PDB entry 6syt

View 6syt on RCSB PDB site
Description: structure of the smg1-smg8-smg9 complex
Deposited on 2019-10-01, released 2019-12-11
The last revision was dated 2020-10-07, with a file datestamp of 2020-10-02.
Experiment type: EM
Resolution: 3.45 Å
R-factor: N/A
AEROSPACI score: 0.17 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1
    Species: Homo sapiens [TaxId:9606]
    Gene: SMG1, ATX, KIAA0421, LIP
    Database cross-references and differences (RAF-indexed):
    • PDB 6SYT (Start-361)
    • Uniprot Q96Q15 (362-1689)
      • conflict (794)
    • PDB 6SYT (1689-1777)
    • Uniprot Q96Q15 (1778-2029)
    • PDB 6SYT (2029-2085)
    • Uniprot Q96Q15 (2086-2107)
    • PDB 6SYT (2107-2137)
    • Uniprot Q96Q15 (2138-2282)
    • PDB 6SYT (2282-2324)
    • Uniprot Q96Q15 (2325-3711)
      • engineered mutation (2385)
  • Chain 'B':
    Compound: Protein SMG8
    Species: Homo sapiens [TaxId:9606]
    Gene: SMG8, ABC2, C17orf71
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Protein SMG9
    Species: Homo sapiens [TaxId:9606]
    Gene: SMG9, C19orf61
    Database cross-references and differences (RAF-indexed):
  • Heterogens: IHP, ATP, MG

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6sytA (A:)
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxfstnfrdtvdilvgwhidhtqkpsltqqvsgwlqslepfwvadlafsttllgqfledm
    eayaedlshvasgesvdedvpppsvslpklaallrvfstvvrsigerfspirgppiteay
    vtdvlyrvmrcvtaanqvffseavltaanecvgvllgsldpsmtihcdmvitygldqlen
    cqtcgtdyiisvlnlltliveqintklpssfveklfipsskllflryhkekevvavahav
    yqavlslknipvletayklilgemtcalnnllhslqlpeacseikheafknhvfnvdnak
    fvvifdlsalttignaknsligmwalsptvfallsknlmivhsdlavhfpaiqyavlytl
    yshctrhdhfissslsssspslfdgavistvttatkkhfsiilnllgillkkdnlnqdtr
    kllmtwaleaavlmrksetyaplfslpsfhkfckgllantlvedvniclqacsslhalss
    slpddllqrcvdvcrvqlvhsgtrirqafgkllksipldvvlsnnnhteiqeislalrsh
    mskapsntfhpqdfsdvisfilygnshrtgkdnwlerlfyscqrldkrdqstiprnllkt
    davlwqwaiweaaqftvlsklrtplgraqdtfqtiegiirslaahtlnpdqdvsqwttad
    ndeghgnnqlrlvlllqylenleklmynayegcanaltsppkvirtffytnrqtcqdwlt
    rirlsimrvgllagqpavtvrhgfdlltemkttslsqgnelevtimmvvealcelhcpea
    iqgiavwsssivgknllwinsvaqqaegrfekasveyqehlcamtgvdccissfdksvlt
    lanagrnsaspkhslngesrktvlskptdsspevinylgnkacecyisiadwaavqewqn
    aihdlkkstsstslnlkadfnyikslssfesgkfvecteqlellpgeninllaggskeki
    dmkkllpnmlspdprelqksievqllrssvclatalnpieqdqkwqsitenvvkylkqts
