[English] 日本語
Yorodumi
- EMDB-13034: Cryo-EM structure of the cellular negative regulator TFS4 bound t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13034
TitleCryo-EM structure of the cellular negative regulator TFS4 bound to the archaeal RNA polymerase
Map dataSharpened map from Autosharpen, Phenix v1.15.2
Sample
  • Complex: TFS4 bound to the RNA polymerase
    • Protein or peptide: x 14 types
  • Ligand: x 3 types
Keywordsnegative regulator / inhibitor / Archaea / Sso TFS4 / trancript cleavage factor / TRANSCRIPTION
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / RNA polymerase III activity / RNA polymerase II activity / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / defense response to virus ...3 iron, 4 sulfur cluster binding / RNA polymerase III activity / RNA polymerase II activity / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / defense response to virus / protein dimerization activity / negative regulation of DNA-templated transcription / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo7 ...RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo7 / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / 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 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / RNA polymerases M / 15 Kd subunits signature. / : / 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, 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. / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / 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 / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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, 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 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo12 ...DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo13 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo4 / Transcription factor S4
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic) / Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsPilotto S / Fouqueau T
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust207446/Z/17/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of RNA polymerase inhibition by viral and host factors.
Authors: Simona Pilotto / Thomas Fouqueau / Natalya Lukoyanova / Carol Sheppard / Soizick Lucas-Staat / Luis Miguel Díaz-Santín / Dorota Matelska / David Prangishvili / Alan C M Cheung / Finn Werner /
Abstract: RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution ...RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.
History
DepositionJun 4, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7oqy
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13034.png

Downloads & links

-
Map

FileDownload / File: emd_13034.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from Autosharpen, Phenix v1.15.2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.09 Å/pix.
x 332 pix.
= 360.22 Å		1.09 Å/pix.
x 332 pix.
= 360.22 Å		1.09 Å/pix.
x 332 pix.
= 360.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.2 / Movie #1: 3.2
Minimum - Maximum-35.127827000000003 - 51.285446
Average (Standard dev.)0.000000000003778 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions332332332
Spacing332332332
CellA=B=C: 360.22 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z332332332
origin x/y/z0.0000.0000.000
length x/y/z360.220360.220360.220
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ332332332
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS332332332
D min/max/mean-35.12851.2850.000

-
Supplemental data

-
Additional map: Sharpened map from postprocess, relion v3.0. The map...

Fileemd_13034_additional_1.map
AnnotationSharpened map from postprocess, relion v3.0. The map was obtained from Multibody refinement and it corresponds to the smaller body with higher flexibility
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half1 map from 3D refinement, relion v3.0

Fileemd_13034_half_map_1.map
AnnotationHalf1 map from 3D refinement, relion v3.0
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half2 map from 3D refinement, relion v3.0

Fileemd_13034_half_map_2.map
AnnotationHalf2 map from 3D refinement, relion v3.0
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : TFS4 bound to the RNA polymerase

EntireName: TFS4 bound to the RNA polymerase
Components
  • Complex: TFS4 bound to the RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit A'
    • Protein or peptide: DNA-directed RNA polymerase subunit B
    • Protein or peptide: DNA-directed RNA polymerase subunit A''
    • Protein or peptide: DNA-directed RNA polymerase subunit D
    • Protein or peptide: DNA-directed RNA polymerase subunit E
    • Protein or peptide: DNA-directed RNA polymerase, subunit F
    • Protein or peptide: DNA-directed RNA polymerase, subunit G
    • Protein or peptide: DNA-directed RNA polymerase subunit H
    • Protein or peptide: DNA-directed RNA polymerase subunit K
    • Protein or peptide: DNA-directed RNA polymerase subunit L
    • Protein or peptide: DNA-directed RNA polymerase subunit N
    • Protein or peptide: DNA-directed RNA polymerase subunit P
    • Protein or peptide: Conserved protein
    • Protein or peptide: DNA-directed RNA polymerase, subunit M (RpoM-2)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: FE3-S4 CLUSTER

+
Supramolecule #1: TFS4 bound to the RNA polymerase

SupramoleculeName: TFS4 bound to the RNA polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 414 KDa

