[English] 日本語
Yorodumi
- EMDB-36908: Cryo-EM structure of yeast Rat1-bound Pol II pre-termination tran... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36908
TitleCryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 2 (Pol II Rat1-PTTC2)
Map data
Sample
  • Complex: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 and Spt5(PTC2)
    • Protein or peptide: x 15 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsTranscription termination / Pol II / Rat1/Rai1 Spt5 / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase II termination complex / sno(s)RNA processing / negative regulation of transcription elongation by RNA polymerase I / positive regulation of termination of RNA polymerase II transcription / RNA NAD+-cap (NAD+-forming) hydrolase activity / positive regulation of transcription elongation by RNA polymerase I / termination of RNA polymerase II transcription, poly(A)-coupled / Las1 complex / termination of RNA polymerase II transcription, exosome-dependent / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA ...RNA polymerase II termination complex / sno(s)RNA processing / negative regulation of transcription elongation by RNA polymerase I / positive regulation of termination of RNA polymerase II transcription / RNA NAD+-cap (NAD+-forming) hydrolase activity / positive regulation of transcription elongation by RNA polymerase I / termination of RNA polymerase II transcription, poly(A)-coupled / Las1 complex / termination of RNA polymerase II transcription, exosome-dependent / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / regulation of transcription-coupled nucleotide-excision repair / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / 5'-3' RNA exonuclease activity / regulation of rRNA processing / RNA polymerase I core binding / DSIF complex / intracellular mRNA localization / nuclear mRNA surveillance / rDNA heterochromatin / RNA polymerase I general transcription initiation factor binding / RPB4-RPB7 complex / snRNP binding / U4 snRNA binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA Polymerase I Transcription Initiation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Processing of Capped Intron-Containing Pre-mRNA / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / spliceosomal complex assembly / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / U5 snRNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / translesion synthesis / U2 snRNA binding / RNA polymerase II, core complex / U6 snRNA binding / positive regulation of autophagy / enzyme regulator activity / U1 snRNA binding / translation initiation factor binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / mRNA splicing, via spliceosome / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / rRNA processing / peroxisome / ribosome biogenesis / single-stranded DNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Similarity search - Function
5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain / RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease / Spt5 C-terminal nonapeptide repeat binding Spt4 ...5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain / RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB9 ...DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Decapping nuclease RAI1 / 5'-3' exoribonuclease 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZeng Y / Zhang Y
Funding support China, 2 items
OrganizationGrant numberCountry
Other governmentJCYJ-SHFY-2022-012 China
Other government2018YFA0900700 China
CitationJournal: Nature / Year: 2024
Title: Structural basis of exoribonuclease-mediated mRNA transcription termination.
Authors: Yuan Zeng / Hong-Wei Zhang / Xiao-Xian Wu / Yu Zhang /
Abstract: Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II ...Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II (Pol II). Here we report two cryogenic electron microscopy structures of Saccharomyces cerevisiae Pol II pre-termination transcription complexes bound to the 5'-to-3' exoribonuclease Rat1 and its partner Rai1. Our structures show that Rat1 displaces the elongation factor Spt5 to dock at the Pol II stalk domain. Rat1 shields the RNA exit channel of Pol II, guides the nascent RNA towards its active centre and stacks three nucleotides at the 5' terminus of the nascent RNA. The structures further show that Rat1 rotates towards Pol II as it shortens RNA. Our results provide the structural mechanism for the Rat1-mediated termination of mRNA transcription by Pol II in yeast and the exoribonuclease-mediated termination of mRNA transcription in other eukaryotes.
History
DepositionJul 23, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36908.png

Downloads & links

-
Map

FileDownload / File: emd_36908.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.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.9454819 - 2.3667789
Average (Standard dev.)-0.001496735 (±0.04746232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_36908_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_36908_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_36908_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : RNA Polymerase II pre-termination complex bound with Rat1-Rai1 an...

EntireName: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 and Spt5(PTC2)
Components
  • Complex: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 and Spt5(PTC2)
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB2
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4
    • DNA: DNA (38-MER)
    • RNA: RNA
    • DNA: DNA (38-MER)
    • Protein or peptide: Transcription elongation factor SPT5
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB4
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB7
    • Protein or peptide: 5'-3' exoribonuclease 2
    • Protein or peptide: Decapping nuclease RAI1
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 an...