    riaigplrlstltvsqslpvlstlqlycssalentvsnrlstedcliplfsealrsckqh
    dvrpwmqalrytmyqnqllekikeqtvpirshlmelgltaakfarkrgnvslatrllaqc
    sevqlgktttaqdlvqhfkklstqgqvdekwgpeldiektkllytagqsthamemlssca
    isfcksvkaeyavaksiltlakwiqaewkeisgqlkqvyraqhqqnftglstlskniltl
    ielpsvntmeeeypriesestvhigvgepdfilgqlyhlssvqapevakswaalaswayr
    wgrkvvdnasxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxegvikvwrkvvdrifslyklsc
    sayftflklnagqipldeddprlhlshrveqstddmivmatlrllrllvkhagelrqyle
    hglettptapwrgiipqlfsrlnhpevyvrqsicnllcrvaqdsphlilypaivgtisls
    sesqasgnkfstaiptllgniqgeellvseceggsppasqdsnkdepksglnedqammqd
    cyskivdklssanptmvlqvqmlvaelrrvtvlwdelwlgvllqqhmyvlrriqqledev
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxphekwfqdnygdai
    enaleklkxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxyilrleeispwlaamtnteial
    pgevsardtvtihsvggtitilptktkpkkllflgsdgksypylfkgledlhlderimqf
    lsivntmfatinrqetprfharhysvtplgtrsgliqwvdgatplfglykrwqqreaalq
    aqkxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxwplhvmkavleelme
    atppnllakelwsscttpdewwrvtqsyarstavmsmvgyiiglgarhldnvlidmttge
    vvhidynvcfekgkslrvpekvpfrmtqnietalgvtgvegvfrlsceqvlhimrrgret
    lltlleafvydplvdwtaggeagfagavyggggqqaeskqskremereitrslfssrvae
    ikvnwfknrdemlvvlpkldgsldeylslqeqltdveklqgklleeieflegaegvdhps
    htlqhrysehtqlqtqqravqeaiqvklnefeqwithyqaafnnleatqlasllqeistq
    mdlgppsyvpataflqnagqahlisqceqlegevgallqqrrsvlrgcleqlhhyatval
    qypkaifqkhrieqwktwmeelicnttvercqelyrkyemqyapqppptvcqfitatemt
    lqryaadinsrlirqverlkqeavtvpvcedqlkeiercikvflhengeegslslasvii
    salctltrrnlmmegaassageqlvdltsrdgawfleelcsmsgnvtclvqllkqchlvp
    qdldipnpmeasetvhlangvytslqelnsnfrqiifpealrclmkgeytlesmlheldg
    lieqttdgvplqtlveslqaylrnaamgleeethahyidvarllhaqygeliqprngsvd
    etpkmsagqmllvafdgmfaqvetafsllveklnkmeipiawrkidiirearstqvnffd
    ddnhrqvleeifflkrlqtikeffrlcgtfsktlsgsssledqntvngpvqivnvktlfr
    nscfsedqmakpikaftadfvrqlliglpnqalgltlcsfisalgvdiiaqveakdfgae
    skvsvddlckkavehniqigkfsqlvmnratvlassydtawkkhdlvrrletsissckts
    lqrvqlhiamfqwqhedllinrpqamsvtppprsailtsmkkklhtlsqietsiatvqek
    laalessieqrlkwagganpalapvlqdfeatiaerrnlvlkesqrasqvtflcsniihf
    eslrtrtaealnldaalfelikrcqqmcsfasqfnssvselelrllqrvdtglehpigss
    ewllsahkqltqdmstqraiqtekeqqietvcetiqnlvdniktvltghnrqlgdvkhll
    kamakdeeaaladgedvpyensvrqflgeykswqdniqtvlftlvqamgqvrsqehveml
    qeitptlkelktqsqsiynnlvsfasplvtdatnecssptssatyqpsfaaavrsntgqk