+
Macromolecule #1: DNA-directed RNA polymerase subunit A'

MacromoleculeName: DNA-directed RNA polymerase subunit A' / type: protein_or_peptide / ID: 1 / Details: DNA-dependent RNA polymerase subunit RPOA' (RPO1N) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 99.929055 KDa
SequenceString: MSEKIIRGVK FGVLSPNEIR QMSVTAIITS EVYDEDGTPI EGGVMDPKLG VIEPGQKCPV CGNTLAGCPG HFGHIELIKP VIHIGYVKH IYDFLRSTCW RCGRIKIKEQ DLERYKRIYN AIKLRWPSAA RRLVEYIKKI SIKNLECPHC GEKQFKIKLE K PYNFNEER ...String:
MSEKIIRGVK FGVLSPNEIR QMSVTAIITS EVYDEDGTPI EGGVMDPKLG VIEPGQKCPV CGNTLAGCPG HFGHIELIKP VIHIGYVKH IYDFLRSTCW RCGRIKIKEQ DLERYKRIYN AIKLRWPSAA RRLVEYIKKI SIKNLECPHC GEKQFKIKLE K PYNFNEER NGSIVKLSPS EIRDRLERIP DSDVELLGYD PKSSRPEWMI LTVLPVPPIT IRPSITIESG IRAEDDLTHK LV DIIRLNE RLKESIEAGA PQLIIEDLWD LLQYHVATYF DNEIPGLPPA KHRSGRPLRT LAQRLKGKEG RFRGNLSGKR VDF SARTVI SPDPNLSIDE VGIPYTIARM LTVPERVTNI NIERIRQYII NGPDKWPGAN YVIKPDGRRI DLRYVKDRKE LASS ITAGY VVERHLVDGD VVLFNRQPSL HRISMMAHKV RVLPGRTFRL NLLDCPPYNA DFDGDEMNLH VPQSEEAIAE ARELM LVHK NIITPRYGGP IIGGGQDYIS GAYLLSVKTT LLTVEEVATI LGVTDFVGEL GEPAILAPKP YYTGKQVISL FLPKDF NFH GPANISKGPR ACKDEICPHD SFIVIKNGLL LEGVFDKKAI GNQQPESMLH WSIREYGTEY GKWLMDNVFK MFIRFLE MR GFTMTLEDIT IPDEAQNEIT TKIKEGYSQV DEYIRKFNEG QLEPIPGRTI EESLESYILD TLDKLRKVAG EIATKYLD P FNNVYIMAIT GARGSELNIT QMTALLGQQS VRGERIRRGY RERTLSLFKY GDIAPEARGF VKNSFMRGLS PYEMFFHAA GGREGLVDTA VKTSQSGYMQ RRLINALSDL RIEYDGTVRS LYGDIVQVVY GDDAVHPMYS AHSKSVNVNR VIERVIGWKR