SupramoleculeName: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 and Spt5(PTC2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

+
Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 191.821578 KDa
SequenceString: MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG ...String:
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG NTQPTIRKDG LKLVGSWKKD RATGDADEPE LRVLSTEEIL NIFKHISVKD FTSLGFNEVF SRPEWMILTC LP VPPPPVR PSISFNESQR GEDDLTFKLA DILKANISLE TLEHNGAPHH AIEEAESLLQ FHVATYMDND IAGQPQALQK SGR PVKSIR ARLKGKEGRI RGNLMGKRVD FSARTVISGD PNLELDQVGV PKSIAKTLTY PEVVTPYNID RLTQLVRNGP NEHP GAKYV IRDSGDRIDL RYSKRAGDIQ LQYGWKVERH IMDNDPVLFN RQPSLHKMSM MAHRVKVIPY STFRLNLSVT SPYNA DFDG DEMNLHVPQS EETRAELSQL CAVPLQIVSP QSNKPCMGIV QDTLCGIRKL TLRDTFIELD QVLNMLYWVP DWDGVI PTP AIIKPKPLWS GKQILSVAIP NGIHLQRFDE GTTLLSPKDN GMLIIDGQII FGVVEKKTVG SSNGGLIHVV TREKGPQ VC AKLFGNIQKV VNFWLLHNGF STGIGDTIAD GPTMREITET IAEAKKKVLD VTKEAQANLL TAKHGMTLRE SFEDNVVR F LNEARDKAGR LAEVNLKDLN NVKQMVMAGS KGSFINIAQM SACVGQQSVE GKRIAFGFVD RTLPHFSKDD YSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGS DAAFEKRYRV DLLNTDHTLD PSLLESGSEI LGDLKLQVLL DEEYKQLVKD RKFLREVFVD GEANWPLPVN I RRIIQNAQ QTFHIDHTKP SDLTIKDIVL GVKDLQENLL VLRGKNEIIQ NAQRDAVTLF CCLLRSRLAT RRVLQEYRLT KQ AFDWVLS NIEAQFLRSV VHPGEMVGVL AAQSIGEPAT QMTLNTFHFA GVASKKVTSG VPRLKEILNV AKNMKTPSLT VYL EPGHAA DQEQAKLIRS AIEHTTLKSV TIASEIYYDP DPRSTVIPED EEIIQLHFSL LDEEAEQSFD QQSPWLLRLE LDRA AMNDK DLTMGQVGER IKQTFKNDLF VIWSEDNDEK LIIRCRVVRP KSLDAETEAE EDHMLKKIEN TMLENITLRG VENIE RVVM MKYDRKVPSP TGEYVKEPEW VLETDGVNLS EVMTVPGIDP TRIYTNSFID IMEVLGIEAG RAALYKEVYN VIASDG SYV NYRHMALLVD VMTTQGGLTS VTRHGFNRSN TGALMRCSFE ETVEILFEAG ASAELDDCRG VSENVILGQM APIGTGA FD VMIDEESLVK YMPEQKITEI EDGQDGGVTP YSNESGLVNA DLDVKDELMF SPLVDSGSND AMAGGFTAYG GADYGEAT S PFGAYGEAPT SPGFGVSSPG FSPTSPTYSP TSPAYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP SYSPTSPSY SPTSPNYSPT SPSYSPTSPG YSPGSPAYSP KQDEQKHNEN ENSR

