Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1), composite map

2026-01-21 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2024-08-29 2026-01-21 2026-01-21 2026-01-21 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM071940 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI101057 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) RO1AI152408 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI177658 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI113157 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM145249 United States National Natural Science Foundation of China (NSFC) 32570759 China Trypanosoma brucei mitochondrial RNA-editing catalytic complex 1, U-deletion (RECC1), composite map Liu YT Jih J Zhou ZH Aphasizhev R RNA editing, tRNA, OB-fold, mitochondria, RNA BINDING PROTEIN Liu YT Vacas AF Jih J Zhao X Yu C Lee JKJ Suematsu T Solayman M Wang H Wang X Huang L Zhang L Aphasizheva I Zhou ZH Aphasizhev R Structural basis of the mitochondrial RNA editing cascade in trypanosomes To Be Published 0353 EMD-46785 consensus EM volume

T. brucei RECC1 consensus map

EMD-46786 focused EM volume

T. brucei RECC1 left wing focused refinement map

EMD-46787 focused EM volume

T. brucei RECC1 right wing focused refinement map

EMD-46789 focused EM volume

T. brucei RECC1 tail focused refinement map

9dei FULLOVERLAP EMDB EMD-46791 associated EM volume

Trypanosoma brucei mitochondrial RNA editing catalytic complex, U-deletion (RECC1)

EMDB EMD-46785 consensus EM volume

T. brucei RECC1 consensus map

EMDB EMD-46786 focused EM volume

T. brucei RECC1 left wing focused refinement map

EMDB EMD-46787 focused EM volume

T. brucei RECC1 right wing focused refinement map

EMDB EMD-46789 focused EM volume

T. brucei RECC1 tail focused refinement map

RECC1 RECC1 0 1 2 3 4 5 6 7 8 9 10 11

From T. brucei mitochondrial T2 isolate

Trypanosoma brucei Lister 427 Mitochondria RECC1 core 1 1 2 3 4

Endonuclease-containing heterotetrameric core

Trypanosoma brucei Lister 427 Mitochondria RECC1 left wing 1 5 6 7

Peripheral tetramer of OB-fold-containing A-proteins (A2, A3, and two copies of A6)

Trypanosoma brucei Lister 427 Mitochondria RECC1 right wing 1 5 7 8 9

Peripheral tetramer of OB-fold-containing A-proteins (A2, A4, A5, and A6)

Trypanosoma brucei Lister 427 Mitochondria RECC1 tail 1 5 6 10

Peripheral tetramer of OB-fold-containing A-proteins (A1, A3, and two copies of A6)

