[English] 日本語
Yorodumi
- EMDB-31622: human Pol III pre-termination complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31622
Titlehuman Pol III pre-termination complex
Map datahuman RNA polymerase III pre-termination complex (PTC)
Sample
  • Complex: human RNA polymerase III elongation complex
    • Complex: human RNA polymerase III elongation
      • Protein or peptide: x 17 types
    • Complex: RNA and DNA
      • RNA: x 1 types
      • DNA: x 2 types
  • Ligand: x 3 types
Function / homology
Function and homology information


snRNA transcription by RNA polymerase III / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / calcitonin gene-related peptide receptor activity / DNA/RNA hybrid binding / regulation of transcription by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / regulation of transcription by RNA polymerase III / DNA polymerase III complex / Cytosolic sensors of pathogen-associated DNA ...snRNA transcription by RNA polymerase III / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / calcitonin gene-related peptide receptor activity / DNA/RNA hybrid binding / regulation of transcription by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / regulation of transcription by RNA polymerase III / DNA polymerase III complex / Cytosolic sensors of pathogen-associated DNA / 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 / RNA polymerase III activity / positive regulation of innate immune response / Abortive elongation of HIV-1 transcript in the absence of Tat / nucleobase-containing compound metabolic process / MicroRNA (miRNA) biogenesis / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / termination of RNA polymerase III transcription / PIWI-interacting RNA (piRNA) biogenesis / RNA polymerase I activity / mRNA Splicing - Minor Pathway / 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 / tRNA transcription by RNA polymerase III / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / neuropeptide signaling pathway / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / positive regulation of interferon-beta production / mRNA Splicing - Major Pathway / acrosomal vesicle / protein-DNA complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / ribonucleoside binding / Formation of TC-NER Pre-Incision Complex / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / defense response to virus / Estrogen-dependent gene expression / cell population proliferation / transcription by RNA polymerase II / nucleic acid binding / protein stabilization / nuclear body / protein dimerization activity / nucleotide binding / intracellular membrane-bounded organelle / innate immune response / centrosome / DNA-templated transcription / chromatin binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
DNA-directed RNA polymerase III subunit RPC5, C-terminal / DNA-directed RNA polymerase III subunit RPC5 C-terminal / DNA-directed RNA polymerase III subunit RPC4 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III, subunit Rpc31 / DNA-directed RNA polymerase III subunit Rpc31 / Pol III subunit C11, C-terminal zinc ribbon / DNA-directed RNA polymerase III subunit Rpc5 / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC1, C-terminal ...DNA-directed RNA polymerase III subunit RPC5, C-terminal / DNA-directed RNA polymerase III subunit RPC5 C-terminal / DNA-directed RNA polymerase III subunit RPC4 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III, subunit Rpc31 / DNA-directed RNA polymerase III subunit Rpc31 / Pol III subunit C11, C-terminal zinc ribbon / DNA-directed RNA polymerase III subunit Rpc5 / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC1, C-terminal / RPC5 protein / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / RNA polymerase Rpc34 / RNA polymerase III Rpc82, C -terminal / RNA polymerase Rpc34-like / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase Rpc34 subunit / RNA polymerase III subunit RPC82 / DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 helix-turn-helix domain / DNA-directed RNA polymerase, subunit E/RPC8 / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / 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 / DNA-directed RNA polymerase subunit Rpo11 / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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, 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. / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4
Similarity search - Domain/homology
DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC7 / DNA-directed RNA polymerase III subunit RPC9 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 ...DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC7 / DNA-directed RNA polymerase III subunit RPC9 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase III subunit RPC3 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerase III subunit RPC10 / DNA-directed RNA polymerase III subunit RPC8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / Resolution: 3.6 Å
AuthorsHou H / Xu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31821002 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural insights into RNA polymerase III-mediated transcription termination through trapping poly-deoxythymidine.
Authors: Haifeng Hou / Yan Li / Mo Wang / Aijun Liu / Zishuo Yu / Ke Chen / Dan Zhao / Yanhui Xu /
Abstract: Termination of the RNA polymerase III (Pol III)-mediated transcription requires the conversion of an elongation complex (EC) to a pre-termination complex (PTC) on poly-deoxythymidine (dT)-containing ...Termination of the RNA polymerase III (Pol III)-mediated transcription requires the conversion of an elongation complex (EC) to a pre-termination complex (PTC) on poly-deoxythymidine (dT)-containing non-template strand, a mechanism distinct from Pol I and Pol II. Here, our in vitro transcription elongation assay showed that 5-7 dT-containing DNA template led to transcription termination of Pol III, but not Pol I or Pol II. We assembled human Pol III PTC on a 7 dT-containing DNA template and determined the structure at 3.6 Å resolution. The structure reveals that poly-dT are trapped in a narrow exit tunnel formed by RPC2. A hydrophobic gate of the exit tunnel separates the bases of two connected deoxythymidines and may prevent translocation of the non-template strand. The fork loop 2 stabilizes both template and non-template strands around the transcription fork, and may further prevent strand translocation. Our study shows that the Pol III-specific exit tunnel and FL2 allow for efficient translocation of non-poly-dT sequence during transcription elongation but trap poly-dT to promote DNA retention of Pol III, revealing molecular mechanism of poly-dT-dependent transcription termination of Pol III.
History
DepositionAug 4, 2021-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateNov 10, 2021-
Current statusNov 10, 2021Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7fjj
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31622.png