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

+
Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 2
Details: Residues (1225B-1259B) are an affinity tag(containing a TEV-6xHis-3xFlag tag) we modified in the genome of target strain for convenient protein purification.
Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 143.336766 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG ...String:
MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG RLPIMLRSKN CYLSEATESD LYKLKECPFD MGGYFIINGS EKVLIAQERS AGNIVQVFKK AAPSPISHVA EI RSALEKG SRFISTLQVK LYGREGSSAR TIKATLPYIK QDIPIVIIFR ALGIIPDGEI LEHICYDVND WQMLEMLKPC VED GFVIQD RETALDFIGR RGTALGIKKE KRIQYAKDIL QKEFLPHITQ LEGFESRKAF FLGYMINRLL LCALDRKDQD DRDH FGKKR LDLAGPLLAQ LFKTLFKKLT KDIFRYMQRT VEEAHDFNMK LAINAKTITS GLKYALATGN WGEQKKAMSS RAGVS QVLN RYTYSSTLSH LRRTNTPIGR DGKLAKPRQL HNTHWGLVCP AETPEGQACG LVKNLSLMSC ISVGTDPMPI ITFLSE WGM EPLEDYVPHQ SPDATRVFVN GVWHGVHRNP ARLMETLRTL RRKGDINPEV SMIRDIREKE LKIFTDAGRV YRPLFIV ED DESLGHKELK VRKGHIAKLM ATEYQDIEGG FEDVEEYTWS SLLNEGLVEY IDAEEEESIL IAMQPEDLEP AEANEEND L DVDPAKRIRV SHHATTFTHC EIHPSMILGV AASIIPFPDH NQSPRNTYQS AMGKQAMGVF LTNYNVRMDT MANILYYPQ KPLGTTRAME YLKFRELPAG QNAIVAIACY SGYNQEDSMI MNQSSIDRGL FRSLFFRSYM DQEKKYGMSI TETFEKPQRT NTLRMKHGT YDKLDDDGLI APGVRVSGED VIIGKTTPIS PDEEELGQRT AYHSKRDAST PLRSTENGIV DQVLVTTNQD G LKFVKVRV RTTKIPQIGD KFASRHGQKG TIGITYRRED MPFTAEGIVP DLIINPHAIP SRMTVAHLIE CLLSKVAALS GN EGDASPF TDITVEGISK LLREHGYQSR GFEVMYNGHT GKKLMAQIFF GPTYYQRLRH MVDDKIHARA RGPMQVLTRQ PVE GRSRDG GLRFGEMERD CMIAHGAASF LKERLMEASD AFRVHICGIC GLMTVIAKLN HNQFECKGCD NKIDIYQIHI PYAA KLLFQ ELMAMNITPR LYTDRSRDFE NLYFQGHHHH HHDYKDHDGD YKDHDIDYKD DDDK

UniProtKB: DNA-directed RNA polymerase II subunit RPB2

+
Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 35.330457 KDa
SequenceString: MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA ...String:
MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA KWGPAAAIEF EYDPWNKLKH TDYWYEQDSA KEWPQSKNCE YEDPPNEGDP FDYKAQADTF YMNVESVGSI PV DQVVVRG IDTLQKKVAS ILLALTQMDQ DKVNFASGDN NTASNMLGSN EDVMMTGAEQ DPYSNASQMG NTGSGGYDNA W

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

+
Macromolecule #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 25.117094 KDa
SequenceString: MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY ...String:
MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY RLKESQLPRI QRADPVALYL GLKRGEVVKI IRKSETSGRY ASYRICM

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

+
Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 17.931834 KDa
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTLK EKAIPKDQRA TTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR IAMKELAEKK IPLVIRRYLP DGSFEDWSVE ELIVDL

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

+
Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 16.525363 KDa
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTPA NDSSATRSWR PPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG GLLMRLEGNY RNLNNLKQEN AYLLIRR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

+
Macromolecule #7: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 14.308161 KDa
SequenceString:
MTTFRFCRDC NNMLYPREDK ENNRLLFECR TCSYVEEAGS PLVYRHELIT NIGETAGVVQ DIGSDPTLPR SDRECPKCHS RENVFFQSQ QRRKDTSMVL FFVCLSCSHI FTSDQKNKRT QFS

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

+
Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 8.290732 KDa
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKRD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

+
Macromolecule #9: DNA-directed RNA polymerase II subunit RPB11

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 13.633493 KDa
SequenceString:
MNAPDRFELF LLGEGESKLK IDPDTKAPNA VVITFEKEDH TLGNLIRAEL LNDRKVLFAA YKVEHPFFAR FKLRIQTTEG YDPKDALKN ACNSIINKLG ALKTNFETEW NLQTLAADDA F

UniProtKB: DNA-directed RNA polymerase II subunit RPB11

+
Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 7.729969 KDa
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

