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- EMDB-77809: Cryo-EM structure of Pyrococcus furiosus RNA polymerase without s... -

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Basic information

Entry
Database: EMDB / ID: EMD-77809
TitleCryo-EM structure of Pyrococcus furiosus RNA polymerase without stalk (no Rpo4/Rpo7)
Map data
Sample
  • Complex: RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo1N
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo1C
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo3
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo11
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo5
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo10
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo6
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo12
  • Ligand: ZINC ION
KeywordsRNA polymerase / Clamp conformation / Euryarchaea / Stalk / TRANSCRIPTION
Function / homology
Function and homology information


transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / DNA-directed RNA polymerase complex / transcription by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / magnesium ion binding ...transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / DNA-directed RNA polymerase complex / transcription by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / magnesium ion binding / DNA-templated transcription / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site ...DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / 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. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / 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. / 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / 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 polymerase Rpb1, domain 1 / 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, 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, 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 Rpo10 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo11
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.56 Å
AuthorsFordjour GNR / Armache J-P / Murakami KS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM156623 United States
CitationJournal: J Biol Chem / Year: 2026
Title: Clamp conformational flexibility and dynamics in archaeal and eukaryotic RNA polymerases revealed by cryo-EM.
Authors: George N R Fordjour / Leon Palao / Kenji Murakami / Jean-Paul Armache / Katsuhiko S Murakami /
Abstract: All cellular RNA polymerases (RNAPs) across Bacteria, Archaea, and Eukarya share a conserved catalytic core, yet bacterial and archaeal-eukaryotic RNAPs diverged after separation from the last ...All cellular RNA polymerases (RNAPs) across Bacteria, Archaea, and Eukarya share a conserved catalytic core, yet bacterial and archaeal-eukaryotic RNAPs diverged after separation from the last universal common ancestor. This evolutionary split produced distinct subunit compositions and fundamentally different requirements for external factors during transcription initiation. Bacterial RNAP relies on a σ factor, whereas archaeal-eukaryotic RNAPs require a more extensive set of general transcription factors (GTFs) to bind promoter DNA, unwind the duplex, and position the template strand within the active site cleft. Notably, despite the close structural similarity between archaeal and eukaryotic RNAPs, the requirement for GTFs became further specialized after the emergence of Eukarya. This divergence raises the question of whether differences in intrinsic conformational flexibility and dynamics of these RNAPs contribute to distinct promoter-loading pathways. In this study, we addressed this question using cryo-electron microscopy (cryo-EM) to examine archaeal RNAPs from Euryarchaeota and Crenarchaeota alongside yeast RNAP II. Archaeal RNAP displays a highly dynamic DNA binding clamp domain that samples a broad spectrum of open and closed states, whereas RNAP II predominantly adopts a closed clamp state. Both archaeal and eukaryotic RNAPs can be found in stalk-bound and stalk-less forms. Comparative structural analyses further reveal a unique conformational transition in crenarchaeal RNAP associated with clamp opening. Together, these findings define the intrinsic clamp-conformational landscapes across the archaeal-eukaryotic lineage and suggest that evolutionary tuning of clamp flexibility and dynamics contributes to distinct GTF-dependent promoter-loading mechanisms.
History
DepositionJun 29, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77809.png

Downloads & links

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Map

FileDownload / File: emd_77809.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 400 pix.
= 377.6 Å		0.94 Å/pix.
x 400 pix.
= 377.6 Å		0.94 Å/pix.
x 400 pix.
= 377.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.944 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.1746483 - 0.69565356
Average (Standard dev.)-0.00037954282 (±0.02673197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 377.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_77809_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_77809_half_map_2.map
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Sample components

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Entire : RNA polymerase

EntireName: RNA polymerase
Components
  • Complex: RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo1N
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo1C
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo3
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo11
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo5
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo10
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo6
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo12
  • Ligand: ZINC ION

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Supramolecule #1: RNA polymerase

SupramoleculeName: RNA polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)

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Macromolecule #1: DNA-directed RNA polymerase subunit Rpo1N