Downloads & links

-
Map

FileDownload / File: emd_31622.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman RNA polymerase III pre-termination complex (PTC)
Voxel sizeX=Y=Z: 1.054 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.02426493 - 0.079786226
Average (Standard dev.)1.6753036e-05 (±0.0020496834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 379.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0541.0541.054
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z379.440379.440379.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0240.0800.000

-
Supplemental data

-
Additional map: local refined map of PTC core

Fileemd_31622_additional_1.map
Annotationlocal refined map of PTC core
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : human RNA polymerase III elongation complex

EntireName: human RNA polymerase III elongation complex
Components
  • Complex: human RNA polymerase III elongation complex
    • Complex: human RNA polymerase III elongation
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC1Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC2Polymerase
      • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC1
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC9Polymerase
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC8Polymerase
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC10Polymerase
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC2
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC5Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC4Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC3Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC6Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC7Polymerase
    • Complex: RNA and DNA
      • RNA: RNA (5'-R(*CP*CP*GP*GP*GP*UP*GP*CP*UP*G)-3')
      • DNA: non-template DNA
      • DNA: template DNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster

+
Supramolecule #1: human RNA polymerase III elongation complex

SupramoleculeName: human RNA polymerase III elongation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Molecular weightTheoretical: 700 KDa

+
Supramolecule #2: human RNA polymerase III elongation

SupramoleculeName: human RNA polymerase III elongation / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#17
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

+
Supramolecule #3: RNA and DNA

SupramoleculeName: RNA and DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #18-#20