+
Macromolecule #14: Transcription elongation factor SPT5

MacromoleculeName: Transcription elongation factor SPT5 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 116.758031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHMSD NSDTNVSMQD HDQQFADPVV VPQSTDTKDE NTSDKDTVDS GNVTTTESTE RAESTSNIPP LDGEEKEAKS EPQQPEDNA ETAATEQVSS SNGPATDDAQ ATLNTDSSEA NEIVKKEEGS DERKRPREED TKNSDGDTKD EGDNKDEDDD E DDDDDDDD ...String:
MHHHHHHMSD NSDTNVSMQD HDQQFADPVV VPQSTDTKDE NTSDKDTVDS GNVTTTESTE RAESTSNIPP LDGEEKEAKS EPQQPEDNA ETAATEQVSS SNGPATDDAQ ATLNTDSSEA NEIVKKEEGS DERKRPREED TKNSDGDTKD EGDNKDEDDD E DDDDDDDD EDDDDEAPTK RRRQERNRFL DIEAEVSDDE DEDEDEEDSE LVREGFITHG DDEDDEASAP GARRDDRLHR QL DQDLNKT SEEDAQRLAK ELRERYGRSS SKQYRAAAQD GYVPQRFLLP SVDTATIWGV RCRPGKEKEL IRKLLKKKFN LDR AMGKKK LKILSIFQRD NYTGRIYIEA PKQSVIEKFC NGVPDIYISQ KLLIPVQELP LLLKPNKSDD VALEEGSYVR IKRG IYKGD LAMVDQISEN NLEVMLKIVP RLDYGKFDEI DPTTQQRKSR RPTFAHRAPP QLFNPTMALR LDQANLYKRD DRHFT YKNE DYIDGYLYKS FRIQHVETKN IQPTVEELAR FGSKEGAVDL TSVSQSIKKA QAAKVTFQPG DRIEVLNGEQ RGSKGI VTR TTKDIATIKL NGFTTPLEFP ISTLRKIFEP GDHVTVINGE HQGDAGLVLM VEQGQVTFMS TQTSREVTIT ANNLSKS ID TTATSSEYAL HDIVELSAKN VACIIQAGHD IFKVIDETGK VSTITKGSIL SKINTARARV SSVDANGNEI KIGDTIVE K VGSRREGQVL YIQTQQIFVV SKKIVENAGV FVVNPSNVEA VASKDNMLSN KMDLSKMNPE IISKMGPPSS KTFQQPIQS RGGREVALGK TVRIRSAGYK GQLGIVKDVN GDKATVELHS KNKHITIDKH KLTYYNREGG EGITYDELVN RRGRVPQARM GPSYVSAPR NMATGGIAAG AAATSSGLSG GMTPGWSSFD GGKTPAVNAH GGSGGGGVSS WGGASTWGGQ GNGGASAWGG A GGGASAWG GQGTGATSTW GGASAWGNKS SWGGASTWAS GGESNGAMST WGGTGDRSAY GGASTWGGNN NNKSTRDGGA SA WGNQDDG NRSAWNNQGN KSNYGGNSTW GGH

UniProtKB: Transcription elongation factor SPT5

+
Macromolecule #15: DNA-directed RNA polymerase II subunit RPB4

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB4 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 25.451191 KDa
SequenceString: MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK EALVERRRAF KRSQKKHKKK HLKHENAND ETTAVEDEDD DLDEDDVNAD DDDFMHSETR EKELESIDVL LEQTTGGNNK DLKNTMQYLT NFSRFRDQET V GAVIQLLK ...String:
MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK EALVERRRAF KRSQKKHKKK HLKHENAND ETTAVEDEDD DLDEDDVNAD DDDFMHSETR EKELESIDVL LEQTTGGNNK DLKNTMQYLT NFSRFRDQET V GAVIQLLK STGLHPFEVA QLGSLACDTA DEAKTLIPSL NNKISDDELE RILKELSNLE TLY

UniProtKB: DNA-directed RNA polymerase II subunit RPB4

+
Macromolecule #16: DNA-directed RNA polymerase II subunit RPB7

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 19.081053 KDa
SequenceString:
MFFIKDLSLN ITLHPSFFGP RMKQYLKTKL LEEVEGSCTG KFGYILCVLD YDNIDIQRGR ILPTDGSAEF NVKYRAVVFK PFKGEVVDG TVVSCSQHGF EVQVGPMKVF VTKHLMPQDL TFNAGSNPPS YQSSEDVITI KSRIRVKIEG CISQVSSIHA I GSIKEDYL GAI