    tqpdvmsqnarkliqknlatsadtppstvpgtgksvacspkkavrdpktgkavqernsya
    vsvwkrvkaklegrdvdpnrrmsvaeqvdyvikeatnldnlaqlyegwtawv
    

    Sequence, based on observed residues (ATOM records):
    >6sytA (A:)
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xfstnfrdtvdilvgsltqqvsgwlqsleafsttllgqfledmeayaedlssvslpklaa
    llrvfstvvrsiayvtdvlyrvmrcvtaanqvffseavltaanecvgvllgsldpsmtih
    cdmvitygldqlencqtcgtdyiisvlnlltliveqintklpssfveklfipsskllflr
    yhkekevvavahavyqavlslknipvletayklilgemtcalnnllhslqlpeacseikh
    eafknhvfnvdnakfvvifdlsalttignaknlsptvfallsknlmivhsdlavhfpaiq
    yavlytlyshctrhdhfissskkhfsiilnllgillkkdnlnqdtrkllmtwaleaavlm
    rksetyaplfslpsfhkfckgllantlvedvniclqacsslhalssslpddllqrcvdvc
    rvqlvhsgtrirqafgkllksipldvvlsnnnhteiqeislalrshmskapsntfhpqdf
    sdvisfilygnshrtnwlerlfyscqrldktiprnllktdavlwqwaiweaaqftvlskl
    rtplgraqdtfqtiegiirslaahtlnpdqdvsqwttadndeghgnnqlrlvlllqylen
    leklmynayegcanaltrtffytnrqtcqdwltrirlsimrvgllagqpavtvrhgfdll
    temktnelevtimmvvealcelhcpeaiqgiavwsssinllwinsvaqqaegrfekasve
    yqehlcamtgvdccissfdksvltlansspevinylgnkacecyisiadwaavqewqnai
    hdlkkstsstslnlkadfnyikslssfesgkfvecteqlellpgeninldmkkllpnmls
    pdprelqksievqllrssvclatalnwqsitenvvkylkqtsriaigplrlstltvsqsl
    pvlstlqlycssalentvsnrlstedcliplfsealrsckqhdvrpwmqalrytmyqnql
    lekikeqtvpirshlmelgltaakfarkrgnvslatrllaqcsettaqdlvqhfkkwgpe
    ldiektkllytagqsthamemlsscaisfcksvkaeyavaksiltlakwiqaewkeisgq
    lkqvyraqhqlstlskniltlielpsesestvhigvgepdfilgqlyhlssvqapevaks
    waalaswayrwgrkvvdnasxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxegvikvwrkvvdrifslyklscsayftflklnastddmivmatlrllrllvkhagelr
    qylehgletpwrgiipqlfsrlnhpevyvrqsicnllcrvaqdsphlilypaivgtiqam
    mqdcyskivdklssanptmvlqvqmlvaelrrvtwdelwlgvllqqhmyvlxxxxxxxxx
    xxxxxxxphekwfqdnygdaienaleklkxxxxxxxxxxxxxxxxyilrleeitnteial
    pgvtihsvgtitilptkpkkllflgsdsypylfkgledlhlderimqflsivntmfatin
    rqetprfharhysvtplgtrsgliqwvdgatplfglykrwqqreaalqaqkxxxxxxxxx
    xxxxxxxxxwplhvmkavleelmeatppnllakelwsscttpdewwrvtqsyarstavms
    mvgyiiglgarhldnvlidmttgevvhidynvcfekgkslrvpekvpfrmtqnietalgv
    tgvegvfrlsceqvlhimrrgretlltlleafvydplvdwtsyavsvwkrvkaklegrdv
    dpnrrmsvaeqvdyvikeatnldnlaqlyegwtawv
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6sytB (B:)
    magpvslrdllmgasawmgsespggsptegggsaaggpeppwredeicvvgifgktalrl
    nsekfslvntvcdrqvfplfrhqdpgdpgpgirteagavgeaggaedpgaaaggsvrgsg
    avaegnrteagsqdysllqayysqeskvlyllltsicdnsqllracralqsgeaggglsl