+
Macromolecule #1: DNA-directed RNA polymerase III subunit RPC1

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 155.860125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVKEQFRETD VAKKISHICF GMKSPEEMRQ QAHIQVVSKN LYSQDNQHAP LLYGVLDHRM GTSEKDRPCE TCGKNLADCL GHYGYIDLE LPCFHVGYFR AVIGILQMIC KTCCHIMLSQ EEKKQFLDYL KRPGLTYLQK RGLKKKISDK CRKKNICHHC G AFNGTVKK ...String:
MVKEQFRETD VAKKISHICF GMKSPEEMRQ QAHIQVVSKN LYSQDNQHAP LLYGVLDHRM GTSEKDRPCE TCGKNLADCL GHYGYIDLE LPCFHVGYFR AVIGILQMIC KTCCHIMLSQ EEKKQFLDYL KRPGLTYLQK RGLKKKISDK CRKKNICHHC G AFNGTVKK CGLLKIIHEK YKTNKKVVDP IVSNFLQSFE TAIEHNKEVE PLLGRAQENL NPLVVLNLFK RIPAEDVPLL LM NPEAGKP SDLILTRLLV PPLCIRPSVV SDLKSGTNED DLTMKLTEII FLNDVIKKHR ISGAKTQMIM EDWDFLQLQC ALY INSELS GIPLNMAPKK WTRGFVQRLK GKQGRFRGNL SGKRVDFSGR TVISPDPNLR IDEVAVPVHV AKILTFPEKV NKAN INFLR KLVQNGPEVH PGANFIQQRH TQMKRFLKYG NREKMAQELK YGDIVERHLI DGDVVLFNRQ PSLHKLSIMA HLARV KPHR TFRFNECVCT PYNADFDGDE MNLHLPQTEE AKAEALVLMG TKANLVTPRN GEPLIAAIQD FLTGAYLLTL KDTFFD RAK ACQIIASILV GKDEKIKVRL PPPTILKPVT LWTGKQIFSV ILRPSDDNPV RANLRTKGKQ YCGKGEDLCA NDSYVTI QN SELMSGSMDK GTLGSGSKNN IFYILLRDWG QNEAADAMSR LARLAPVYLS NRGFSIGIGD VTPGQGLLKA KYELLNAG Y KKCDEYIEAL NTGKLQQQPG CTAEETLEAL ILKELSVIRD HAGSACLREL DKSNSPLTMA LCGSKGSFIN ISQMIACVG QQAISGSRVP DGFENRSLPH FEKHSKLPAA KGFVANSFYS GLTPTEFFFH TMAGREGLVD TAVKTAETGY MQRRLVKSLE DLCSQYDLT VRSSTGDIIQ FIYGGDGLDP AAMEGKDEPL EFKRVLDNIK AVFPCPSEPA LSKNELILTT ESIMKKSEFL C CQDSFLQE IKKFIKGVSE KIKKTRDKYG INDNGTTEPR VLYQLDRITP TQVEKFLETC RDKYMRAQME PGSAVGALCA QS IGEPGTQ MTLKTFHFAG VASMNITLGV PRIKEIINAS KAISTPIITA QLDKDDDADY ARLVKGRIEK TLLGEISEYI EEV FLPDDC FILVKLSLER IRLLRLEVNA ETVRYSICTS KLRVKPGDVA VHGEAVVCVT PRENSKSSMY YVLQFLKEDL PKVV VQGIP EVSRAVIHID EQSGKEKYKL LVEGDNLRAV MATHGVKGTR TTSNNTYEVE KTLGIEAART TIINEIQYTM VNHGM SIDR RHVMLLSDLM TYKGEVLGIT RFGLAKMKES VLMLASFEKT ADHLFDAAYF GQKDSVCGVS ECIIMGIPMN IGTGLF KLL HKADRDPNPP KRPLIFDTNE FHIPLVT

