or peptide: x 4 types
    • Complex: TATA-box-binding protein and transcription factors
      • Protein or peptide: x 2 types
      • DNA: x 1 types
    • Complex: Promoter
      • Protein or peptide: x 2 types
  • Ligand: x 1 types
Function / homology
Function and homology information


snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II ...snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II / RNA polymerase III general transcription initiation factor activity / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / germinal vesicle / RNA polymerase II general transcription initiation factor binding / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / cell division site / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II complex binding / protein acetylation / 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 / transcription initiation at RNA polymerase III promoter / viral transcription / acetyltransferase activity / RNA Polymerase I Transcription Initiation / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / TFIIB-class transcription factor binding / positive regulation of transcription initiation by RNA polymerase II / spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / transcription by RNA polymerase III / core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / promoter-specific chromatin binding / protein-DNA complex / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / kinetochore / RNA polymerase II transcription regulator complex / cell junction / chromosome / spermatogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / nuclear body / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin / nucleolus / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
snRNA-activating protein complex subunit 5 / snRNA-activating protein complex subunit 19, SNAPc subunit 19 / snRNA-activating protein complex subunit 1 / snRNA-activating protein complex, subunit 3 / Small nuclear RNA activating complex (SNAPc), subunit 1 / snRNA-activating protein complex (SNAPc), subunit 3 / Myb-like domain profile. / Myb-like DNA-binding domain / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit ...snRNA-activating protein complex subunit 5 / snRNA-activating protein complex subunit 19, SNAPc subunit 19 / snRNA-activating protein complex subunit 1 / snRNA-activating protein complex, subunit 3 / Small nuclear RNA activating complex (SNAPc), subunit 1 / snRNA-activating protein complex (SNAPc), subunit 3 / Myb-like domain profile. / Myb-like DNA-binding domain / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Myb-type HTH DNA-binding domain profile. / Zinc finger, TFIIB-type / SANT domain / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Myb domain / TBP domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
snRNA-activating protein complex subunit 5 / TATA-box-binding protein / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIB / snRNA-activating protein complex subunit 1 / snRNA-activating protein complex subunit 4 / snRNA-activating protein complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRengachari S / Schilbach S / Kaliyappan T / Gouge J / Zumer K / Schwarz J / Urlaub H / Dienemann C / Vannini A / Cramer P
Funding support Germany, United Kingdom, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
Cancer Research UKCR-UK C47547/A21536 United Kingdom
Wellcome Trust200818/Z/16/Z United Kingdom
Citation
Journal: Nat Struct Mol Biol / Year: 2022
Title: Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II.
Authors: Srinivasan Rengachari / Sandra Schilbach / Thangavelu Kaliyappan / Jerome Gouge / Kristina Zumer / Juliane Schwarz / Henning Urlaub / Christian Dienemann / Alessandro Vannini / Patrick Cramer /
Abstract: RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at ...RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at non-coding genes, such as small nuclear RNA (snRNA) genes, is less well understood at the structural level. Here, we study Pol II initiation at snRNA gene promoters and show that the snRNA-activating protein complex (SNAPc) enables DNA opening and transcription initiation independent of TFIIE and TFIIH in vitro. We then resolve cryo-EM structures of the SNAPc-containing Pol IIpre-initiation complex (PIC) assembled on U1 and U5 snRNA promoters. The core of SNAPc binds two turns of DNA and recognizes the snRNA promoter-specific proximal sequence element (PSE), located upstream of the TATA box-binding protein TBP. Two extensions of SNAPc, called wing-1 and wing-2, bind TFIIA and TFIIB, respectively, explaining how SNAPc directs Pol II to snRNA promoters. Comparison of structures of closed and open promoter complexes elucidates TFIIH-independent DNA opening. These results provide the structural basis of Pol II initiation at non-coding RNA gene promoters.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II
Authors: Rengachari S / Schilbach S / Kaliyappan T / Gouge J / Zumer K / Schwarz J / Urlaub H / Dienemann C / Vannini A / Cramer P
History
DepositionMay 20, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15009.png

