Cryo-EM structure of the ATV RNAP Inhibitory Protein (RIP) bound to the DNA-binding channel of the host's RNA polymerase

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION em_3d_fitting_list em_admin pdbx_initial_refinement_model _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update 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 pdbx_validate_close_contact struct_conn struct_conn_type _em_admin.last_update _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id PDBe PDBe 2021-06-02 2021-08-25 2021-08-25 2026-09-02 Wellcome Trust 207446/Z/17/Z United Kingdom Cryo-EM structure of the ATV RNAP Inhibitory Protein (RIP) bound to the DNA-binding channel of the host's RNA polymerase Pilotto S Fouqueau T viral inhibitor, transcription inhibition, ATV, archaeal virus, Archaea, VIRAL PROTEIN 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 7oq4 FULLOVERLAP PDB 7OK0 unspecified

apo-RNA polymerase

EMDB EMD-13026 associated EM volume

Complex of archaeal RNA-polymerase with the ATV inhibitory protein RIP Complex of archaeal RNA-polymerase with the ATV inhibitory protein RIP 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

The RNA polymerase was incubated with a 10-fold excess of RIP for 5 min at 338 K followed by cross-linking with BS3

0.421 DNA-directed RNA polymerase subunit A' Sulfolobus acidocaldarius DSM 639 0.09992905499999999 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 DSM 639 0.12664710199999998 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 DSM 639 0.04450743 1 LEVO MIDEKLKGYIDKRLNEIKDKIPDKLHEDLRAAIMDINGVELTEEDIDRIIDLTIREYQQSLIEPGEAIGVVTAQSVGEPG TQMTLRTFHFAGIRELNVTLGLPRLIEIVDARKVPSTPMMTIYLTDEYKTDKDKALDIARRIEYTRVENVVSSVSVDISN MSITLQFDQEMLKDKGVSIEEIKKIITKLKLGEIRIEDNDEYSFTIYFEKIDSIMALFKMREKILNTKIKGVKGIKRAIV QKKGDEYVIITDGSNLEGIMNVTGVDINKIQTNNIHEVEEVLGIEAARELISREIKKVLEEQGLDVDMRHIVLVSDIMTR TGDIRQIGRHGVTGEKSSVLARAAFEVTVKHLLDAAARGEREEFKGVIENIIIGQPIRLGTGIVELTMKPNMR P11514 2.7.7.6 DNA-directed RNA polymerase subunit D Sulfolobus acidocaldarius DSM 639 0.029858752 1 LEVO MPISLIERNGLRLRLVLENYPLEFVNSIRRASILYVPVMAVDEVYFIENNSPLYDEILAHRLALVPFVSDEALEHYRPPE ECAECKENCDGCYNRVYLDVEAKDQPLMIYSRDLKSEDQMITPVSGAIPIVLLGSKQKISLEARLRLGYGKEHIKYSPVS VSIVRYYPKVTVLGNCEKAVEVCPEGVFAMENNKLVVKNELSCILCEECLKYCAGSVSIESVENKFILEIESVGSLKPER ILIEASKSLLRKLSELKSKLEAGK P39471 2.7.7.6 DNA-directed RNA polymerase subunit E Sulfolobus acidocaldarius DSM 639 0.020496749999999998 1 LEVO MFKLVRAKGIVRIPPEYFGQSVDEIAIKILRQEYQEKLIKDIGVVLGIVNAKASEEGFIIFGDGATYHEVEFDMLVYTPI IHEVIEGEVSQVDNYGVYVNMGPVDGLVHISQITDDNLKFDSNRGILIGEKSKKSIQKGDRVRAMIISASMSSGRLPRIA LTMKQPYLGKIEWINQEIAKASK P39466 2.7.7.6 DNA-directed RNA polymerase, subunit F Sulfolobus acidocaldarius DSM 639 0.013070987 1 LEVO MSYSLKTIEEHFVPYSIAKKYIKELIDTGSSSNLIQKTFDYLNSISRCDEDSASKIMKELEEIVKREDVRAVLASICPTT VEEVRSVLVIDPSTIYSTEQIQKIIEIIKKYVES Q4JB12 2.7.7.6 DNA-directed RNA polymerase, subunit G Sulfolobus acidocaldarius DSM 639 0.015292757999999998 1 Sulfolobus acidocaldarius DSM 639 LEVO MKEMMQGTCKISSIEKGALKNLYVVKMDCDNDLKIEFDITKELSIFSKDEEVTFIISREKPEYSEKDFCAHGYLFLERQQ EDGSFIDEISLYGLIVKILSKNGLINSKLFKMMDHVYYCVKKKAHHHHHH Q4JAY4 2.7.7.6 DNA-directed RNA polymerase subunit H Sulfolobus acidocaldarius DSM 639 0.009477059 1 LEVO MRSSSKKKIDISNHELVPKHEILQLEEAYKLVKELGIKPEQLPWIRASDPVAKSIGAKPGDIIKITRKSPFTGESVTYRY VITG P11521 2.7.7.6 DNA-directed RNA polymerase subunit K Sulfolobus acidocaldarius DSM 639 0.010251989999999999 1 LEVO MTIDKINEIFKENWKNKLTKYEIARIISARALQLSMGALPLIDTSNLKSDDVISIAEEELKRGVLPITIRRIYPNGQVEL ISVRKIENR P39463 2.7.7.6 DNA-directed RNA polymerase subunit L Sulfolobus acidocaldarius DSM 639 0.010061790999999999 1 LEVO MEIKVIKEEQNYLELQIDGEEHTIGNLLKGMLLKVPGVKFAAYSLPHPLITSITIKILTDGSISAREALIKAIELAENYA NLFIDEVKKI P46217 2.7.7.6 DNA-directed RNA polymerase subunit N Sulfolobus acidocaldarius DSM 639 0.007673108 1 LEVO MIIPIRCFTCGAVVADKWEPFSNRVMGGEDPEKVLTELGVNRYCCRRMLLSHVNIIREIIHYTRPI P39472 2.7.7.6 DNA-directed RNA polymerase subunit P Sulfolobus acidocaldarius DSM 639 0.005662912 1 LEVO MAKYRCGKCWKELDDDQLKTLPGVRCPYCGYRIIYMVRKPTVKIVKAI Q4JAE8 2.7.7.6 Conserved protein Sulfolobus acidocaldarius DSM 639 0.012331662 1 LEVO MSEDDSKKEPEPEETEAEIKHEEISREEDDEGGEFSTVTISDIEMLLKDTEIWDKLLRNELSIEEAKKMFDDVARSYSKA DKKKRRVEKKPKKGKVTKKSDEEEE Q4JAJ6 RNAP inhibitory protein Acidianus two-tailed virus 0.017321936