+
Macromolecule #2: DNA-directed RNA polymerase III subunit RPC2

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.953891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDVLAEEFGN LTPEQLAAPI PTVEEKWRLL PAFLKVKGLV KQHIDSFNYF INVEIKKIMK ANEKVTSDAD PMWYLKYLNI YVGLPDVEE SFNVTRPVSP HECRLRDMTY SAPITVDIEY TRGSQRIIRN ALPIGRMPIM LRSSNCVLTG KTPAEFAKLN E CPLDPGGY ...String:
MDVLAEEFGN LTPEQLAAPI PTVEEKWRLL PAFLKVKGLV KQHIDSFNYF INVEIKKIMK ANEKVTSDAD PMWYLKYLNI YVGLPDVEE SFNVTRPVSP HECRLRDMTY SAPITVDIEY TRGSQRIIRN ALPIGRMPIM LRSSNCVLTG KTPAEFAKLN E CPLDPGGY FIVKGVEKVI LIQEQLSKNR IIVEADRKGA VGASVTSSTH EKKSRTNMAV KQGRFYLRHN TLSEDIPIVI IF KAMGVES DQEIVQMIGT EEHVMAAFGP SLEECQKAQI FTQMQALKYI GNKVRRQRMW GGGPKKTKIE EARELLASTI LTH VPVKEF NFRAKCIYTA VMVRRVILAQ GDNKVDDRDY YGNKRLELAG QLLSLLFEDL FKKFNSEMKK IADQVIPKQR AAQF DVVKH MRQDQITNGM VNAISTGNWS LKRFKMDRQG VTQVLSRLSY ISALGMMTRI SSQFEKTRKV SGPRSLQPSQ WGMLC PSDT PEGEACGLVK NLALMTHITT DMEDGPIVKL ASNLGVEDVN LLCGEELSYP NVFLVFLNGN ILGVIRDHKK LVNTFR LMR RAGYINEFVS ISTNLTDRCV YISSDGGRLC RPYIIVKKQK PAVTNKHMEE LAQGYRNFED FLHESLVEYL DVNEEND CN IALYEHTINK DTTHLEIEPF TLLGVCAGLI PYPHHNQSPR NTYQCAMGKQ AMGTIGYNQR NRIDTLMYLL AYPQKPMV K TKTIELIEFE KLPAGQNATV AVMSYSGYDI EDALVLNKAS LDRGFGRCLV YKNAKCTLKR YTNQTFDKVM GPMLDAATR KPIWRHEILD ADGICSPGEK VENKQVLVNK SMPTVTQIPL EGSNVPQQPQ YKDVPITYKG ATDSYIEKVM ISSNAEDAFL IKMLLRQTR RPEIGDKFSS RHGQKGVCGL IVPQEDMPFC DSGICPDIIM NPHGFPSRMT VGKLIELLAG KAGVLDGRFH Y GTAFGGSK VKDVCEDLVR HGYNYLGKDY VTSGITGEPL EAYIYFGPVY YQKLKHMVLD KMHARARGPR AVLTRQPTEG RS RDGGLRL GEMERDCLIG YGASMLLLER LMISSDAFEV DVCGQCGLLG YSGWCHYCKS SCHVSSLRIP YACKLLFQEL QSM NIIPRL KLSKYNE

+
Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1

MacromoleculeName: DNA-directed RNA polymerases I and III subunit RPAC1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.301672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAASQAVEEM RSRVVLGEFG VRNVHTTDFP GNYSGYDDAW DQDRFEKNFR VDVVHMDENS LEFDMVGIDA AIANAFRRIL LAEVPTMAV EKVLVYNNTS IVQDEILAHR LGLIPIHADP RLFEYRNQGD EEGTEIDTLQ FRLQVRCTRN PHAAKDSSDP N ELYVNHKV ...String:
MAASQAVEEM RSRVVLGEFG VRNVHTTDFP GNYSGYDDAW DQDRFEKNFR VDVVHMDENS LEFDMVGIDA AIANAFRRIL LAEVPTMAV EKVLVYNNTS IVQDEILAHR LGLIPIHADP RLFEYRNQGD EEGTEIDTLQ FRLQVRCTRN PHAAKDSSDP N ELYVNHKV YTRHMTWIPL GNQADLFPEG TIRPVHDDIL IAQLRPGQEI DLLMHCVKGI GKDHAKFSPV ATASYRLLPD IT LLEPVEG EAAEELSRCF SPGVIEVQEV QGKKVARVAN PRLDTFSREI FRNEKLKKVV RLARVRDHYI FSVESTGVLP PDV LVSEAI KVLMGKCRRF LDELDAVQMD

+
Macromolecule #4: DNA-directed RNA polymerase III subunit RPC9

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC9 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.89399 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEVKDANSAL LSNYEVFQLL TDLKEQRKES GKNKHSSGQQ NLNTITYETL KYISKTPCRH QSPEIVREFL TALKSHKLTK AEKLQLLNH RPVTAVEIQL MVEESEERLT EEQIEALLHT VTSILPAEPE AEQKKNTNSN VAMDEEDPA

+
Macromolecule #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.584223 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQSGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN ...String:
MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQSGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN QLPRIQAGDP VARYFGIKRG QVVKIIRPSE TAGRYITYRL VQ

+
Macromolecule #6: 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: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.491026 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIITD

