2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update PDBe PDBe 2021-05-17 2021-08-25 2021-08-25 2026-09-02 Wellcome Trust 207446/Z/17/Z United Kingdom Cryo-EM structure of the Sulfolobus acidocaldarius RNA polymerase at 2.88 A Pilotto S Fouqueau T RNA polymerase, transcription, Archaea, Crenarchaea Pilotto S Fouqueau T Lukoyanova N Sheppard C Lucas-Staat S Diaz-Santin LM Matelska D Prangishvili D Cheung ACM Werner F Structural basis of RNA polymerase inhibition by viral and host factors. Nat Commun UK 12 5523 5523 2021 34535646 doi:10.1038/s41467-021-25666-5 2041-1723 EMD-13026 other EM volume
Cryo-EM structure of the archaeal RNA polymerase inhibited by RIP
 EMD-13034 other EM volume
Cryo-EM structure of the archaeal RNA polymerase inhibited by TFS4
 7ok0 FULLOVERLAP EMDB EMD-12960 associated EM volume
Cryo-EM structure of the Sulfolobus acidocaldarius RNA polymerase at 2.88 A
 EMDB EMD-13026 other EM volume
Cryo-EM structure of the archaeal RNA polymerase inhibited by RIP
 EMDB EMD-13034 other EM volume
Cryo-EM structure of the archaeal RNA polymerase inhibited by TFS4
 PDB 7OQ4 unspecified PDB 7OQY unspecified apo-RNA polymerase apo-RNA polymerase 0 1 2 3 4 5 6 7 8 9 10 11 12 13
13 subunits
0.404 DNA-directed RNA polymerase subunit A' Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.09992905499999999
DNA-directed RNA polymerase subunit RPO1
1 LEVO MSEKIIRGVKFGVLSPNEIRQMSVTAIITSEVYDEDGTPIEGGVMDPKLGVIEPGQKCPVCGNTLAGCPGHFGHIELIKP VIHIGYVKHIYDFLRSTCWRCGRIKIKEQDLERYKRIYNAIKLRWPSAARRLVEYIKKISIKNLECPHCGEKQFKIKLEK PYNFNEERNGSIVKLSPSEIRDRLERIPDSDVELLGYDPKSSRPEWMILTVLPVPPITIRPSITIESGIRAEDDLTHKLV DIIRLNERLKESIEAGAPQLIIEDLWDLLQYHVATYFDNEIPGLPPAKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDF SARTVISPDPNLSIDEVGIPYTIARMLTVPERVTNINIERIRQYIINGPDKWPGANYVIKPDGRRIDLRYVKDRKELASS ITAGYVVERHLVDGDVVLFNRQPSLHRISMMAHKVRVLPGRTFRLNLLDCPPYNADFDGDEMNLHVPQSEEAIAEARELM LVHKNIITPRYGGPIIGGGQDYISGAYLLSVKTTLLTVEEVATILGVTDFVGELGEPAILAPKPYYTGKQVISLFLPKDF NFHGPANISKGPRACKDEICPHDSFIVIKNGLLLEGVFDKKAIGNQQPESMLHWSIREYGTEYGKWLMDNVFKMFIRFLE MRGFTMTLEDITIPDEAQNEITTKIKEGYSQVDEYIRKFNEGQLEPIPGRTIEESLESYILDTLDKLRKVAGEIATKYLD PFNNVYIMAITGARGSELNITQMTALLGQQSVRGERIRRGYRERTLSLFKYGDIAPEARGFVKNSFMRGLSPYEMFFHAA GGREGLVDTAVKTSQSGYMQRRLINALSDLRIEYDGTVRSLYGDIVQVVYGDDAVHPMYSAHSKSVNVNRVIERVIGWKR P11512 2.7.7.6 DNA-directed RNA polymerase subunit B Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.12664710199999998
DNA-directed RNA polymerase subunit RPO2
1 LEVO MLDTESRWAIAESFFKTRGLVRQHLDSFNDFLRNKLQQVIYEQGEIVTEVPGLKIKLGKIRYEKPSIRETDKGPMREITP MEARLRNLTYSSPIFLSMIPVENNIEGEPIEIYIGDLPIMLKSVADPTSNLPIDKLIEIGEDPKDPGGYFIVNGSEKVII AQEDLATNRVLVDYGKSGSNITHVAKVTSSAAGYRVQVMIERLKDSTIQISFATVPGRIPFAIIMRALGFVTDRDIVYAV SLDPQIQNELLPSLEQASSITSAEEALDFIGNRVAIGQKRENRIQKAEQVIDKYFLPHLGTSPEDRKKKGYYLASAVNKI LELYLGRREPDDKDHYANKRVRLAGDLFTSLFRVAFKAFVKDLVYQLEKSKVRGRRLSLTALVRADIITERIRHALATGN WVGGRTGVSQLLDRTNWLSMLSHLRRVVSSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALLAQVSVGINE SVVERVAYELGVVSVEDVIRRISEQNEDVEKYMSWSKVYLNGRLLGYYEDGKELAKKIRESRRQGKLSDEVNVAYIATDY