[English] 日本語
Yorodumi
- EMDB-64271: CryoEM structure of T.thermophilus transcription initiation compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64271
TitleCryoEM structure of T.thermophilus transcription initiation complex bound to Gp4A-C, -1 dA in the template DNA strand
Map data
Sample
  • Complex: T.thermophilus transcription initiation complex
    • Complex: RNAP core enzyme
      • Protein or peptide: x 4 types
    • Complex: RNAP subunit sigma A
      • Protein or peptide: x 1 types
    • Complex: DNA scaffold
      • DNA: x 2 types
  • Ligand: x 5 types
KeywordsComplex / TRANSCRIPTION
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
: / DNA-directed RNA polymerase subunit beta', hybrid domain / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. ...: / DNA-directed RNA polymerase subunit beta', hybrid domain / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsDuan W / Kaushik A / Serganov A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112904 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21GM151508 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM088118-09 United States
CitationJournal: Nat Chem Biol / Year: 2025
Title: Molecular basis for noncanonical transcription initiation from NpA alarmones.
Authors: Wenqian Duan / Abhishek Kaushik / Ilona C Unarta / Yue Wu / Mengjie M J Liu / Jacob W Weaver / Bing Wang / William J Rice / Daniel J Luciano / Joel G Belasco / Xuhui Huang / Evgeny Nudler / Alexander Serganov /
Abstract: Stress-induced dinucleoside tetraphosphates (NpNs, where N is adenosine, guanosine, cytosine or uridine) are ubiquitous in living organisms, yet their function has been largely elusive for over 50 ...Stress-induced dinucleoside tetraphosphates (NpNs, where N is adenosine, guanosine, cytosine or uridine) are ubiquitous in living organisms, yet their function has been largely elusive for over 50 years. Recent studies have revealed that RNA polymerase can influence the cellular lifetime of transcripts by incorporating these alarmones into RNA as 5'-terminal caps. Here we present structural and biochemical data that reveal the molecular basis of noncanonical transcription initiation from NpAs by Escherichia coli and Thermus thermophilus RNA polymerases. Our results show the influence of the first two nucleotide incorporation steps on capping efficiency and the different interactions of NpAs with transcription initiation complexes. These data provide critical insights into the substrate selectivity that dictates levels of Np capping in bacterial cells.
History
DepositionApr 21, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_64271.png

Downloads & links

-
Map

FileDownload / File: emd_64271.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 322.8 Å		1.08 Å/pix.
x 300 pix.
= 322.8 Å		1.08 Å/pix.
x 300 pix.
= 322.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.33635694 - 1.1052705
Average (Standard dev.)0.001840299 (±0.04462416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 322.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_64271_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64271_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : T.thermophilus transcription initiation complex

EntireName: T.thermophilus transcription initiation complex
Components
  • Complex: T.thermophilus transcription initiation complex
    • Complex: RNAP core enzyme
      • Protein or peptide: DNA-directed RNA polymerase subunit alpha
      • Protein or peptide: DNA-directed RNA polymerase subunit beta
      • Protein or peptide: DNA-directed RNA polymerase subunit beta'
      • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Complex: RNAP subunit sigma A
      • Protein or peptide: RNA polymerase sigma factor SigA
    • Complex: DNA scaffold
      • DNA: template DNA strand
      • DNA: non-template DNA strand
  • Ligand: MAGNESIUM ION
  • Ligand: CHAPSO
  • Ligand: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate
  • Ligand: CYTIDINE-5'-MONOPHOSPHATE
  • Ligand: ZINC ION

+
Supramolecule #1: T.thermophilus transcription initiation complex

SupramoleculeName: T.thermophilus transcription initiation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

+
Supramolecule #2: RNAP core enzyme

SupramoleculeName: RNAP core enzyme / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

+
Supramolecule #3: RNAP subunit sigma A

SupramoleculeName: RNAP subunit sigma A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

+
Supramolecule #4: DNA scaffold

SupramoleculeName: DNA scaffold / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Synthetically produced: Yes