    phaeahefwkhqeklqclsllylfsvchilllvhptcsfditydrvfraldglrqkvlpl
    lktaikdcpvgkdwklncrpcpprllflfqlngalkvepprnqdpahpdkpkkhspkrrl
    qhaledqiyrifrksrvltnqsinclftvpanqafvyivpgsqeedpvgmlldqlrshct
    vkdpesllvpaplsgprryqvmrqhsrqqlsfhidsssssssgqlvdftlreflwqhvel
    vlskkgfddsvgrnpqpshfelptyqkwisaasklyevaidgkeedlgsptgeltskils
    sikvlegfldidtkfsenrcqkalpmahsayqsnlphnytmtvhknqlaqalrvysqhar
    gpafhkyamqlhedcykfwsnghqlceersltdqhcvhkfhslpksgekpeadrnppvly
    hnsrarstgacncgrkqaprddpfdikaanydfyqlleekccgkldhinfpvfepstpdp
    apaknesspappdsdadklkekepqtqgestslslalslgqstdslgtypadpqaggdnp
    evhgqvevktekrpnfvdrqastveylpgmlhsncpkgllpkfsswslvklgpaksynfh
    tgldqqgfipgtnylmpwdivirtraedegdldtnswpapnkaipgkrsavvmgrgrrrd
    diarafvgfeyedsrgrrfmcsgpdkvmkvmgsgpkesalkalnsdmplyilsssqgrgl
    kphyaqlmrlfvvvpdaplqiilmpqvqpgpppcpvfypekqeitlppdglwvlrfpyay
    vtergpcfppkenvqlmsykvlrgvlkavtq
    

    Sequence, based on observed residues (ATOM records):
    >6sytB (B:)
    pvslrdllmgeppwredeicvvgifgktalrlnsekfslvntvcdrqvfplfrqdysllq
    ayysqeskvlyllltsicdnsqllracralqsgphaeahefwkhqeklqclsllylfsvc
    hilllvhptcsfditydrvfraldglrqkvlpllktaikdcpvgkdwklncrpcpprllf
    lfqlngalkspkrrlqhaledqiyrifrksrvltnqsinclftvpanqafvyivpgsqee
    dpvgmlldqlrshctftlreflwqhvelvlskkgfddsvgrnpqpshfelptyqkwisaa
    sklyevskilssikvlfldidtkfsenrcqkalpmahsayvhknqlaqalrvysqhargp
    afhkyamqlhedcykfw
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6sytC (C:)
    msesghsqpglygierrrrwkepgsggpqnlsgpggrerdyiapwererrdaseetstsv
    mqktpiilskppaerskqpppptapaappapaplekpivlmkpreegkgpvavtgastpe
    gtappppaapappkgekegqrptqpvyqiqnrgmgtaapaamdpvvgqakllppermkhs
    iklvddqmnwcdsaieylldqtdvlvvgvlglqgtgksmvmsllsantpeedqrtyvfra
    qsaemkerggnqtsgidffitqerivfldtqpilspsildhlinndrklppeynlphtyv
    emqslqiaaflftvchvvivvqdwftdlslyrflqtaemvkpstpspshesssssgsdeg
    teyyphlvflqnkarredfcprklrqmhlmidqlmahshlrykgtlsmlqcnvfpglppd
    fldsevnlflvpfmdseaesenppragpgssplfsllpgyrghpsfqslvsklrsqvmsm
    arpqlshtilteknwfhyaariwdgvrkssalaeysrlla
    

    Sequence, based on observed residues (ATOM records):
    >6sytC (C:)
    llppermkhsiklvddqmnwcdsaieylldqtdvlvvgvlglqgtgksmvmsllsantpe
    edqrtyvfraqsaemkerggnqtsgidffitqerivfldtqpilspsildhlinnynlph
    tyvemqslqiaaflftvchvvivvqdwftdlslyrflqtaemvkpsteyyphlvflqnka
    rredfcprklrqmhlmidqlmahshlrykgtlsmlqcnvfpglppdfldsevnlflvpfm
    dplfsllpgyrghpsfqslvsklrsqvmsmarpqlshtilteknwfhyaariwdgvrkss
    alaeysrll