LNEVHINCDAGRVRRPLIIVNNGTPLVDTEDIKKLKNGEITFDDLVKQGKIEFIDAEEEENAYVALNPQDLTPDHTHLEI WPSAILGIIASIIPYPEHNQSPRNTYQSAMAKQSLGLYASNYQIRTDTRAHLLHYPQMPLVQTRMLGVIGYNDRPAGANA ILAIMSYTGYNMEDSIIMNKSSIERGMYRSTFFRLYSTEEVKYPGGQEDKIITPEAGVKGYKGKDYYRLLEDNGVVSPEV EVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGENGIVDLVLITETLEGNKLVKVRVRDLRIPEIGDKFATRH GQKGVVGILIDQVDMPYTAKGIVPDIILNPHALPSRMTIGQIMEAIGGKYAALSGKPVDATPFLETPKLQEMQKEILKLG HLPDSTEVVYDGRTGQKLKSRILFGIVYYQKLHHMVADKMHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGT AMLIKDRLLDNSDKAVVYICDQCGYVGWYDRSKNRYVCPVHGDKSVLHPVTVSYAFKLLIQELMSMVISPRLILGEKVNL GGASNE P11513 2.7.7.6 DNA-directed RNA polymerase subunit A'' Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.04450743
DNA-directed RNA polymerase subunit RPO1
1 LEVO MIDEKLKGYIDKRLNEIKDKIPDKLHEDLRAAIMDINGVELTEEDIDRIIDLTIREYQQSLIEPGEAIGVVTAQSVGEPG TQMTLRTFHFAGIRELNVTLGLPRLIEIVDARKVPSTPMMTIYLTDEYKTDKDKALDIARRIEYTRVENVVSSVSVDISN MSITLQFDQEMLKDKGVSIEEIKKIITKLKLGEIRIEDNDEYSFTIYFEKIDSIMALFKMREKILNTKIKGVKGIKRAIV QKKGDEYVIITDGSNLEGIMNVTGVDINKIQTNNIHEVEEVLGIEAARELISREIKKVLEEQGLDVDMRHIVLVSDIMTR TGDIRQIGRHGVTGEKSSVLARAAFEVTVKHLLDAAARGEREEFKGVIENIIIGQPIRLGTGIVELTMKPNMR P11514 2.7.7.6 DNA-directed RNA polymerase subunit D Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.029858752
DNA-directed RNA polymerase subunit RPO3
1 LEVO MPISLIERNGLRLRLVLENYPLEFVNSIRRASILYVPVMAVDEVYFIENNSPLYDEILAHRLALVPFVSDEALEHYRPPE ECAECKENCDGCYNRVYLDVEAKDQPLMIYSRDLKSEDQMITPVSGAIPIVLLGSKQKISLEARLRLGYGKEHIKYSPVS VSIVRYYPKVTVLGNCEKAVEVCPEGVFAMENNKLVVKNELSCILCEECLKYCAGSVSIESVENKFILEIESVGSLKPER ILIEASKSLLRKLSELKSKLEAGK P39471 2.7.7.6 DNA-directed RNA polymerase subunit E Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.020496749999999998
DNA-directed RNA polymerase subunit RPO7
1 LEVO MFKLVRAKGIVRIPPEYFGQSVDEIAIKILRQEYQEKLIKDIGVVLGIVNAKASEEGFIIFGDGATYHEVEFDMLVYTPI IHEVIEGEVSQVDNYGVYVNMGPVDGLVHISQITDDNLKFDSNRGILIGEKSKKSIQKGDRVRAMIISASMSSGRLPRIA LTMKQPYLGKIEWINQEIAKASK P39466 2.7.7.6 DNA-directed RNA polymerase, subunit F Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.013070987
DNA-directed RNA polymerase subunit RPO4
1 LEVO MSYSLKTIEEHFVPYSIAKKYIKELIDTGSSSNLIQKTFDYLNSISRCDEDSASKIMKELEEIVKREDVRAVLASICPTT VEEVRSVLVIDPSTIYSTEQIQKIIEIIKKYVES Q4JB12 2.7.7.6 DNA-directed RNA polymerase, subunit G Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.015292757999999998
DNA-directed RNA polymerase subunit RPO8
1 Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) LEVO MKEMMQGTCKISSIEKGALKNLYVVKMDCDNDLKIEFDITKELSIFSKDEEVTFIISREKPEYSEKDFCAHGYLFLERQQ EDGSFIDEISLYGLIVKILSKNGLINSKLFKMMDHVYYCVKKKAHHHHHH Q4JAY4 2.7.7.6 DNA-directed RNA polymerase subunit H Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.009477059
DNA-directed RNA polymerase subunit RPO5
1 LEVO MRSSSKKKIDISNHELVPKHEILQLEEAYKLVKELGIKPEQLPWIRASDPVAKSIGAKPGDIIKITRKSPFTGESVTYRY VITG P11521 2.7.7.6 DNA-directed RNA polymerase subunit K Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.010251989999999999
DNA-directed RNA polymerase subunit RPO6