Trypanosoma brucei Lister 427 Mitochondria tRNA 1 11

Bridges RECC1 core and left wing

Trypanosoma brucei Lister 427 Mitochondria KREPB5; RNA-editing catalytic complex core protein, B5 Trypanosoma brucei Lister 427 0.043818895 1 LEVO MRRAVVLHTAAPMCALTGKCVEDWESHRKSFDMRIFELLKGRVTSPTEPLPIKQIYATIANPCRLVEEFTCAKTTRRLGR LHTALSFLRRHNVLLHSLLFHVKETQTWNTTPDFDRLALYGESSLRHEVRARTLRLFPGIDSETYAALTSSVLSEEALHG LFDRLLMKALVGEKPVGKMRDWSLTPNQCGQMLCAIVGEMSWFAARTKATDRTHNNALFPPSDALILHVLCCHVLESLPA ELLYNVLEPKVQRIKENWVNEPMSIPEQLHLKPRTIGSLSLSLVAKPLTEEEGRRKEVAVSAEKCQLSLTPERVIGSVRS TMLPRWNYKRFEERRYHILESDKRQVLPLAMSPVGRGDVSLASEQMPDERRRELVALALGGRYR KREPB8; RNA editing catalytic complex core protein, B8 Trypanosoma brucei Lister 427 0.041881055 1 LEVO MHRGPPALLHNVGVATRSKSFAASTKLPGRLTPLPSTSSTLQPTNTLLSSSAGIASLRQLVSASTLTSTSTSGKKRVGSL DAHCRLLSRGTSADSYMPMTSRSFDVFEGNNKQAWLDLKTGWCHLCQEPLGATMGVHIGDRDHTNLQYFLFLYAAHGRRW SSEEVLRSCLATAPTVHNYATRHTTWDHLHVMDDALRRAELEALLFHLTHPPQQALSHVLQGRSPLGFWYSGERMWKLRI SRLVTQVFPPISAGMMTNFTQKCWGRSNGERMYDALRLQRIKAYYGWQPYESKEKKAFFVRQLLWELLSVEVRDEVDELT KHMADLALRRMAFEMIFLQSMEYMHKVQYVYDLMGRPTVDELAAMNLL C9ZW42 MP90 Trypanosoma brucei Lister 427 0.090093039 1 LEVO MGLHWPLARSSNWCHMRALSNEHLRRRVGAAVRSIASTAPCFALERVEVAHSHAYSRRGVTVGFTSSSSSPSGKTGSGGL SPASQSLHSSSSFDASNGDVLANYVNFVADDATGPAATKENGAQPMRSLRSASAVENLLFTDAAKNYCRLCMEEVQVTPK AHISTPYRGSHTNHTCREVVLDSLALLAIRGYPIDDVYFVWADTLYQSSVFQRIPELVSPRWTVDKRSEVLAKILFMLKD MGVIDISLAAQAPDLFDNTAQQVHHRRRVAFERLEYIGDNSWGNHLSNRMMLLFPDRQWTYSQNAYTFNCFRDACEMNVT LEFMFDTLRVGELLPPGVREKLGTGKIKADVVEAVIGELHVTLWGLEPQLYDSVCFVEINGVGEARLAALVQHCLTEIYD LIVLSYVQELSGSAVPLAKQIAADRIWNSVYPPVRKAKDRAPGGRKSRSTVVNVVGVGEVRQLPSLPSLFPAASKRPTRA PHPLRRLRKLGEIPEETVCAGTNKDVFVHLIESYERLDMLDDSLLPTLNMRRLQDVQFSKLKRQLVPSLSPAALEELHNC KELDAESVTPHKVGDKEVATDERVLDLEEVYFRDKYFDLFPTPLPNEVVTKEGDCDKRQSGASTSRAVIISLPRGFDGSR PCNRAQLHMARNTIYPSLTERPAHSPTAGITKGDRVCLFSLSVYVPPDTKRPSAGVVTDKNLHFGEFAFHGVRIKGIECA SEPECISRRSNAPGSDVGTSLNRSSWKEGGDNSCGTLTVEDGTGENSVVGEDGDTGVNGGEGKAEDATGKHLLRAKWCRE NPFFPRASLPLLGISVGA C9ZIA9 RNA editing complex protein MP46 Trypanosoma brucei Lister 427 0.046525059 1 LEVO MLRVENLRRSMTRLARHSLIRAVPFSPLSVGSSTDQTFGAPTRTPFRSHTCLLCDVSYESWGDHAESTTHIARHAICRTF VSPERHNAVMQQLWKHIRLDFGYVDEVTHKKEDRRRMRLASTMRHLQEKGVLHHSLPRVTVDAQSEVSLTVESDSFVNYM FLGESFARQETLDRVARLMPRAEALELSSIISFVLSKRRLAHFFDIFDMRKMVLNGDSSDDKASADGDVPPTIPRLQQDG