Downloads & links

-
Map

FileDownload / File: emd_15009.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0205
Minimum - Maximum-0.04218926 - 0.100573
Average (Standard dev.)1.4414956e-05 (±0.0024733997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15009_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_15009_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_15009_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : General transcription factors and SNAPc bound to U1 promoter

EntireName: General transcription factors and SNAPc bound to U1 promoter
Components
  • Complex: General transcription factors and SNAPc bound to U1 promoter
    • Complex: SNAPc
      • DNA: Non-template strandCoding strand
      • Protein or peptide: Transcription initiation factor IIA subunit 1
      • Protein or peptide: Transcription initiation factor IIA subunit 2
      • Protein or peptide: snRNA-activating protein complex subunit 1SNAPC1
      • Protein or peptide: snRNA-activating protein complex subunit 3
    • Complex: TATA-box-binding protein and transcription factors
      • Protein or peptide: Transcription initiation factor IIB
      • Protein or peptide: TATA-box-binding protein
      • DNA: Template strandTranscription (biology)
    • Complex: Promoter
      • Protein or peptide: snRNA-activating protein complex subunit 4
      • Protein or peptide: snRNA-activating protein complex subunit 5
  • Ligand: ZINC ION

+
Supramolecule #1: General transcription factors and SNAPc bound to U1 promoter

SupramoleculeName: General transcription factors and SNAPc bound to U1 promoter
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#10

+
Supramolecule #2: SNAPc

SupramoleculeName: SNAPc / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2, #5-#8
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: TATA-box-binding protein and transcription factors

SupramoleculeName: TATA-box-binding protein and transcription factors / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1, #3-#4
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #4: Promoter

SupramoleculeName: Promoter / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #9-#10
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Transcription initiation factor IIB

MacromoleculeName: Transcription initiation factor IIB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.877949 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASTSRLDAL PRVTCPNHPD AILVEDYRAG DMICPECGLV VGDRVIDVGS EWRTFSNDKA TKDPSRVGDS QNPLLSDGDL STMIGKGTG AASFDEFGNS KYQNRRTMSS SDRAMMNAFK EITTMADRIN LPRNIVDRTN NLFKQVYEQK SLKGRANDAI A SACLYIAC ...String:
MASTSRLDAL PRVTCPNHPD AILVEDYRAG DMICPECGLV VGDRVIDVGS EWRTFSNDKA TKDPSRVGDS QNPLLSDGDL STMIGKGTG AASFDEFGNS KYQNRRTMSS SDRAMMNAFK EITTMADRIN LPRNIVDRTN NLFKQVYEQK SLKGRANDAI A SACLYIAC RQEGVPRTFK EICAVSRISK KEIGRCFKLI LKALETSVDL ITTGDFMSRF CSNLCLPKQV QMAATHIARK AV ELDLVPG RSPISVAAAA IYMASQASAE KRTQKEIGDI AGVADVTIRQ SYRLIYPRAP DLFPTDFKFD TPVDKLPQL

+
Macromolecule #3: TATA-box-binding protein

MacromoleculeName: TATA-box-binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.729938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDQNNSLPPY AQGLASPQGA MTPGIPIFSP MMPYGTGLTP QPIQNTNSLS ILEEQQRQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQ QQQQQQAVAA AAVQQSTSQQ ATQGTSGQAP QLFHSQTLTT APLPGTTPLY PSPMTPMTPI TPATPASESS G IVPQLQNI ...String:
MDQNNSLPPY AQGLASPQGA MTPGIPIFSP MMPYGTGLTP QPIQNTNSLS ILEEQQRQQQ QQQQQQQQQQ QQQQQQQQQQ QQQQQQQQQ QQQQQQAVAA AAVQQSTSQQ ATQGTSGQAP QLFHSQTLTT APLPGTTPLY PSPMTPMTPI TPATPASESS G IVPQLQNI VSTVNLGCKL DLKTIALRAR NAEYNPKRFA AVIMRIREPR TTALIFSSGK MVCTGAKSEE QSRLAARKYA RV VQKLGFP AKFLDFKIQN MVGSCDVKFP IRLEGLVLTH QQFSSYEPEL FPGLIYRMIK PRIVLLIFVS GKVVLTGAKV RAE IYEAFE NIYPILKGFR KTT