1 LEVO MTIDKINEIFKENWKNKLTKYEIARIISARALQLSMGALPLIDTSNLKSDDVISIAEEELKRGVLPITIRRIYPNGQVEL ISVRKIENR P39463 2.7.7.6 DNA-directed RNA polymerase subunit L Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.010061790999999999
DNA-directed RNA polymerase subunit RPO11
1 LEVO MEIKVIKEEQNYLELQIDGEEHTIGNLLKGMLLKVPGVKFAAYSLPHPLITSITIKILTDGSISAREALIKAIELAENYA NLFIDEVKKI P46217 2.7.7.6 DNA-directed RNA polymerase subunit N Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.007673108
DNA-directed RNA polymerase subunit RPO10
1 LEVO MIIPIRCFTCGAVVADKWEPFSNRVMGGEDPEKVLTELGVNRYCCRRMLLSHVNIIREIIHYTRPI P39472 2.7.7.6 DNA-directed RNA polymerase subunit P Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.005662912
DNA-directed RNA polymerase subunit RPO12
1 LEVO MAKYRCGKCWKELDDDQLKTLPGVRCPYCGYRIIYMVRKPTVKIVKAI Q4JAE8 2.7.7.6 Conserved protein Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 0.012331662
DNA-directed RNA polymerase subunit 13
1 LEVO MSEDDSKKEPEPEETEAEIKHEEISREEDDEGGEFSTVTISDIEMLLKDTEIWDKLLRNELSIEEAKKMFDDVARSYSKA DKKKRRVEKKPKKGKVTKKSDEEEE Q4JAJ6 MAGNESIUM ION 2.4305e-05 1 MG ZINC ION 6.5409e-05 6 ZN FE3-S4 CLUSTER 0.000295795 1 F3S singleParticle particle 0.06 7.0 20.0 C8H18N2O4S HEPES 200.0 NaCl sodium chloride 5.0 MgCl2 magnesium chloride 100.0 ZnSO4 zinc sulfate UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY GLOW DISCHARGE AIR
The grid was coated with graphene oxide prior to use
 ETHANE 94 277 FEI VITROBOT MARK IV
The sample was crosslinked with bis(sulfosuccinimidyl)suberate (BS3)
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.3 2.5 81000.0 NITROGEN GATAN K3 (6k x 4k) 5760 4092 1 1676 44.46
Images were collected in movie-mode for a total of 40 frames in super-resolution mode and with a tilt of 30 degrees
 1
Movie stacks were aligned and summed using MotionCor2
1286432 Gctf
CTF aplitude was further corrected on selected particles after 3D recostruction to correct the 30 degrees tilt used during data collection
PHASE FLIPPING AND AMPLITUDE CORRECTION C1 2.9 FSC 0.143 CUT-OFF RELION 3.0 423157 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 2 RELION 3.0
the particles were split 50% in each class providing 2 identical maps. The particles of both classes were pooled together prior 3D refinement and postprocessing.
 emd_12960.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 332 332 332 0 0 0 332 332 332 360.22 360.22 360.22 90.0 90.0 90.0 Z Y X -22.123083000000001 54.864739999999998 -0.000000000003985 1.0 1.085 1.085 1.085 4.0 AUTHOR sharpened map obtained from Autosharpen (Phenix v.1.15), box size 332 pixels FLEXIBLE FIT CC REAL 57.777200000000001 emd_12960_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 332 332 332 0 0 0 332 332 332 360.22 360.22 360.22 90.0 90.0 90.0 X Y Z -0.018172272 0.10032345 0.00007616919 0.001898057 1.085 1.085 1.085 AUTHOR half2 map obtained from Refine3D (Relion v.3.0), box size 332 pixels emd_12960_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 332 332 332 0 0 0 332 332 332 360.22 360.22 360.22 90.0 90.0 90.0 X Y Z -0.018070085 0.09474672 0.00007683755 0.0018979773 1.085 1.085 1.085 AUTHOR half1 map obtained from Refine3D (Relion v.3.0), box size 332 pixels