Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 2)

2025-12-31 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBj PDBj 2024-12-26 2025-12-31 2025-12-31 2025-12-31 Japan Society for the Promotion of Science (JSPS) 16H04759 Japan Japan Society for the Promotion of Science (JSPS) 16KK0166 Japan Japan Society for the Promotion of Science (JSPS) 20H02916 Japan Japan Society for the Promotion of Science (JSPS) 24H00505 Japan Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 2) Ouchi R Numata T CRISPR-Cas effector, ANTIVIRAL PROTEIN Ouchi R Numata T A new in vitro reconstitution system of type III-B CRISPR-Cas effector for functional and structural studies To Be Published 0353 9l7d FULLOVERLAP EMDB EMD-62873 associated EM volume

Archaeoglobus fulgidus type III-B CRISPR-Cas effector Archaeoglobus fulgidus type III-B CRISPR-Cas effector 0 1 2 3 4 5 6 7 Archaeoglobus fulgidus DSM 4304 0.346 Type III-B CRISPR module RAMP protein Cmr4 Archaeoglobus fulgidus DSM 4304 0.041252254

His-tagged protein

2 Escherichia coli BL21(DE3) LEVO MGSSHHHHHHSQDPMFDMFEKAVVFGLYSITPVHAGSGAELSVIALPIQRERHTGFPVIWGQSLKGVLRSRFRQLELDEK IEVESQKWKWKEKTKEVLKEKADEFIKKVEERKRDPLLTEIVFGPATDGASEHAGAVSVGDAKILLFPVRSAKGVFAFVT SPIVIQRLKEDFELVSEIENDIELKQILSRFKVELSNNETIAGNALILNGENKVILEDIVLKVKSDSNVIENLVEVLKTL FGDNFFGKPIESIKERIAIVSDDVFKSFTRFSTEIVARVRIDAEKGTVARGGLWYEEFLPSDTLMYSLIAVGSPKKENLP KEVDNTQKIVNVLKVTFNNAFLQIGGDETVGKGFVKVRAGVLTGGHKGN O28416 Cmr1 C-terminal domain-containing protein Archaeoglobus fulgidus 0.038016969 1 Escherichia coli BL21(DE3) LEVO MCMYSATFTLEAITPVFMRGANQSKAEIRAASIKGLMRWWFRALSGSYFGNDVEGLRRVEEYVFGSTKRESRVVVEVVKE HVEERFCPLPMVWKKKKGVTTRVSQRAIAPGSKFTLLLTSDDEEVLKLACYSLIGLVYFGGIGFRCSRGAGSLKISSLKS DVQLIDLPKNKNQLGQMVNDLTVEIAKILKKTFLCDHENKNCTSYSSFWCFYLFLWGEKAELEEVYYRSNNLENERLTLL DLFEKEFKNKNNHLSNYGYRDFVFGLPRGTKKDRRASPIKVGITELSEKYHVRVSVFKTKIFKPGMNVKWDNIFVFLENI GAERIYPER O28411 GGDEF domain-containing protein Archaeoglobus fulgidus DSM 4304 0.11521185199999999 1 Escherichia coli BL21(DE3) LEVO MGQYFRVSGKYRGRENLPREVNKMADNEFWLNKIRAFFHDPPDKSFELKTHERRASFILGELKPSKSLKRIIKNADIQAS SLQRVDLEKSIHKKELKSTFDRIHNTEKYEYIGQPIIRHPVTGEIKEYGTILANLPQTQREVYDVDDEGKEDYEEQFQEI LSRILKIEKKVFDDFKNRYSDPKDLYISLWAFYAEKLKEALEEEFSASFAEEFVNLPAYTLSPDHTLFDHADATSAIFGA EIDGKKPVLVLFKISPVQKFIADARKEKDLWAASHMLSTLTFKAISFIADKFGPDVVIYPHLRGNPFFHAWLHSKKIWEF SDSHSLKIASVPNKFLALVGVSDEKELNNLREGIRNEIESFLADLFDKLWNEVIVGALEHSDALKHLGDKKEIHKEILLK RFTLTLSSLKIHDVDVSGSKEEAYEKVKDFVRSLGLPNAIESKYLQWLDMLGSVEASNNRPTKYDLYSLYYEILTVLNAI ESTHFDKPAEPAGYKCTLCGEHLAIGGESREMMENVWGKIHKRWPSHLRSNERLCAVCAVKRFYPKFIETLDIFEGVGKV VPDIESVSEVAMCRRTKHGITWKEVYDYLRGLKNVDDEKLLGKLENLKHSVQTLINNVKSELKSRKVYPEEFLEGLNRNF SNEILYSERLRDFNTLLDTLGFDAAKLGLDDVKNYETMISELRERLSEVYKMLGEPPKYYAILMMDGDEMGKLLSGEKLK TAEHYLHSAILERVSDALRVKAKTVRRLITPAAHSSISRALKNFSVNHVPDVVRKGNGTLIYSGGDDVLVLLPVDTAFDV ATELAMTFSTSWNGWEMLPGNKLSAGLLIVHYKHPLYDALEKTRELLQKAKKLGRNAIAVGLLKRSGSYYESVVNFETLE DAKAVANLLVKEQVSPRIIYELLNFADVISKEFLHQLVKYEAVRHSIDKNLAEEFQSVFARGHQGVRVELEGNDEEINKY ISDGANLETFLDKYEKAVDVIRKQVRGFLNLVKILYESIRGGAK O28412 Type III-B CRISPR