KAVILFSCLGELQMFSRRDRSHSVATRSAAEQLVLNVLGTHVMENIIGELVHEALQTVVEEGTAVWREHCGELKHKLFEG TKAASPPIATTPNPVSNSGGPEVTADVNDQMWVDLCRLYVLDKNGSVPQLQPTVKRHSWHDVARALTLELTVPNPVNKSA VFAAAAPRLATKKK Q86MV9 MP18 RNA editing complex protein, putative Trypanosoma brucei Lister 427 0.018097566 5 LEVO MLALTSRRLLLQQTFMRCCKSVNSVTLVGVVHDIQSGFVYEDAVTQFTLTTTSIDTTHPTQEVVVEKDHHTIRCFGELFS AEVKQKVKEGNVVCVNGRLRLSPQLEPSCNKHFYFPYIQVQPPHGQVAVIHGDRRTVPAAVNPAVEDIKSEKEGAGGDQS GVPS D0A2P0 RNA-editing complex protein MP42 Trypanosoma brucei Lister 427 0.042318461 2 LEVO MKRVTSHISRFLPLVLSQRGLSTYASPHVSSMRYYGATKCLLASTPDTPSFQCGECGKAFRLINALNHHIMTKHAGKAKA MMNKGGKLEEVNPEEIKNKPQGAMSQPTSPPPSSSTSGTEAASTSPTHSSFPGIPFSPVGGIGLVGTPVGAASHVVNTTT TAANSASGNALSDENADKKTFVCTICQKTFRLEAALQHHYQAKHNMEMPTSSSSSGGASAQPVLQGGATTAGVGSVGFSH TEEETGRSAMGTQYVHSQETILPQAPQYHLDVAPNAPEEGEVAAHWRCVNHCVMLGVVQNIQEGFVFEDKVLQFTLITDF EGPSPGDPDKDFHTVRVFDSDYSSRVKEQLRDGEWFLVTGRLRMVPQYDGSMRKYYHYPVIQVHPGCGSVLKV Q95W13 KREPA2 Trypanosoma brucei Lister 427 0.062983031 2 LEVO MYRRFFRSAAVKHLGTTSAQCLMRATKYPCGAMCRNASSCHPQTLGYQQRFQSTTDKKFHCSVCKKPFRLEMAAKLHLQQ AHGGDGSVEAGPGPGVEASSVNVVSTPVPSPISPVERTFVDEEERRPRRMRPTPKPLHQPDRDIPAAAMEEMLGVWDKIG LNRLEGNFVHSTMVMKVFAAPPDVSEIPLYEHVAPEGENPFDSLDHMTTGTVDATYVGHDAFAEVDLVDPFVAAPDQTLN PFRAGKVRNPFTRISPTQREVVKPLQPPQPKEEPLKAPVTPFGQLPMFGQTREPSASFAAAAVSVQAAANPNEVSSPFAA AVSSSPFVGQVASPFAPAQDVAGSPFEASPCAASSPFVTAGGQETSPFAAPSTPASFGQGSLFPPMGTGAPGFTAITETE QRQQELEHGCPTCGKKFSTFEGAAMHSKSKHGIVLESKKVKDRLNRKGVPDLPAYVPSPVDLSSTSPFGTRSAIGASWAE TELIPHAQCVSNITIVGRVLDVSQASENVSHVTVFVEGERSGEEETLTLCCFGEVSQKIRGTLKRNATIFASGTLRLHPV YEASNNKYYVSPVVHVSMPTGTLAVIT A0A3L6L0V2 RNA editing complex protein Trypanosoma brucei Lister 427 0.023769062 1 LEVO MWVRSLLLCIRRDPLQRAVDVAYASGMLLGSGSSRGTTHFSETTAFTSSNFAADLRGGRVGLAGDGGTKCEDRNGELVRG RIQFASRCAEGPFVGASPTVTSCAHIEGVVRQVECGYVGGDRVLQFIIEVEEVPASGGTPMRLPLAVRWRPGSEVAQNRM DEWQKEMERLVGRRVLASGRLQVEECFDSGSRRLYKTPSLVLPATSTVEMISLQELEC D0A2N9 KREPA5 Trypanosoma brucei Lister 427 0.019081923999999997 1 LEVO MFSSTFRRLAIRPLNRVTMVGAMHDIQVGFLDRCSVFQFTLTCTVLDFQKVAEPQPKSPGSLPSSTRTAPNANGEEVEKH INKEQYTVRCLGSEAYTEALKNYLDDGCIVRVIGRLKTTEVVDAGKKQPFPCIIVEQGRWSTVSLVHSLRKQRRDWQLQN ILTSVATLE A0A3L6L2P3 RNA-editing complex protein MP81 Trypanosoma brucei Lister 427 0.08130718799999999 1 LEVO MRRLTRRSDRLCGKGNGGSCLQMSPTHVGAVVTWSLNRLMPLHTRTIPLRCSLPTPESGTTEPRELCFYETFELTGEDVH