+
Macromolecule #5: Transcription initiation factor IIA subunit 1

MacromoleculeName: Transcription initiation factor IIA subunit 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.544551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANSANTNTV PKLYRSVIED VINDVRDIFL DDGVDEQVLM ELKTLWENKL MQSRAVDGFH SEEQQLLLQV QQQHQPQQQQ HHHHHHHQQ AQPQQTVPQQ AQTQQVLIPA SQQATAPQVI VPDSKLIQHM NASNMSAAAT AATLALPAGV TPVQQILTNS G QLLQVVRA ...String:
MANSANTNTV PKLYRSVIED VINDVRDIFL DDGVDEQVLM ELKTLWENKL MQSRAVDGFH SEEQQLLLQV QQQHQPQQQQ HHHHHHHQQ AQPQQTVPQQ AQTQQVLIPA SQQATAPQVI VPDSKLIQHM NASNMSAAAT AATLALPAGV TPVQQILTNS G QLLQVVRA ANGAQYIFQP QQSVVLQQQV IPQMQPGGVQ APVIQQVLAP LPGGISPQTG VIIQPQQILF TGNKTQVIPT TV AAPTPAQ AQITATGQQQ PQAQPAQTQA PLVLQVDGTG DTSSEEDEDE EEDYDDDEEE DKEKDGAEDG QVEEEPLNSE DDV SDEEGQ ELFDTENVVV CQYDKIHRSK NKWKFHLKDG IMNLNGRDYI FSKAIGDAEW

+
Macromolecule #6: Transcription initiation factor IIA subunit 2

MacromoleculeName: Transcription initiation factor IIA subunit 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.469091 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAYQLYRNTT LGNSLQESLD ELIQSQQITP QLALQVLLQF DKAINAALAQ RVRNRVNFRG SLNTYRFCDN VWTFVLNDVE FREVTELIK VDKVKIVACD GKNTGSNTTE

+
Macromolecule #7: snRNA-activating protein complex subunit 1

MacromoleculeName: snRNA-activating protein complex subunit 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.074473 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGTPPGLQTD CEALLSRFQE TDSVRFEDFT ELWRNMKFGT IFCGRMRNLE KNMFTKEALA LAWRYFLPPY TFQIRVGALY LLYGLYNTQ LCQPKQKIRV ALKDWDEVLK FQQDLVNAQH FDAAYIFRKL RLDRAFHFTA MPKLLSYRMK KKIHRAEVTE E FKDPSDRV ...String:
MGTPPGLQTD CEALLSRFQE TDSVRFEDFT ELWRNMKFGT IFCGRMRNLE KNMFTKEALA LAWRYFLPPY TFQIRVGALY LLYGLYNTQ LCQPKQKIRV ALKDWDEVLK FQQDLVNAQH FDAAYIFRKL RLDRAFHFTA MPKLLSYRMK KKIHRAEVTE E FKDPSDRV MKLITSDVLE EMLNVHDHYQ NMKHVISVDK SKPDKALSLI KDDFFDNIKN IVLEHQQWHK DRKNPSLKSK TN DGEEKME GNSQETERCE RAESLAKIKS KAFSVVIQAS KSRRHRQVKL DSSDSDSASG QGQVKATRKK EKKERLKPAG RKM SLRNKG NVQNIHKEDK PLSLSMPVIT EEEENESLSG TEFTASKKRR KH