+
Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 35.056164 KDa
SequenceString: MLDSKLKAPV FTVRTQGREY GEFVLEPLER GFGVTLGNPL RRILLSSIPG TAVTSVYIED VLHEFSTIPG VKEDVVEIIL NLKELVVRF LNPSLQTVTL LLKAEGPKEV KARDFLPVAD VEIMNPDLHI ATLEEGGRLN MEVRVDRGVG YVPAEKHGIK D RINAIPVD ...String:
MLDSKLKAPV FTVRTQGREY GEFVLEPLER GFGVTLGNPL RRILLSSIPG TAVTSVYIED VLHEFSTIPG VKEDVVEIIL NLKELVVRF LNPSLQTVTL LLKAEGPKEV KARDFLPVAD VEIMNPDLHI ATLEEGGRLN MEVRVDRGVG YVPAEKHGIK D RINAIPVD AVFSPVRRVA FQVEDTRLGQ RTDLDKLTLR IWTDGSVTPL EALNQAVEIL REHLTYFSNP QAAAVAAPEE AK EPEAPPE QEEELDLPLE ELGLSTRVLH SLKEEGIESV RALLALNLKD LKNIPGIGER SLEEIKEALE KKGFTLKE

UniProtKB: DNA-directed RNA polymerase subunit alpha

+
Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 125.436539 KDa
SequenceString: MEIKRFGRIR EVIPLPPLTE IQVESYRRAL QADVPPEKRE NVGIQAAFRE TFPIEEEDKG KGGLVLDFLE YRLGEPPFPQ DECREKDLT YQAPLYARLQ LIHKDTGLIK EDEVFLGHIP LMTEDGSFII NGADRVIVSQ IHRSPGVYFT PDPARPGRYI A SIIPLPKR ...String:
MEIKRFGRIR EVIPLPPLTE IQVESYRRAL QADVPPEKRE NVGIQAAFRE TFPIEEEDKG KGGLVLDFLE YRLGEPPFPQ DECREKDLT YQAPLYARLQ LIHKDTGLIK EDEVFLGHIP LMTEDGSFII NGADRVIVSQ IHRSPGVYFT PDPARPGRYI A SIIPLPKR GPWIDLEVEP NGVVSMKVNK RKFPLVLLLR VLGYDQETLA RELGAYGELV QGLMDESVFA MRPEEALIRL FT LLRPGDP PKRDKAVAYV YGLIADPRRY DLGEAGRYKA EEKLGIRLSG RTLARFEDGE FKDEVFLPTL RYLFALTAGV PGH EVDDID HLGNRRIRTV GELMTDQFRV GLARLARGVR ERMLMGSEDS LTPAKLVNSR PLEAAIREFF SRSQLSQFKD ETNP LSSLR HKRRISALGP GGLTRERAGF DVRDVHRTHY GRICPVETPE GANIGLITSL AAYARVDELG FIRTPYRRVV GGVVT DEVV YMTATEEDRY TIAQANTPLE GNRIAAERVV ARRKGEPVIV SPEEVEFMDV SPKQVFSVNT NLIPFLEHDD ANRALM GSN MQTQAVPLIR AQAPVVMTGL EERVVRDSLA ALYAEEDGEV AKVDGNRIVV RYEDGRLVEY PLRRFYRSNQ GTALDQR PR VVVGQRVRKG DLLADGPASE NGFLALGQNV LVAIMPFDGY NFEDAIVISE ELLKRDFYTS IHIERYEIEA RDTKLGPE R ITRDIPHLSE AALRDLDEEG VVRIGAEVKP GDILVGRTSF KGESEPTPEE RLLRSIFGEK ARDVKDTSLR VPPGEGGIV VRTVRLRRGD PGVELKPGVR EVVRVYVAQK RKLQVGDKLA NRHGNKGVVA KILPVEDMPH LPDGTPVDVI LNPLGVPSRM NLGQILETH LGLAGYFLGQ RYISPIFDGA KEPEIKELLA QAFEVYFGKR KGEGFGVDKR EVEVLRRAEK LGLVTPGKTP E EQLKELFL QGKVVLYDGR TGEPIEGPIV VGQMFIMKLY HMVEDKMHAR STGPYSLITQ QPLGGKAQFG GQRFGEMEVW AL EAYGAAH TLQEMLTLKS DDIEGRNAAY EAIIKGEDVP EPSVPESFRV LVKELQALAL DVQTLDEKDN PVDIFEGLAS KR