+
Macromolecule #7: DNA-directed RNA polymerase III subunit RPC8

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.938846 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVLVEMVDT VRIPPWQFER KLNDSIAEEL NKKLANKVVY NVGLCICLFD ITKLEDAYVF PGDGASHTKV HFRCVVFHPF LDEILIGKI KGCSPEGVHV SLGFFDDILI PPESLQQPAK FDEAEQVWVW EYETEEGAHD LYMDTGEEIR FRVVDESFVD T SPTGPSSA ...String:
MFVLVEMVDT VRIPPWQFER KLNDSIAEEL NKKLANKVVY NVGLCICLFD ITKLEDAYVF PGDGASHTKV HFRCVVFHPF LDEILIGKI KGCSPEGVHV SLGFFDDILI PPESLQQPAK FDEAEQVWVW EYETEEGAHD LYMDTGEEIR FRVVDESFVD T SPTGPSSA DATTSSEELP KKEAPYTLVG SISEPGLGLL SWWTSN

+
Macromolecule #8: 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: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.162273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGTL DDGEYNPTDD RPSRADQFE YVMYGKVYRI EGDETSTEAA TRLSAYVSYG GLLMRLQGDA NNLHGFEVDS RVYLLMKKLA F

+
Macromolecule #9: DNA-directed RNA polymerase III subunit RPC10

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.338104 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MLLFCPGCGN GLIVEEGQRC HRFACNTCPY VHNITRKVTN RKYPKLKEVD DVLGGAAAWE NVDSTAESCP KCEHPRAYFM QLQTRSADE PMTTFYKCCN AQCGHRWRD

+
Macromolecule #10: 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: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.655123 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

+
Macromolecule #11: DNA-directed RNA polymerases I and III subunit RPAC2

MacromoleculeName: DNA-directed RNA polymerases I and III subunit RPAC2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.259222 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEEDQELERK ISGLKTSMAE GERKTALEMV QAAGTDRHCV TFVLHEEDHT LGNSLRYMIM KNPEVEFCGY TTTHPSESKI NLRIQTRGT LPAVEPFQRG LNELMNVCQH VLDKFEASIK DYKDQKASRN ESTF

+
Macromolecule #12: 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: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.018244 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

+
Macromolecule #13: DNA-directed RNA polymerase III subunit RPC5

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC5 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.004031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MANEEDDPVV QEIDVYLAKS LAEKLYLFQY PVRPASMTYD DIPHLSAKIK PKQQKVELEM AIDTLNPNYC RSKGEQIALN VDGACADET STYSSKLMDK QTFCSSQTTS NTSRYAAALY RQGELHLTPL HGILQLRPSF SYLDKADAKH REREAANEAG D SSQDEAED ...String:
MANEEDDPVV QEIDVYLAKS LAEKLYLFQY PVRPASMTYD DIPHLSAKIK PKQQKVELEM AIDTLNPNYC RSKGEQIALN VDGACADET STYSSKLMDK QTFCSSQTTS NTSRYAAALY RQGELHLTPL HGILQLRPSF SYLDKADAKH REREAANEAG D SSQDEAED DVKQITVRFS RPESEQARQR RVQSYEFLQK KHAEEPWVHL HYYGLRDSRS EHERQYLLCP GSSGVENTEL VK SPSEYLM MLMPPSQEEE KDKPVAPSNV LSMAQLRTLP LADQIKILMK NVKVMPFANL MSLLGPSIDS VAVLRGIQKV AML VQGNWV VKSDILYPKD SSSPHSGVPA EVLCRGRDFV MWKFTQSRWV VRKEVATVTK LCAEDVKDFL EHMAVVRINK GWEF ILPYD GEFIKKHPDV VQRQHMLWTG IQAKLEKVYN LVKETMPKKP DAQSGPAGLV CGDQRIQVAK TKAQQNHALL ERELQ RRKE QLRVPAVPPG VRIKEEPVSE EGEEDEEQEA EEEPMDTSPS GLHSKLANGL PLGRAAGTDS FNGHPPQGCA STPVAR ELK AFVEATFQRQ FVLTLSELKR LFNLHLASLP PGHTLFSGIS DRMLQDTVLA AGCKQILVPF PPQTAASPDE QKVFALW ES GDMSDQHRQV LLEIFSKNYR VRRNMIQSRL TQECGEDLSK QEVDKVLKDC CVSYGGMWYL KGTVQS