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo1N / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 103.265844 KDa
SequenceString: MKKVIGSIEF GILSPQEIRK MSAVEVTVPD TYDDDGYPIE GGVMDKRMGV IDPGLRCETC GGRAGECPGH FGHIELARPV IHVGFAKTI YRILESTCRE CGRIKLTDEE IEEYMKKIEL ARNRRSEFNE IIKEIHKKAK ERMVCPHCGA PQYPIKFEKP T IYWEIRKD ...String:
MKKVIGSIEF GILSPQEIRK MSAVEVTVPD TYDDDGYPIE GGVMDKRMGV IDPGLRCETC GGRAGECPGH FGHIELARPV IHVGFAKTI YRILESTCRE CGRIKLTDEE IEEYMKKIEL ARNRRSEFNE IIKEIHKKAK ERMVCPHCGA PQYPIKFEKP T IYWEIRKD EQGNEYRHRL MPTEVRDWLE KIPDKDLPLL GLDPEKSRPE WMVLTVLPVP PVTARPSITL ETGIRAEDDL TH KLVDIIR INNRLKQNIE AGAPQLIIED LWDLLQYHVT TYINNEAPGV PPAKHKSGRP LKTLAQRLKG KEGRFRGNLS GKR VNFSAR TVISPDPMIS INEVGVPVEV AMELTVPEKV TEFNIERLRK MVLNGPDKYP GANYVIDPEG RRRRIMDSNK ETLA NQLDI GWTVERHLMD GDIVLFNRQP SLHRMSIMAH RVRVMPYRTF RLNLAVCPPY NADFDGDEMN LHVPQTEEAQ AEARI LMEV QNHIISPRYG GPIIGGIQDH ISGGYLLTRE GAYFTRDEVE QMLMFAGVDI TELPEPDKYD ENGNPLWSGK TIFSLL LPE DLTVWYRNKL CDEPERCEAL EKLIEEKLMP DPEEVRKLAY DGFVYIQNGK LLSGAIDKKA YGREDGIILD LIVREYG VE RARQFLDQVT KLTIWVITHK GFTTGIDDED LPEEARDRIR EIIREAEERV NKLIEAYKRG ELEPLPGKSL EDTLESLI M AVLAEARDNA GAVAEKYLGM DNHTVIMAKT GARGKILNIT QMAALLGQQS IRGKRLYRGF RGRVLSHFKP GDLGARAKG FVVNSYKSGL TPQEYFFHAM GGREGLVDTA VRTAQSGYMQ RRLINALQDL KVEYDGTVRS PEGIIVQFKY GEDGVDPMKS WRGKTVDVD RIIVRTLLKM RGNNKAKV

UniProtKB: DNA-directed RNA polymerase subunit Rpo1N

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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: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 127.188898 KDa
SequenceString: MRGPTVVDVT PDDLWIVMES YWQEKGLVRQ HLDSYNAFIE RGLQEVVNEF GGIKPDIPDF EVKFGKIRVG EPEFQEPHGQ RKPLYPMDA RIRNLTYAAP LYLEMIPVIK GVEQDPVEVR IGELPIMLKS KVCRLYGLSD EELIKLGEDP KDPGGYFIIN G SERVIVSI ...String:
MRGPTVVDVT PDDLWIVMES YWQEKGLVRQ HLDSYNAFIE RGLQEVVNEF GGIKPDIPDF EVKFGKIRVG EPEFQEPHGQ RKPLYPMDA RIRNLTYAAP LYLEMIPVIK GVEQDPVEVR IGELPIMLKS KVCRLYGLSD EELIKLGEDP KDPGGYFIIN G SERVIVSI EDIAPNRTLV EKDERQEKYI AKVFSYRHGY RALVAVERRK DGILYVDIPN VPKPVKFVYV MRALGLERDK DI VEAVGND PEVQQIMFDN LEDASDITTQ QEALEFIGKL VAPGQAREYR LKRAEYVIDN NLLPHMGVSP EDRIKKAYYL GMM ALKVIE LSLGRRPEDD KDHYANKRLR LAGDLLKDLF RVAFSQLVKD IQYQMTKTYQ RKGDKYTFGN IHRFIRNSIR PDVL TERIE HALATGAWPG GRTGVSQLLD RTNYMSTLSH LRRVTSPLDR EQPHFEARDL HGTHWGRICP TETPEGPNCG LVKNL ALMA QITTAVPEEE IREYLMSLGI VPIEVRRPDP TLWRVYLNGV LIGTIEDGKA LVQRIRQDRR SGKISDVINV AYYEDV KEV YVNSDDGRVR RPLIIVENGV PKLTKEHVQA VKEGRLKWSD LIKMGIIEYL DAEEEENAYV AMWPWEVTEE HTHLELM PA AILGLPASLV PYPEHNAAPR NTYGAGMAKQ SLGLGWANFR IRVDTRGHLL HYPQIPLVNS RIMKAVGYED RPAGQNFV V AVLAYQGYNM EDAIIINKAS IERGLARSTF FRTYEAEEKK YLGGQTDKFE IPDPTVRGYR GEKYYRNLDE DGLIFPESK VEGKDVLVGR TSPPRFLEER GLGTVSLQER RETSVAVRPS EKGVVDKVII TETGDGTKLV KVTVRDLRIP ELGDKFASRH GQKGVIGLI VPQEDMPWTE SGIVPDLIVN PHGIPSRMTV GQLIEAIGGK VASLKGRRVD GTAFIGEPEE KLRKELEELG F KHTGREIM YDGITGKRLE ADIFIGVIYY QRLHHMVADK IHARSRGPVQ VLTKQPTEGR AREGGLRFGE MERDVLVGHG AA MLLIERL LEESDKTEVW VCENCGHIAL EDKRRRRVYC PVCGEEERIS KVEMSYAFKL LLDELKAMVI RPKLNLSERV