YLLLHEAHVKHGVLLNVPPQLAPNGTPPEVPEVIMPAAQLERMGGMKLAYEPTHLPPPLHTTGARQLVLDESFYTTPTKE KKATTTAVSHVSESTAASGGRGGASATAAGTALPPRLPPDPTMKFHCSACGKAFRLKFSADHHVKLNHGSDPKAAVVDGP GEGGLLGGAVTITTAKVAKHSSSAASGTASRAGDSATLDVKQQPDPQKELSASGISAVKIPYSKAVLSLPDDELVDELLI DVWDAVAAQRDDVPKSNSANIFLPFASVVTGTADRRKEMEAVARPTARATPEGAAPGIKRPGAMAGGAVAVGKGRSGGQI LPIRELIKKYPNPFGDSPNAAVQDLENEPLNPFLPEEELAAQLQVACEEDTVVTPSACTTDVSTGSVIGKKGSLEKLKEK LRGTRPSMAASAAKRRFTCPICVEKQQTLQQQQSENVGSGFCTDIPSFRLLDALLDHVESVHGEELTEDQLRELYAKQRQ STLYPQKSSTGDGAGSRETPDDSEKKEGSVGNTSMDELKSLPEEVRRVVPPAPVEQDALAVHIRAGSNALMIGRIADVQH GFLGAMTVTQYVLEVDGDERINSKGVTTPASACTPDPASTKAVEAKGEEGEVVEPEKEFIVIRCMGDNFPASLLKDQVKL GSRVLVQGTLRMNRHVDDVSKRLHAYPFIQVVPPLGYVKVVG Q95W15 tRNA-valine (anticodon AAC) Trypanosoma brucei Lister 427 0.024480467 1 CGCUGAUGGUCUAGGUGGUUAUGACGUCGCUUUAACACGGCGAAGGUCUCGGGUUCGAGUCCCGAUCGGCGUACCA ZINC ION 6.5409e-05 5 ZN MAGNESIUM ION 2.4305e-05 3 MG GUANOSINE-5'-MONOPHOSPHATE 0.000363221 1 5GP water 1.8015e-05 367 HOH singleParticle particle 7.6 60.0 KCl Potassium chloride 25.0 Tris-HCl Tris hydrochloride 10.0 MgCl2 Magnesium chloride 5.0 OG n-Octylglucoside 1.0 CaCl2 Calcium chloride Quantifoil R1.2/1.3 GOLD 300 GRAPHENE CONTINUOUS PLASMA CLEANING 60 ETHANE 100 277 FEI VITROBOT MARK IV

From T. brucei mitochondrial T2 isolate

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 3.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 23092 2.0 45.0 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.6 2.8000000000000003 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 FEI FALCON IV (4k x 4k) 40988 3.5 45.0 2

Falcon 4i and K3 Bioquantum images were combined for processing.

cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION C1 FOURIER SPACE 2.99 FSC 0.143 CUT-OFF cryoSPARC 452724 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC cryoSPARC emd_46791.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 422.40002 422.40002 422.40002 90.0 90.0 90.0 Z Y X -39.675249999999998 71.537009999999995 0.006750229 1.0837945 1.1 1.1 1.1 3.5 AUTHOR ::::EMDATABANK.org::::EMD-46791:::: RNA-editing catalytic complex 1 (RECC1), composite map AB INITIO MODEL

Consensus map and focused refinement maps were combined to generate a composite map for final model refinement.

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