UniProtKB: DNA-directed RNA polymerase subunit Rpo1N

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

MacromoleculeName: DNA-directed RNA polymerase subunit B / type: protein_or_peptide / ID: 2 / Details: DNA-dependent RNA polymerase subunit RPOB (RPO2) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Molecular weightTheoretical: 126.647102 KDa
SequenceString: MLDTESRWAI AESFFKTRGL VRQHLDSFND FLRNKLQQVI YEQGEIVTEV PGLKIKLGKI RYEKPSIRET DKGPMREITP MEARLRNLT YSSPIFLSMI PVENNIEGEP IEIYIGDLPI MLKSVADPTS NLPIDKLIEI GEDPKDPGGY FIVNGSEKVI I AQEDLATN ...String:
MLDTESRWAI AESFFKTRGL VRQHLDSFND FLRNKLQQVI YEQGEIVTEV PGLKIKLGKI RYEKPSIRET DKGPMREITP MEARLRNLT YSSPIFLSMI PVENNIEGEP IEIYIGDLPI MLKSVADPTS NLPIDKLIEI GEDPKDPGGY FIVNGSEKVI I AQEDLATN RVLVDYGKSG SNITHVAKVT SSAAGYRVQV MIERLKDSTI QISFATVPGR IPFAIIMRAL GFVTDRDIVY AV SLDPQIQ NELLPSLEQA SSITSAEEAL DFIGNRVAIG QKRENRIQKA EQVIDKYFLP HLGTSPEDRK KKGYYLASAV NKI LELYLG RREPDDKDHY ANKRVRLAGD LFTSLFRVAF KAFVKDLVYQ LEKSKVRGRR LSLTALVRAD IITERIRHAL ATGN WVGGR TGVSQLLDRT NWLSMLSHLR RVVSSLARGQ PNFEARDLHG TQWGRMCPFE TPEGPNSGLV KNLALLAQVS VGINE SVVE RVAYELGVVS VEDVIRRISE QNEDVEKYMS WSKVYLNGRL LGYYEDGKEL AKKIRESRRQ GKLSDEVNVA YIATDY LNE VHINCDAGRV RRPLIIVNNG TPLVDTEDIK KLKNGEITFD DLVKQGKIEF IDAEEEENAY VALNPQDLTP DHTHLEI WP SAILGIIASI IPYPEHNQSP RNTYQSAMAK QSLGLYASNY QIRTDTRAHL LHYPQMPLVQ TRMLGVIGYN DRPAGANA I LAIMSYTGYN MEDSIIMNKS SIERGMYRST FFRLYSTEEV KYPGGQEDKI ITPEAGVKGY KGKDYYRLLE DNGVVSPEV EVKGGDVLIG KVSPPRFLQE FKELSPEQAK RDTSIVTRHG ENGIVDLVLI TETLEGNKLV KVRVRDLRIP EIGDKFATRH GQKGVVGIL IDQVDMPYTA KGIVPDIILN PHALPSRMTI GQIMEAIGGK YAALSGKPVD ATPFLETPKL QEMQKEILKL G HLPDSTEV VYDGRTGQKL KSRILFGIVY YQKLHHMVAD KMHARARGPV QILTRQPTEG RAREGGLRFG EMERDCLIGF GT AMLIKDR LLDNSDKAVV YICDQCGYVG WYDRSKNRYV CPVHGDKSVL HPVTVSYAFK LLIQELMSMV ISPRLILGEK VNL GGASNE

UniProtKB: DNA-directed RNA polymerase subunit Rpo2

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

MacromoleculeName: DNA-directed RNA polymerase subunit A'' / type: protein_or_peptide / ID: 3
Details: DNA-dependent RNA polymerase subunit RPOA'' (RPO1C)
Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 44.50743 KDa
SequenceString: MIDEKLKGYI DKRLNEIKDK IPDKLHEDLR AAIMDINGVE LTEEDIDRII DLTIREYQQS LIEPGEAIGV VTAQSVGEPG TQMTLRTFH FAGIRELNVT LGLPRLIEIV DARKVPSTPM MTIYLTDEYK TDKDKALDIA RRIEYTRVEN VVSSVSVDIS N MSITLQFD ...String:
MIDEKLKGYI DKRLNEIKDK IPDKLHEDLR AAIMDINGVE LTEEDIDRII DLTIREYQQS LIEPGEAIGV VTAQSVGEPG TQMTLRTFH FAGIRELNVT LGLPRLIEIV DARKVPSTPM MTIYLTDEYK TDKDKALDIA RRIEYTRVEN VVSSVSVDIS N MSITLQFD QEMLKDKGVS IEEIKKIITK LKLGEIRIED NDEYSFTIYF EKIDSIMALF KMREKILNTK IKGVKGIKRA IV QKKGDEY VIITDGSNLE GIMNVTGVDI NKIQTNNIHE VEEVLGIEAA RELISREIKK VLEEQGLDVD MRHIVLVSDI MTR TGDIRQ IGRHGVTGEK SSVLARAAFE VTVKHLLDAA ARGEREEFKG VIENIIIGQP IRLGTGIVEL TMKPNMR