+
Macromolecule #14: DNA-directed RNA polymerase III subunit RPC4

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.471875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSEGNAAGEP STPGGPRPLL TGARGLIGRR PAPPLTPGRL PSIRSRDLTL GGVKKKTFTP NIISRKIKEE PKEEVTVKKE KRERDRDRQ REGHGRGRGR PEVIQSHSIF EQGPAEMMKK KGNWDKTVDV SDMGPSHIIN IKKEKRETDE ETKQILRMLE K DDFLDDPG ...String:
MSEGNAAGEP STPGGPRPLL TGARGLIGRR PAPPLTPGRL PSIRSRDLTL GGVKKKTFTP NIISRKIKEE PKEEVTVKKE KRERDRDRQ REGHGRGRGR PEVIQSHSIF EQGPAEMMKK KGNWDKTVDV SDMGPSHIIN IKKEKRETDE ETKQILRMLE K DDFLDDPG LRNDTRNMPV QLPLAHSGWL FKEENDEPDV KPWLAGPKEE DMEVDIPAVK VKEEPRDEEE EAKMKAPPKA AR KTPGLPK DVSVAELLRE LSLTKEEELL FLQLPDTLPG QPPTQDIKPI KTEVQGEDGQ VVLIKQEKDR EAKLAENACT LAD LTEGQV GKLLIRKSGR VQLLLGKVTL DVTMGTACSF LQELVSVGLG DSRTGEMTVL GHVKHKLVCS PDFESLLDHK HR

+
Macromolecule #15: DNA-directed RNA polymerase III subunit RPC3

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.692555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTQAEIKLCS LLLQEHFGEI VEKIGVHLIR TGSQPLRVIA HDTGTSLDQV KKALCVLVQH NLVSYQVHKR GVVEYEAQCS RVLRMLRYP RYIYTTKTLY SDTGELIVEE LLLNGKLTMS AVVKKVADRL TETMEDGKTM DYAEVSNTFV RLADTHFVQR C PSVPTTEN ...String:
MTQAEIKLCS LLLQEHFGEI VEKIGVHLIR TGSQPLRVIA HDTGTSLDQV KKALCVLVQH NLVSYQVHKR GVVEYEAQCS RVLRMLRYP RYIYTTKTLY SDTGELIVEE LLLNGKLTMS AVVKKVADRL TETMEDGKTM DYAEVSNTFV RLADTHFVQR C PSVPTTEN SDPGPPPPAP TLVINEKDMY LVPKLSLIGK GKRRRSSDED AAGEPKAKRP KYTTDNKEPI PDDGIYWQAN LD RFHQHFR DQAIVSAVAN RMDQTSSEIV RTMLRMSEIT TSSSAPFTQP LSSNEIFRSL PVGYNISKQV LDQYLTLLAD DPL EFVGKS GDSGGGMYVI NLHKALASLA TATLESVVQE RFGSRCARIF RLVLQKKHIE QKQVEDFAMI PAKEAKDMLY KMLS ENFMS LQEIPKTPDH APSRTFYLYT VNILSAARML LHRCYKSIAN LIERRQFETK ENKRLLEKSQ RVEAIIASMQ ATGAE EAQL QEIEEMITAP ERQQLETLKR NVNKLDASEI QVDETIFLLE SYIECTMKRQ