+
Macromolecule #8: snRNA-activating protein complex subunit 3

MacromoleculeName: snRNA-activating protein complex subunit 3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.812605 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAEGSRGGPT CSGVGGRQDP VSGSGGCNFP EYELPELNTR AFHVGAFGEL WRGRLRGAGD LSLREPPASA LPGSQAADSD REDAAVARD LDCSLEAAAE LRAVCGLDKL KCLEDGEDPE VIPENTDLVT LGVRKRFLEH REETITIDRA CRQETFVYEM E SHAIGKKP ...String:
MAEGSRGGPT CSGVGGRQDP VSGSGGCNFP EYELPELNTR AFHVGAFGEL WRGRLRGAGD LSLREPPASA LPGSQAADSD REDAAVARD LDCSLEAAAE LRAVCGLDKL KCLEDGEDPE VIPENTDLVT LGVRKRFLEH REETITIDRA CRQETFVYEM E SHAIGKKP ENSADMIEEG ELILSVNILY PVIFHKHKEH KPYQTMLVLG SQKLTQLRDS IRCVSDLQIG GEFSNTPDQA PE HISKDLY KSAFFYFEGT FYNDKRYPEC RDLSRTIIEW SESHDRGYGK FQTARMEDFT FNDLCIKLGF PYLYCHQGDC EHV IVITDI RLVHHDDCLD RTLYPLLIKK HWLWTRKCFV CKMYTARWVT NNDSFAPEDP CFFCDVCFRM LHYDSEGNKL GEFL AYPYV DPGTFN

+
Macromolecule #9: snRNA-activating protein complex subunit 4

MacromoleculeName: snRNA-activating protein complex subunit 4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 159.645172 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDVDAEREKI TQEIKELERI LDPGSSGSHV EISESSLESD SEADSLPSED LDPADPPISE EERWGEASND EDDPKDKTLP EDPETCLQL NMVYQEVIQE KLAEANLLLA QNREQQEELM RDLAGSKGTK VKDGKSLPPS TYMGHFMKPY FKDKVTGVGP P ANEDTREK ...String:
MDVDAEREKI TQEIKELERI LDPGSSGSHV EISESSLESD SEADSLPSED LDPADPPISE EERWGEASND EDDPKDKTLP EDPETCLQL NMVYQEVIQE KLAEANLLLA QNREQQEELM RDLAGSKGTK VKDGKSLPPS TYMGHFMKPY FKDKVTGVGP P ANEDTREK AAQGIKAFEE LLVTKWKNWE KALLRKSVVS DRLQRLLQPK LLKLEYLHQK QSKVSSELER QALEKQGREA EK EIQDINQ LPEEALLGNR LDSHDWEKIS NINFEGSRSA EEIRKFWQNS EHPSINKQEW SREEEERLQA IAAAHGHLEW QKI AEELGT SRSAFQCLQK FQQHNKALKR KEWTEEEDRM LTQLVQEMRV GSHIPYRRIV YYMEGRDSMQ LIYRWTKSLD PGLK KGYWA PEEDAKLLQA VAKYGEQDWF KIREEVPGRS DAQCRDRYLR RLHFSLKKGR WNLKEEEQLI ELIEKYGVGH WAKIA SELP HRSGSQCLSK WKIMMGKKQG LRRRRRRARH SVRWSSTSSS GSSSGSSGGS SSSSSSSSEE DEPEQAQAGE GDRALL SPQ YMVPDMDLWV PARQSTSQPW RGGAGAWLGG PAASLSPPKG SSASQGGSKE ASTTAAAPGE ETSPVQVPAR AHGPVPR SA QASHSADTRP AGAEKQALEG GRRLLTVPVE TVLRVLRANT AARSCTQKEQ LRQPPLPTSS PGVSSGDSVA RSHVQWLR H RATQSGQRRW RHALHRRLLN RRLLLAVTPW VGDVVVPCTQ ASQRPAVVQT QADGLREQLQ QARLASTPVF TLFTQLFHI DTAGCLEVVR ERKALPPRLP QAGARDPPVH LLQASSSAQS TPGHLFPNVP AQEASKSASH KGSRRLASSR VERTLPQASL LASTGPRPK PKTVSELLQE KRLQEARARE ATRGPVVLPS QLLVSSSVIL QPPLPHTPHG RPAPGPTVLN VPLSGPGAPA A AKPGTSGS WQEAGTSAKD KRLSTMQALP LAPVFSEAEG TAPAASQAPA LGPGQISVSC PESGLGQSQA PAASRKQGLP EA PPFLPAA PSPTPLPVQP LSLTHIGGPH VATSVPLPVT WVLTAQGLLP VPVPAVVSLP RPAGTPGPAG LLATLLPPLT ETR AAQGPR APALSSSWQP PANMNREPEP SCRTDTPAPP THALSQSPAE ADGSVAFVPG EAQVAREIPE PRTSSHADPP EAEP PWSGR LPAFGGVIPA TEPRGTPGSP SGTQEPRGPL GLEKLPLRQP GPEKGALDLE KPPLPQPGPE KGALDLGLLS QEGEA ATQQ WLGGQRGVRV PLLGSRLPYQ PPALCSLRAL SGLLLHKKAL EHKATSLVVG GEAERPAGAL QASLGLVRGQ LQDNPA YLL LRARFLAAFT LPALLATLAP QGVRTTLSVP SRVGSESEDE DLLSELELAD RDGQPGCTTA TCPIQGAPDS GKCSASS CL DTSNDPDDLD VLRTRHARHT RKRRRLV