module-associated protein Cmr3 Archaeoglobus fulgidus DSM 4304 0.039043328 1 Escherichia coli BL21(DE3) LEVO MILVMKPYDSLLFREPRPFDVNNHVARTILPLPQTLAGAVRSAIYVKYGSKVKDLIGFGKEEPEFEILGHFFYRYDGKFE LLVESPHDVTQNLGLVKPHRIDKLGITILMDSEGIKFRPFNGFLKFSGLIDYLQGRIAEDSVVERQKIFKKERRVGIALT KAKVTKEEHFYQVEMLRFSDDCGIAVWVEDGVDFDDEGILGVGGERRFVKFEKREEPECITNLRSKWKKIRDKINETGRL KIYLATPAILGAKGYSSKLDYDLLGDIGIERVRSVNFIGGKPVIFSGWDFVTRKPKPTRYAVPAGSVYFVEFEGEVKLDM PYLKLGKLTKLGYGLCFMGVW O28413 Type III-B CRISPR module RAMP protein Cmr6 Archaeoglobus fulgidus DSM 4304 0.039469902 1 Escherichia coli BL21(DE3) LEVO MKSNVVVKYPVNSELANYAEKFWKKELAIYNLSLILNKMTPFVKRRSESYKSSLSAVKEIFKNVDDFQNFLNSVLRRSLD EYRVFFENYERLFNSFSSKIFSMRTKSRLVVGLGDESVYETSIRLHRNYGVPYIPGSALKGVAKHYAFSILARENGDEIL RIYESVKEDLKARIAKRDKIKKNDVPEDYYLTAAVIQELFEKKFDELGAIRNTRVEIGDTVISVGDIVKIFGTQKEEGSV IFFDAFPTPEQLKDKPNLELDIMNPHYQPYYQHGEPPGDWHSPNPIFFLTVPAGVEFTFAVASRDLDDLAEKAEKLLKEA LKKFGVGAKTSLGYGRFDARDDR O28418 CRISPR system Cmr subunit Cmr5 Archaeoglobus fulgidus DSM 4304 0.017407706999999998 1 Escherichia coli BL21(DE3) LEVO MDIREIEQERASFAFKVVSDIKDKYSQNKKVQGKYSSYAEKAPTIILNNGLGATLAFFLSKLEKPIDDVDYKSINPESFG NAENIAYAFLYKHLSTWLAEGNGKDSAFSGLTNGEDPLKYIMEKTAIDVAISTEEALSILNWIKKFAKAMLEEEL O28417 RNA (5'-R(*UP*GP*UP*AP*GP*UP*AP*UP*GP*CP*GP*GP*UP*CP*CP*UP*UP*GP*CP*GP*GP*C)-3') Pyrococcus furiosus DSM 3638 0.014501588999999999 1 AUUGAAAGUUGUAGUAUGCGGUCCUUGCGGCUGAGAGCACUUCAG MAGNESIUM ION 2.4305e-05 1 MG ADENOSINE-5'-TRIPHOSPHATE 0.000507181 2 ATP ZINC ION 6.5409e-05 1 ZN singleParticle particle 0.8 7.0 20.0 Tris-HCl 200.0 NaCl 1.0 DTT 2.0 MgCl2 Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY ARRAY GLOW DISCHARGE 10 AIR 0.007 ETHANE 100 281 FEI VITROBOT MARK IV JEOL CRYO ARM 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.4000000000000001 1.6 60000.0 NITROGEN In-column Omega Filter GATAN K3 BIOCONTINUUM (6k x 4k) 1 5500 2.597 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION

AlphaFold2 model

C1 3.1 FSC 0.143 CUT-OFF cryoSPARC 4.3.1 66164 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 MAXIMUM LIKELIHOOD cryoSPARC 4.3.1 emd_62873.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 300.8 300.8 300.8 90.0 90.0 90.0 X Y Z -0.4197578 0.9227727 -0.0008131578 0.03210518 0.752 0.752 0.752 0.235 AUTHOR ::::EMDATABANK.org::::EMD-62873:::: AlphaFold in silico model

The initial model containing all protein subunits was constructed by AlphaFold2

emd_62873_msk_1.map emd_62873_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 300.8 300.8 300.8 90.0 90.0 90.0 X Y Z -1.4379504 2.2829838 -0.00081315776 0.06134628 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-62873:::: emd_62873_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 300.8 300.8 300.8 90.0 90.0 90.0 X Y Z -0.67881674 1.2642256 0.000875823 0.06492032 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-62873:::: emd_62873_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 300.8 300.8 300.8 90.0 90.0 90.0 X Y Z -0.6410434 1.1487366 0.0008536001 0.06489337 0.752 0.752 0.752 AUTHOR ::::EMDATABANK.org::::EMD-62873::::