UniProtKB: DNA-directed RNA polymerase subunit beta

+
Macromolecule #3: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 170.997391 KDa
SequenceString: MKKEVRKVRI ALASPEKIRS WSYGEVEKPE TINYRTLKPE RDGLFDERIF GPIKDYECAC GKYKRQRFEG KVCERCGVEV TKSIVRRYR MGHIELATPA AHIWFVKDVP SKIGTLLDLS ATELEQVLYF SKYIVLDPKG AILNGVPVEK RQLLTDEEYR E LRYGKQET ...String:
MKKEVRKVRI ALASPEKIRS WSYGEVEKPE TINYRTLKPE RDGLFDERIF GPIKDYECAC GKYKRQRFEG KVCERCGVEV TKSIVRRYR MGHIELATPA AHIWFVKDVP SKIGTLLDLS ATELEQVLYF SKYIVLDPKG AILNGVPVEK RQLLTDEEYR E LRYGKQET YPLPPGVDAL VKDGEEVVKG QELAPGVVSR LDGVALYRFP RRVRVEYVKK ERAGLRLPLA AWVEKEAYKP GE ILAELPE PYLFRAEEEG VVELKELEEG AFLVLRREDE PVATYFLPVG MTPLVVHGEI VEKGQPLAEA KGLLRMPRQV RAA QVEAEE EGETVYLTLF LEWTEPKDYR VQPHMNVVVP EGARVEAGDK IVAAIDPEEE VIAEAEGVVH LHEPASILVV KARV YPFED DVEVSTGDRV APGDVLADGG KVKSDVYGRV EVDLVRNVVR VVESYDIDAR MGAEAIQQLL KELDLEALEK ELLEE MKHP SRARRAKARK RLEVVRAFLD SGNRPEWMIL EAVPVLPPDL RPMVQVDGGR FATSDLNDLY RRLINRNNRL KKLLAQ GAP EIIIRNEKRM LQEAVDALLD NGRRGAPVTN PGSDRPLRSL TDILSGKQGR FRQNLLGKRV DYSGRSVIVV GPQLKLH QC GLPKRMALEL FKPFLLKKME EKGIAPNVKA ARRMLERQRD IKDEVWDALE EVIHGKVVLL NRAPTLHRLG IQAFQPVL V EGQSIQLHPL VCEAFNADFD GDQMAVHVPL SSFAQAEARI QMLSAHNLLS PASGEPLAKP SRDIILGLYY ITQVRKEKK GAGLEFATPE EALAAHERGE VALNAPIKVA GRETSVGRLK YVFANPDEAL LAVAHGIVDL QDVVTVRYMG KRLETSPGRI LFARIVAEA VEDEKVAWEL IQLDVPQEKN SLKDLVYQAF LRLGMEKTAR LLDALKYYGF TFSTTSGITI GIDDAVIPEE K KQYLEEAD RKLLQIEQAY EMGFLTDRER YDQILQLWTE TTEKVTQAVF KNFEENYPFN PLYVMAQSGA RGNPQQIRQL CG LRGLMQK PSGETFEVPV RSSFREGLTV LEYFISSHGA RKGGADTALR TADSGYLTRK LVDVTHEIVV READCGTTNY ISV PLFQPD EVTRSLRLRK RADIEAGLYG RVLAREVEVL GVRLEEGRYL SMDDVHLLIK AAEAGEIQEV PVRSPLTCQT RYGV CQKCY GYDLSMARPV SIGEAVGIVA AQSIGEPGTQ LTMRTFHTGG VAGAADITQG LPRVIELFEA RRPKAKAVIS EIDGV VRIE ETEEKLSVFV ESEGFSKEYK LPKEARLLVK DGDYVEAGQP LTRGAIDPHQ LLEAKGPEAV ERYLVEEIQK VYRAQG VKL HDKHIEIVVR QMMKYVEVTD PGDSRLLEGQ VLEKWDVEAL NERLIAEGKT PVAWKPLLMG VTKSALSTKS WLSAASF QN TTHVLTEAAI AGKKDELIGL KENVILGRLI PAGTGSDFVR FTQVVDQKTL KAIEEARKEA VEAKERPAAR RGVKREQP G KQA