UniProtKB: DNA-directed RNA polymerase subunit Rpo1C

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

MacromoleculeName: DNA-directed RNA polymerase subunit D / type: protein_or_peptide / ID: 4 / Details: DNA-dependent RNA polymerase subunit RPOD (RPO3) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 29.858752 KDa
SequenceString: MPISLIERNG LRLRLVLENY PLEFVNSIRR ASILYVPVMA VDEVYFIENN SPLYDEILAH RLALVPFVSD EALEHYRPPE ECAECKENC DGCYNRVYLD VEAKDQPLMI YSRDLKSEDQ MITPVSGAIP IVLLGSKQKI SLEARLRLGY GKEHIKYSPV S VSIVRYYP ...String:
MPISLIERNG LRLRLVLENY PLEFVNSIRR ASILYVPVMA VDEVYFIENN SPLYDEILAH RLALVPFVSD EALEHYRPPE ECAECKENC DGCYNRVYLD VEAKDQPLMI YSRDLKSEDQ MITPVSGAIP IVLLGSKQKI SLEARLRLGY GKEHIKYSPV S VSIVRYYP KVTVLGNCEK AVEVCPEGVF AMENNKLVVK NELSCILCEE CLKYCAGSVS IESVENKFIL EIESVGSLKP ER ILIEASK SLLRKLSELK SKLEAGK

UniProtKB: DNA-directed RNA polymerase subunit Rpo3

+
Macromolecule #5: DNA-directed RNA polymerase subunit E

MacromoleculeName: DNA-directed RNA polymerase subunit E / type: protein_or_peptide / ID: 5 / Details: DNA-dependent RNA polymerase subunit RPOE (RPO7) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 20.49675 KDa
SequenceString:
MFKLVRAKGI VRIPPEYFGQ SVDEIAIKIL RQEYQEKLIK DIGVVLGIVN AKASEEGFII FGDGATYHEV EFDMLVYTPI IHEVIEGEV SQVDNYGVYV NMGPVDGLVH ISQITDDNLK FDSNRGILIG EKSKKSIQKG DRVRAMIISA SMSSGRLPRI A LTMKQPYL GKIEWINQEI AKASK

UniProtKB: DNA-directed RNA polymerase subunit Rpo7

+
Macromolecule #6: DNA-directed RNA polymerase, subunit F

MacromoleculeName: DNA-directed RNA polymerase, subunit F / type: protein_or_peptide / ID: 6 / Details: DNA-dependent RNA polymerase subunit RPOF (RPO4) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 13.070987 KDa
SequenceString:
MSYSLKTIEE HFVPYSIAKK YIKELIDTGS SSNLIQKTFD YLNSISRCDE DSASKIMKEL EEIVKREDVR AVLASICPTT VEEVRSVLV IDPSTIYSTE QIQKIIEIIK KYVES

UniProtKB: DNA-directed RNA polymerase subunit Rpo4

+
Macromolecule #7: DNA-directed RNA polymerase, subunit G

MacromoleculeName: DNA-directed RNA polymerase, subunit G / type: protein_or_peptide / ID: 7 / Details: DNA-dependent RNA polymerase subunit RPOG (RPO8) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 15.292758 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
MKEMMQGTCK ISSIEKGALK NLYVVKMDCD NDLKIEFDIT KELSIFSKDE EVTFIISREK PEYSEKDFCA HGYLFLERQQ EDGSFIDEI SLYGLIVKIL SKNGLINSKL FKMMDHVYYC VKKKAHHHHH H

UniProtKB: DNA-directed RNA polymerase subunit Rpo8

+
Macromolecule #8: DNA-directed RNA polymerase subunit H

MacromoleculeName: DNA-directed RNA polymerase subunit H / type: protein_or_peptide / ID: 8 / Details: DNA-dependent RNA polymerase subunit RPOH (RPO5) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 9.477059 KDa
SequenceString:
MRSSSKKKID ISNHELVPKH EILQLEEAYK LVKELGIKPE QLPWIRASDP VAKSIGAKPG DIIKITRKSP FTGESVTYRY VITG

UniProtKB: DNA-directed RNA polymerase subunit Rpo5

+
Macromolecule #9: DNA-directed RNA polymerase subunit K

MacromoleculeName: DNA-directed RNA polymerase subunit K / type: protein_or_peptide / ID: 9 / Details: DNA-dependent RNA polymerase subunit RPOK (RPO6) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 10.25199 KDa
SequenceString:
MTIDKINEIF KENWKNKLTK YEIARIISAR ALQLSMGALP LIDTSNLKSD DVISIAEEEL KRGVLPITIR RIYPNGQVEL ISVRKIENR