Residual sequence from the thrombin cleavage site at the C-terminus of RIP (LVPR)

1 Escherichia coli BL21 LEVO MKNMLHPQKYETHVLDDLMEFYEGVIGYPEIDLRLAGEEAWLKGVNPELAEAVKKIIKTIRRYLEGSPYDGSEKPIPRYI IAEIFSQIAPEVQLLVNALDTEGKYGFLKHIKKLNLNSLAMLSKNYNENDKLWKELENEGYVYLELVPR Q3V4R7 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 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid 200.0 NaCl sodium chloride 5.0 MgCl2 magnesium chloride 100.0 ZnSO4 zinc sulphate 10.0 C3H8O3 glycerol 5.0 C4H10O2S2 dithiothreitol

DTT was added fresh before the incubation of the two species

UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY ARRAY GLOW DISCHARGE AIR

after glow discharged, the grid was coated with graphene oxide

ETHANE 94 277 FEI VITROBOT MARK IV

blotting force: -10 blotting time: 2 sec wait time: 0 sec.

The sample was monodisperse

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 -1.0 -2.5 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20

sample holder was tilted of -30 degrees for the entire data collection

GATAN K2 SUMMIT (4k x 4k) COUNTING 1-45 1 2130 45.5 1

The movie-stacks were aligned and summed using MotionCor2 within Relion 3.0

600640 Gctf PHASE FLIPPING AND AMPLITUDE CORRECTION 2 C1 3.27 FSC 0.143 CUT-OFF RELION 3.0 3D refinement, followed by three cycles of CTF refinement and post processing 151237 NOT APPLICABLE cryoSPARC 2.0 2D classification NOT APPLICABLE cryoSPARC 2.0 3D reconstruction 2 75000.0 cryoSPARC 2.0 3D reconstruction

The classification provided two classes of identical maps, splitting the particles equally in the two classes. For that, the particles of both classes have been pooled together for the final reconstruction

emd_13026.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 314.1 314.1 314.1 90.0 90.0 90.0 X Y Z -0.10906489 0.19450761 0.00018650922 0.0037748057 1.047 1.047 1.047 0.019 AUTHOR ::::EMDATABANK.org::::EMD-13026:::: Post-process map obtained from Relion 3.0 7OH0 PDB experimental model 3FAJ A PDB experimental model FLEXIBLE FIT

The C-terminal tail of RIP was manually built in Coot after the first refinement run.

correlation coefficient REAL 81.4405 emd_13026_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 303.0 303.0 303.0 90.0 90.0 90.0 X Y Z -0.032793477 0.08990841 0.000012325291 0.00295002 1.01 1.01 1.01 AUTHOR ::::EMDATABANK.org::::EMD-13026:::: Half2 map obtained from 3D refinement in Relion 3.0. The A/pix has been corrected later during post-processing. emd_13026_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 303.0 303.0 303.0 90.0 90.0 90.0 X Y Z -0.03169839 0.09563194 0.000012383232 0.002941212 1.01 1.01 1.01 AUTHOR ::::EMDATABANK.org::::EMD-13026:::: Half1 map obtained from 3D refinement in Relion 3.0. The A/pix has been corrected later during post-processing.