UniProtKB: DNA-directed RNA polymerase II subunit RPB7

+
Macromolecule #17: 5'-3' exoribonuclease 2

MacromoleculeName: 5'-3' exoribonuclease 2 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 117.606508 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDMGVPSFF RWLSRKYPKI ISPVLEEQPQ IVDGVILPLD YSASNPNGEL DNLYLDMNGI VHPCSHPENK PPPETEDEM LLAVFEYTNR VLNMARPRKV LVMAVDGVAP RAKMNQQRAR RFRSARDAQI ENEAREEIMR QREEVGEIID D AVRNKKTW ...String:
MGSSHHHHHH SQDMGVPSFF RWLSRKYPKI ISPVLEEQPQ IVDGVILPLD YSASNPNGEL DNLYLDMNGI VHPCSHPENK PPPETEDEM LLAVFEYTNR VLNMARPRKV LVMAVDGVAP RAKMNQQRAR RFRSARDAQI ENEAREEIMR QREEVGEIID D AVRNKKTW DSNAITPGTP FMDKLAAALR YWTAFKLATD PGWKNLQVII SDATVPGEGE HKIMNFIRSQ RADPEYNPNT TH CIYGLDA DLIFLGLATH EPHFKILRED VFAQDNRKRN NLKDTINMTE EEKQFLQKQN SEQPFLWLHI NVLREYLSAE LWV PGLPFT FDLERAIDDW VFMCFFCGND FLPHLPCLDV RENSIDILLD IWKVVLPKLK TYMTCDGVLN LPSVETLLQH LGSR EGDIF KTRHIQEARK KEAFERRKAQ KNMSKGQDRH PTVATEQLQM YDTQGNLAKG SWNLTTSDMV RLKKELMLAN EGNEE AIAK VKQQSDKNNE LMKDISKEEI DDAVSKANKT NFNLAEVMKQ KIINKKHRLE KDNEEEEIAK DSKKVKTEKA ESECDL DAE IKDEIVADVN DRENSETTEV SRDSPVHSTV NVSEGPKNGV FDTDEFVKLF EPGYHERYYT AKFHVTPQDI EQLRKDM VK CYIEGVAWVL MYYYQGCASW NWFYPYHYAP LATDFHGFSH LEIKFEEGTP FLPYEQLMSV LPAASGHALP KIFRSLMS E PDSEIIDFYP EEFPIDMNGK KMSWQGIALL PFIDQDRLLT AVRAQYPLLS DAERARNIRG EPVLLISNKN ANYERFSKK LYSKENNNNN VVVKFQHFKS GLSGIVSKDV EGFELNGKIV CPIQGGSLPN LSTTLILKMS YRLIPLPSRN KSIILNGFIP SEPVLTAYD LDSIMYKYNN QNYSRRWNFG NDLKQNIVPV GPKGITQYKP RTGGYRAFFY FAELSRNNVQ PAHNYGRNSY N SQPGFNNS RYDGGNNNYR QNSNYRNNNY SGNRNSGQYS GNSYSRNNKQ SRYDNSRANR R

UniProtKB: 5'-3' exoribonuclease 2

+
Macromolecule #18: Decapping nuclease RAI1

MacromoleculeName: Decapping nuclease RAI1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 44.571445 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGVSANLFVK QRGSTTALKQ PKEIGFYSRT KDEEYLISDD TNLNYYYLPD AELDRKLDLS SGFQKFKDYY KDFEDRCSLR GLLETIESS ERHKGKKINA DIITFRGIAR KLISCAFDSP SFNTVDLRIV SFNGQLFIKE VPEAVNAAKA SSATEAGRNI N QDLNVFTG ...String:
MGVSANLFVK QRGSTTALKQ PKEIGFYSRT KDEEYLISDD TNLNYYYLPD AELDRKLDLS SGFQKFKDYY KDFEDRCSLR GLLETIESS ERHKGKKINA DIITFRGIAR KLISCAFDSP SFNTVDLRIV SFNGQLFIKE VPEAVNAAKA SSATEAGRNI N QDLNVFTG YKFETLATLS NPLQYTPREV IEKRTKRIVS HGDEYISVVR TGVGNCKLIL GAEVDCIFDF KENGRDNLKH YA ELKCTQQ VANISDTHKF ERKLFRTWLQ CFLVGIPRII YGFKDDHYVL KTVEEFSTEE VPVLLKNNNP QVGSACLEAI KWY GLLTEW LLKMIPRDED PHSQIRAFKL VFENNHLRLS EIEESDEEYS GLIDGEHILS NGFKEWRKSL K

UniProtKB: Decapping nuclease RAI1

+
Macromolecule #11: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.935569 KDa
SequenceString:
(DG)(DC)(DG)(DT)(DG)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DC)(DG) (DA)(DG)(DA)(DG)(DG)(DT)(DA)(DA)(DT) (DT)(DC)(DT)(DG)(DC)(DT)(DT)(DA)(DT)(DC) (DG) (DG)(DT)(DA)(DG)(DA)(DG)(DT)(DG)

+
Macromolecule #13: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.633406 KDa
SequenceString:
(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DC)(DC)(DG) (DA)(DT)(DA)(DA)(DG)(DC)(DA)(DG)(DA)(DA) (DT)(DT)(DA)(DC)(DC)(DT)(DC)(DT)(DC) (DG)(DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DC) (DT) (DA)(DG)(DA)(DC)(DA)(DC)(DG)(DC)

+
Macromolecule #12: RNA

MacromoleculeName: RNA / type: rna / ID: 12 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.446904 KDa
SequenceString:
ACAGAUGUCC UCGAGAGGUA

+
Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #20: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 20 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 0.01 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5vvs

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 265756
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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