+
Macromolecule #10: snRNA-activating protein complex subunit 5

MacromoleculeName: snRNA-activating protein complex subunit 5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.343449 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MLSRLQELRK EEETLLRLKA ALHDQLNRLK VEELALQSMI SSRRGDEMLS SHTVPEQSHD MLVHVDNEAS INQTTLELST KSHVTEEEE EEEEEESDS

+
Macromolecule #2: Non-template strand

MacromoleculeName: Non-template strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.969139 KDa
SequenceString: (DG)(DC)(DA)(DA)(DG)(DT)(DG)(DA)(DC)(DC) (DG)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA)(DA) (DA)(DG)(DA)(DG)(DT)(DG)(DA)(DG)(DG) (DC)(DG)(DT)(DA)(DT)(DG)(DA)(DG)(DG)(DC) (DT) (DG)(DT)(DG)(DT)(DC)(DG) ...String:
(DG)(DC)(DA)(DA)(DG)(DT)(DG)(DA)(DC)(DC) (DG)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA)(DA) (DA)(DG)(DA)(DG)(DT)(DG)(DA)(DG)(DG) (DC)(DG)(DT)(DA)(DT)(DG)(DA)(DG)(DG)(DC) (DT) (DG)(DT)(DG)(DT)(DC)(DG)(DG)(DG) (DG)(DC)(DA)(DG)(DA)(DG)(DG)(DC)(DA)(DC) (DA)(DA) (DC)(DG)(DT)(DT)(DT)(DC)(DA) (DT)(DA)(DC)(DT)(DT)(DA)(DC)(DC)(DT)(DG) (DG)(DC)(DA) (DG)(DG)(DG)(DG)(DA)(DG) (DA)(DT)(DA)(DC)(DC)(DA)(DT)(DG)(DA)(DT)

+
Macromolecule #4: Template strand

MacromoleculeName: Template strand / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.261691 KDa
SequenceString: (DA)(DT)(DC)(DA)(DT)(DG)(DG)(DT)(DA)(DT) (DC)(DT)(DC)(DC)(DC)(DC)(DT)(DG)(DC)(DC) (DA)(DG)(DG)(DT)(DA)(DA)(DG)(DT)(DA) (DT)(DG)(DA)(DA)(DA)(DC)(DG)(DT)(DT)(DG) (DT) (DG)(DC)(DC)(DT)(DC)(DT) ...String:
(DA)(DT)(DC)(DA)(DT)(DG)(DG)(DT)(DA)(DT) (DC)(DT)(DC)(DC)(DC)(DC)(DT)(DG)(DC)(DC) (DA)(DG)(DG)(DT)(DA)(DA)(DG)(DT)(DA) (DT)(DG)(DA)(DA)(DA)(DC)(DG)(DT)(DT)(DG) (DT) (DG)(DC)(DC)(DT)(DC)(DT)(DG)(DC) (DC)(DC)(DC)(DG)(DA)(DC)(DA)(DC)(DA)(DG) (DC)(DC) (DT)(DC)(DA)(DT)(DA)(DC)(DG) (DC)(DC)(DT)(DC)(DA)(DC)(DT)(DC)(DT)(DT) (DT)(DA)(DC) (DA)(DC)(DA)(DC)(DA)(DC) (DG)(DG)(DT)(DC)(DA)(DC)(DT)(DT)(DG)(DC)

+
Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.45 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137246
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
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

Read more