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit Rpo1C

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo1C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 44.468156 KDa
SequenceString: MVSLSTIKSL IEKKGANLPE NVKSELYEKL KKYNEKYKLT KAEIEAIIDD VVKEYERALV EPGEPVGTVA AQSIGEPSTQ MTLNTFHYA GVAEINVTLG LPRIIEIVDA RKNPSTPMMT VYLDEEHRYD RAKAEEVARR IEGTTLENLA RSTTLDLINF E FIVEIDPE ...String:
MVSLSTIKSL IEKKGANLPE NVKSELYEKL KKYNEKYKLT KAEIEAIIDD VVKEYERALV EPGEPVGTVA AQSIGEPSTQ MTLNTFHYA GVAEINVTLG LPRIIEIVDA RKNPSTPMMT VYLDEEHRYD RAKAEEVARR IEGTTLENLA RSTTLDLINF E FIVEIDPE RLERSGLTME KVVKKLESSF KSAEFEVDGY TLIVRPKKAD KISDLRRFAE KIKKHRLKGL SGVGKTIVRK EG DEYVIYT EGSNFKQVLK VPGVDPTRTR TNNIHEIAEV LGIEAARNAI IDEIVSTMQE QGLEVDIRHI MLVADMMTLD GIV RPIGRH GVVGEKSSVL ARAAFEITVQ HLFEAAEKGE VDNLNGVIEN VLIGQPVPVG TGMVKLTMKL PLRPQKEKEE V

UniProtKB: DNA-directed RNA polymerase subunit Rpo1C

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Macromolecule #4: DNA-directed RNA polymerase subunit Rpo3

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 31.688195 KDa
SequenceString: MAGIEVQILE KKEDSIKFVL KGVHVSFANA LRRTILGEVP TFAVDEVEFY ENDSALFDEI IAHRLAMIPL TTPVDRFELD ALELDDYTV TLSLEAEGPG IVYSGDLKSD DPDVKPVNPN IPIVKLAEGQ RLVFNAYAKL GRGKDHAKWQ PGFVYYKYYT I VHISKSIP ...String:
MAGIEVQILE KKEDSIKFVL KGVHVSFANA LRRTILGEVP TFAVDEVEFY ENDSALFDEI IAHRLAMIPL TTPVDRFELD ALELDDYTV TLSLEAEGPG IVYSGDLKSD DPDVKPVNPN IPIVKLAEGQ RLVFNAYAKL GRGKDHAKWQ PGFVYYKYYT I VHISKSIP EWKELKKLAK KRGLPVEETE EEVLVTTIKP FYIPKDFEEY EGKEIWEEIV PNTYIFTVET NGELPVEEIV SI ALKILMR KADRFISELQ KLTSWSHPQF EKHHHHHH

UniProtKB: DNA-directed RNA polymerase subunit Rpo3

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Macromolecule #5: DNA-directed RNA polymerase subunit Rpo11

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo11 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 11.132764 KDa
SequenceString:
MKIEVIKKEE NLLEFYLEGE DHTFANLLVE TLRENPHVKF TAYTIEHPIT MARKPRFRVV TDGEITPEEA LEEAAKKIFE RAKEVLEAW EKAVKS

UniProtKB: DNA-directed RNA polymerase subunit Rpo11

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Macromolecule #6: DNA-directed RNA polymerase subunit Rpo5

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 9.260792 KDa
SequenceString:
MAGKKEFSIF DHVLVPEHRV LSEEEKKALL EKYKITLAQL PQIKASDPAV KALGAKPGDV IEIKRKSPTA GVYYYYRVVV ED

UniProtKB: DNA-directed RNA polymerase subunit Rpo5

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Macromolecule #7: DNA-directed RNA polymerase subunit Rpo10

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo10 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 7.800158 KDa
SequenceString:
MIVPVRCFTC GKVIGDKYYE FKRRVEAGED PEKVLDDLGL ERYCCRRMLL SHVELIDDIM HYRVY

UniProtKB: DNA-directed RNA polymerase subunit Rpo10

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Macromolecule #8: DNA-directed RNA polymerase subunit Rpo6

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 6.24349 KDa
SequenceString:
MFKYTRFEKA RIIGARALQI SMGAPVLIDV PPGITPLEAA ILEFEKGVIP ITVIRPS

UniProtKB: DNA-directed RNA polymerase subunit Rpo6

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Macromolecule #9: DNA-directed RNA polymerase subunit Rpo12

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo12 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 5.77005 KDa
SequenceString:
MVEAVYRCFK CGREVKLDLS ITRDLRCPYC GSKILYKPRP KVPRRVKAI

UniProtKB: DNA-directed RNA polymerase subunit Rpo12

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8orq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 61865
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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