+
Macromolecule #16: DNA-directed RNA polymerase III subunit RPC6

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC6 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.726914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEVKVKVQP PDADPVEIEN RIIELCHQFP HGITDQVIQN EMPHIEAQQR AVAINRLLSM GQLDLLRSNT GLLYRIKDSQ NAGKMKGSD NQEKLVYQII EDAGNKGIWS RDIRYKSNLP LTEINKILKN LESKKLIKAV KSVAASKKKV YMLYNLQPDR S VTGGAWYS ...String:
MAEVKVKVQP PDADPVEIEN RIIELCHQFP HGITDQVIQN EMPHIEAQQR AVAINRLLSM GQLDLLRSNT GLLYRIKDSQ NAGKMKGSD NQEKLVYQII EDAGNKGIWS RDIRYKSNLP LTEINKILKN LESKKLIKAV KSVAASKKKV YMLYNLQPDR S VTGGAWYS DQDFESEFVE VLNQQCFKFL QSKAETARES KQNPMIQRNS SFASSHEVWK YICELGISKV ELSMEDIETI LN TLIYDGK VEMTIIAAKE GTVGSVDGHM KLYRAVNPII PPTGLVRAPC GLCPVFDDCH EGGEISPSNC IYMTEWLEF

+
Macromolecule #17: DNA-directed RNA polymerase III subunit RPC7

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC7 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.95351 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGNKGRGRA AYTFNIEAVG FSKGEKLPDV VLKPPPLFPD TDYKPVPLKT GEGEEYMLAL KQELRETMKR MPYFIETPEE RQDIERYSK RYMKVYKEEW IPDWRRLPRE MMPRNKCKKA GPKPKKAKDA GKGTPLTNTE DVLKKMEELE KRGDGEKSDE E NEEKEGSK ...String:
MAGNKGRGRA AYTFNIEAVG FSKGEKLPDV VLKPPPLFPD TDYKPVPLKT GEGEEYMLAL KQELRETMKR MPYFIETPEE RQDIERYSK RYMKVYKEEW IPDWRRLPRE MMPRNKCKKA GPKPKKAKDA GKGTPLTNTE DVLKKMEELE KRGDGEKSDE E NEEKEGSK EKSKEGDDDD DDDAAEQEEY DEEEQEEEND YINSYFEDGD DFGADSDDNM DEATY

+
Macromolecule #18: RNA (5'-R(*CP*CP*GP*GP*GP*UP*GP*CP*UP*G)-3')

MacromoleculeName: RNA (5'-R(*CP*CP*GP*GP*GP*UP*GP*CP*UP*G)-3') / type: rna / ID: 18 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.208948 KDa
SequenceString:
CCGGGUGCUG

+
Macromolecule #19: non-template DNA

MacromoleculeName: non-template DNA / type: dna / ID: 19 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.602605 KDa
SequenceString: (DC)(DC)(DG)(DC)(DC)(DT)(DG)(DG)(DG)(DA) (DA)(DT)(DA)(DC)(DC)(DG)(DG)(DG)(DT)(DG) (DC)(DT)(DT)(DA)(DC)(DG)(DA)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DC)(DA)(DG)(DA)(DC) (DT) (DA)(DG)(DA)(DG)(DC)(DC) ...String:
(DC)(DC)(DG)(DC)(DC)(DT)(DG)(DG)(DG)(DA) (DA)(DT)(DA)(DC)(DC)(DG)(DG)(DG)(DT)(DG) (DC)(DT)(DT)(DA)(DC)(DG)(DA)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DC)(DA)(DG)(DA)(DC) (DT) (DA)(DG)(DA)(DG)(DC)(DC)(DG)(DC) (DT)(DG)(DT)(DT)(DT)(DC)

+
Macromolecule #20: template DNA

MacromoleculeName: template DNA / type: dna / ID: 20 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.570594 KDa
SequenceString: (DG)(DA)(DA)(DA)(DC)(DA)(DG)(DC)(DG)(DG) (DC)(DT)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DG) (DT)(DC)(DC)(DA)(DG)(DC)(DA)(DC)(DC) (DC)(DG)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DC) (DG) (DG)(DT)(DA)(DT)(DT)(DC) ...String:
(DG)(DA)(DA)(DA)(DC)(DA)(DG)(DC)(DG)(DG) (DC)(DT)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DG) (DT)(DC)(DC)(DA)(DG)(DC)(DA)(DC)(DC) (DC)(DG)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DC) (DG) (DG)(DT)(DA)(DT)(DT)(DC)(DC)(DC) (DA)(DG)(DG)(DC)(DG)(DG)

+
Macromolecule #21: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #22: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 22 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #23: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 23 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

-
Experimental details

-
Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.38 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48593

+
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