UniProtKB: DNA-directed RNA polymerase subunit Rpo6

+
Macromolecule #10: DNA-directed RNA polymerase subunit L

MacromoleculeName: DNA-directed RNA polymerase subunit L / type: protein_or_peptide / ID: 10 / Details: DNA-dependent RNA polymerase subunit RPOL (RPO11) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 10.061791 KDa
SequenceString:
MEIKVIKEEQ NYLELQIDGE EHTIGNLLKG MLLKVPGVKF AAYSLPHPLI TSITIKILTD GSISAREALI KAIELAENYA NLFIDEVKK I

UniProtKB: DNA-directed RNA polymerase subunit Rpo11

+
Macromolecule #11: DNA-directed RNA polymerase subunit N

MacromoleculeName: DNA-directed RNA polymerase subunit N / type: protein_or_peptide / ID: 11 / Details: DNA-dependent RNA polymerase subunit RPON (RPO10) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 7.673108 KDa
SequenceString:
MIIPIRCFTC GAVVADKWEP FSNRVMGGED PEKVLTELGV NRYCCRRMLL SHVNIIREII HYTRPI

UniProtKB: DNA-directed RNA polymerase subunit Rpo10

+
Macromolecule #12: DNA-directed RNA polymerase subunit P

MacromoleculeName: DNA-directed RNA polymerase subunit P / type: protein_or_peptide / ID: 12 / Details: DNA-dependent RNA polymerase subunit RPOP (RPO12) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Molecular weightTheoretical: 5.662912 KDa
SequenceString:
MAKYRCGKCW KELDDDQLKT LPGVRCPYCG YRIIYMVRKP TVKIVKAI

UniProtKB: DNA-directed RNA polymerase subunit Rpo12

+
Macromolecule #13: Conserved protein

MacromoleculeName: Conserved protein / type: protein_or_peptide / ID: 13 / Details: DNA-dependent RNA polymerase subunit RPO13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 12.331662 KDa
SequenceString:
MSEDDSKKEP EPEETEAEIK HEEISREEDD EGGEFSTVTI SDIEMLLKDT EIWDKLLRNE LSIEEAKKMF DDVARSYSKA DKKKRRVEK KPKKGKVTKK SDEEEE

UniProtKB: DNA-directed RNA polymerase subunit Rpo13

+
Macromolecule #14: DNA-directed RNA polymerase, subunit M (RpoM-2)

MacromoleculeName: DNA-directed RNA polymerase, subunit M (RpoM-2) / type: protein_or_peptide / ID: 14 / Details: DNA-directed RNA polymerase subunit RpoM-2 (TFS4) / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Molecular weightTheoretical: 10.422411 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRFCPKCGSF LKVKGNKMVC SKCGYSDHDV EKVILKENVA HENDKTIIAD GETIEGRVAI SLCPRCGSVR AILLNKKKRL YRCMTCNFV YNI

UniProtKB: Transcription factor S4

+
Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #17: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 17 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHepes
200.0 mMNaClsodium chloride
5.0 mMMgCl2magnesium chloride
100.0 microMZnSO4zinc sulfate
5.0 mMC4H10O2S2DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: the grid was coated with graphene oxide after to be glow discharged and before applying the sample
VitrificationCryogen name: ETHANE / Chamber humidity: 94 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsthe sample was applied twice on the grid before vetrification

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1760 / Average exposure time: 2.0 sec. / Average electron dose: 45.2 e/Å2
Details: images were collected as movie-stacks of 40 frames in super resolution mode
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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsAll images were binned 2x, aligned and summed by using MotionCor2
Particle selectionNumber selected: 1161535
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Software - details: 3D refinement / Number images used: 350682
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Software - details: 2D classification
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Software - details: 3D classification
Final 3D classificationNumber classes: 2 / Avg.num./class: 170000 / Software - Name: RELION (ver. 3.0) / Software - details: 3D classification
Details: All particles clustered in only one class which showed some preferred orientations later removed with a home-made script
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7ok0


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: CC
Output model

PDB-7oqy:
Cryo-EM structure of the cellular negative regulator TFS4 bound to the archaeal RNA polymerase

+
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