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- EMDB-74466: Cryo-EM structure of the complete Pyrococcus furiosus RNA polymer... -

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Basic information

Entry
Database: EMDB / ID: EMD-74466
TitleCryo-EM structure of the complete Pyrococcus furiosus RNA polymerase in open clamp conformation
Map data
Sample
  • Organelle or cellular component: RNA polymerase
    • Protein or peptide: x 11 types
  • Ligand: x 1 types
KeywordsRNA polymerase / Conformations / Promoter loading / Euryarchaea / TRANSCRIPTION
Function / homology
Function and homology information


tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription elongation by RNA polymerase I / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription by RNA polymerase II / protein dimerization activity ...tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription elongation by RNA polymerase I / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription by RNA polymerase II / protein dimerization activity / nucleotide binding / magnesium ion binding / DNA-templated transcription / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo7 / 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 E/RPC8 / HRDC domain superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 ...DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo7 / 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 E/RPC8 / HRDC domain superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / 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 / HRDC-like superfamily / 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. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / 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 / 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 Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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 / Nucleic acid-binding, OB-fold
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 Rpo4 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo11
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 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: To Be Published
Title: Clamp conformational flexibility and dynamics in archaeal and eukaryotic RNA polymerases revealed by cryo-EM
Authors: Fordjour GNR / Murakami K / Armache J-P / Murakami KS
History
DepositionDec 15, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74466.png

Downloads & links

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Map

FileDownload / File: emd_74466.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
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

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.944 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-1.2872126 - 1.9614799
Average (Standard dev.)-0.0001129758 (±0.041078012)
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: #2

Fileemd_74466_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74466_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : RNA polymerase

EntireName: RNA polymerase
Components
  • Organelle or cellular component: 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 Rpo7
    • Protein or peptide: DNA-directed RNA polymerase subunit Rpo4
    • 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: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
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 Rpo7

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo7 / 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: 21.731455 KDa
SequenceString:
MYKIVTVKDV VRIPPTMFTM DPKEAAKIIL RETYEGTYDK DEGVILSILE VKDIKDGIII PGDGATYHEV VFDVLVWEPK IHEVVEGYV ADVMPFGAFI RIGPIDGLVH ISQLMDDYVV YDERNKQFVG KEKKYLLKIG DLVRARIINI SAKSKVIREN R IGLTMRQP GLGKFEWIEK EKKKEKEEGK K

UniProtKB: DNA-directed RNA polymerase subunit Rpo7

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Macromolecule #6: DNA-directed RNA polymerase subunit Rpo4

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo4 / 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: 14.116311 KDa
SequenceString:
MIGRGKLGEK YITIAEAKEL LLKRREEEVK AGIEEPLYYE ARLALEHAER FAKLPADKAK EAVEELMNAF EWMSDRIACK IVDIMPEDS MDLRVIFAKE EYQPTQEEMK QILDILDKYR E

UniProtKB: DNA-directed RNA polymerase subunit Rpo4

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Macromolecule #7: DNA-directed RNA polymerase subunit Rpo11

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo11 / 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: 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 #8: DNA-directed RNA polymerase subunit Rpo5

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo5 / 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: 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 #9: DNA-directed RNA polymerase subunit Rpo10

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo10 / 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: 7.800158 KDa
SequenceString:
MIVPVRCFTC GKVIGDKYYE FKRRVEAGED PEKVLDDLGL ERYCCRRMLL SHVELIDDIM HYRVY

UniProtKB: DNA-directed RNA polymerase subunit Rpo10

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Macromolecule #10: DNA-directed RNA polymerase subunit Rpo6

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo6 / type: protein_or_peptide / ID: 10 / 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 #11: DNA-directed RNA polymerase subunit Rpo12

MacromoleculeName: DNA-directed RNA polymerase subunit Rpo12 / type: protein_or_peptide / ID: 11 / 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 #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / 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: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 142876
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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