UniProtKB: DNA-directed RNA polymerase subunit beta'

+
Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 11.533316 KDa
SequenceString:
MAEPGIDKLF GMVDSKYRLT VVVAKRAQQL LRHGFKNTVL EPEERPKMQT LEGLFDDPNA VTWAMKELLT GRLVFGENLV PEDRLQKEM ERLYPVEREE

UniProtKB: DNA-directed RNA polymerase subunit omega

+
Macromolecule #5: RNA polymerase sigma factor SigA

MacromoleculeName: RNA polymerase sigma factor SigA / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 50.900594 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MMKKSKRKNA QAQEAQETEV LVQEEAEELP EFPEGEPDPD LEDPDLTLED DLLDLPEEGE GLDLEEEEE DLPIPKISTS DPVRQYLHEI GQVPLLTLEE EVELARKVEE GMEAIKKLSE ITGLDPDLIR EVVRAKILGS A RVRHIPGL ...String:
MGSSHHHHHH SSGLVPRGSH MMKKSKRKNA QAQEAQETEV LVQEEAEELP EFPEGEPDPD LEDPDLTLED DLLDLPEEGE GLDLEEEEE DLPIPKISTS DPVRQYLHEI GQVPLLTLEE EVELARKVEE GMEAIKKLSE ITGLDPDLIR EVVRAKILGS A RVRHIPGL KETLDPKTVE EIDQKLKSLP KEHKRYLHIA REGEAARQHL IEANLRLVVS IAKKYTGRGL SFLDLIQEGN QG LIRAVEK FEYKRRFKFS TYATWWIRQA INRAIADQAR TIRIPVHMVE TINKLSRTAR QLQQELGREP TYEEIAEAMG PGW DAKRVE ETLKIAQEPV SLETPIGDEK DSFYGDFIPD EHLPSPVDAA TQSLLSEELE KALSKLSERE AMVLKLRKGL IDGR EHTLE EVGAFFGVTR ERIRQIENKA LRKLKYHESR TRKLRDFLD

UniProtKB: RNA polymerase sigma factor SigA

+
Macromolecule #6: template DNA strand

MacromoleculeName: template DNA strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 14.855575 KDa
SequenceString:
(DG)(DC)(DA)(DT)(DC)(DC)(DG)(DT)(DG)(DA) (DG)(DT)(DA)(DG)(DA)(DG)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DA)(DG)(DC)(DA)(DC)(DA) (DA)(DT)(DT)(DT)(DA)(DA)(DC)(DA)(DC)(DT) (DT) (DT)(DT)(DG)(DT)(DC)(DA)(DA)(DG)

+
Macromolecule #7: non-template DNA strand

MacromoleculeName: non-template DNA strand / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 14.863547 KDa
SequenceString:
(DC)(DT)(DT)(DG)(DA)(DC)(DA)(DA)(DA)(DA) (DG)(DT)(DG)(DT)(DT)(DA)(DA)(DA)(DT)(DT) (DG)(DT)(DG)(DC)(DT)(DA)(DT)(DA)(DC) (DT)(DG)(DG)(DG)(DA)(DG)(DC)(DC)(DG)(DT) (DC) (DA)(DC)(DG)(DG)(DA)(DT)(DG)(DC)

+
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #9: CHAPSO

MacromoleculeName: CHAPSO / type: ligand / ID: 9 / Number of copies: 1 / Formula: 1N7
Molecular weightTheoretical: 631.884 Da
Chemical component information

ChemComp-1N7:
CHAPSO / detergent*YM

+
Macromolecule #10: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidany...

MacromoleculeName: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4- ...Name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate
type: ligand / ID: 10 / Number of copies: 1 / Formula: A1IF9
Molecular weightTheoretical: 852.386 Da

+
Macromolecule #11: CYTIDINE-5'-MONOPHOSPHATE

MacromoleculeName: CYTIDINE-5'-MONOPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: C5P
Molecular weightTheoretical: 323.197 Da
Chemical component information

ChemComp-C:
CYTIDINE-5'-MONOPHOSPHATE

+
Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / 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: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 356931
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