PDB entry 6nzd

View 6nzd on RCSB PDB site
Description: cryo-em structure of the lysosomal folliculin complex (flcn-fnip2- raga-ragc-ragulator)
Deposited on 2019-02-13, released 2019-11-06
The last revision was dated 2019-12-18, with a file datestamp of 2019-12-13.
Experiment type: EM
Resolution: 3.6 Å
R-factor: N/A
AEROSPACI score: 0.08 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Ragulator complex protein LAMTOR1
    Species: Homo sapiens [TaxId:9606]
    Gene: LAMTOR1, C11orf59, PDRO, PP7157
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Ragulator complex protein LAMTOR2
    Species: Homo sapiens [TaxId:9606]
    Gene: LAMTOR2, MAPBPIP, ROBLD3, HSPC003
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9Y2Q5 (2-126)
      • expression tag (1)
  • Chain 'C':
    Compound: Ragulator complex protein LAMTOR3
    Species: Homo sapiens [TaxId:9606]
    Gene: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Ragulator complex protein LAMTOR4
    Species: Homo sapiens [TaxId:9606]
    Gene: LAMTOR4, C7orf59
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Hepatitis B virus x interacting protein
    Species: Homo sapiens [TaxId:9606]
    Gene: LAMTOR5, HBXIP, hCG_40252
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Ras-related GTP-binding protein A
    Species: Homo sapiens [TaxId:9606]
    Gene: RRAGA
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Ras-related GTP-binding protein C
    Species: Homo sapiens [TaxId:9606]
    Gene: RRAGC
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9HB90
      • engineered mutation (185)
  • Chain 'H':
    Compound: Folliculin
    Species: Homo sapiens [TaxId:9606]
    Gene: FLCN, BHD
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: Folliculin-interacting protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: FNIP2, FNIPL, KIAA1450, MAPO1
    Database cross-references and differences (RAF-indexed):
  • Heterogens: GDP, L8S

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:
    >6nzdA (A:)
    snaefmaccyssenedsdqdreerkllldpsspptkalngaepnyhslpsartdeqalls
    silaktasniidvsaadsqgmeqheymdrarqystrlavlssslthwkklpplpsltsqp
    hqvlasepipfsdlqqvsriaayaysalsqirvdakeelvvqfgip
    

    Sequence, based on observed residues (ATOM records):
    >6nzdA (A:)
    tdeqallssilaktasniidvsslthwkklpplpsltsqphqvlasepipfsdlqqvsri
    aayaysalsqirvdakeelvv
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6nzdB (B:)
    gamlrpkaltqvlsqantggvqstlllnnegsllaysgygdtdarvtaaiasniwaaydr
    ngnqafnednlkfilmdcmegrvaitrvanlllcmyaketvgfgmlkakaqalvqyleep
    ltqvaas
    

    Sequence, based on observed residues (ATOM records):
    >6nzdB (B:)
    amlrpkaltqvlsqantggvqstlllnnegsllaysgygdtdarvtaaiasniwaaydrn
    gnqafnednlkfilmdcmegrvaitrvanlllcmyaketvgfgmlkakaqalvqyleepl
    tqvaas
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6nzdC (C:)
    maddlkrflykklpsveglhaivvsdrdgvpvikvandnapehalrpgflstfalatdqg
    sklglsknksiicyyntyqvvqfnrlplvvsfiasssantglivslekelaplfeelrqv
    vevs
    

    Sequence, based on observed residues (ATOM records):
    >6nzdC (C:)
    addlkrflykklpsveglhaivvsdrdgvpvikvandnapehalrpgflstfalatdqgs
    klglsknksiicyyntyqvvqfnrlplvvsfiasssantglivslekelaplfeelrqvv
    e
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6nzdD (D:)
    mtsaltqgleripdqlgylvlsegavlassgdlendeqaasaiselvstacgfrlhrgmn
    vpfkrlsvvfgehtllvtvsgqrvfvvkrqnrgrepidv
    

    Sequence, based on observed residues (ATOM records):
    >6nzdD (D:)
    saltqgleripdqlgylvlsegavlassgdlendeqaasaiselvstacgfrlhrgmnvp
    fkrlsvvfgehtllvtvsgqrvfvvkrqnr
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6nzdE (E:)
    mepgaghldghragspslrqalcdgsavmfsskergrctvinfvpleaplrstprsrqvt
    eacggegravplgsepewsvggmeatleqhledtmknpsivgvlctdsqglnlgcrgtls
    dehagvisvlaqqaakltsdptdipvvclesdngnimiqkhdgitvavhkmas
    

    Sequence, based on observed residues (ATOM records):
    >6nzdE (E:)
    meatleqhledtmknpsivgvlctdsqglnlgcrgtlsdehagvisvlaqqaakltsdpt
    dipvvclesdngnimiqkhdgitvavhkmas
    

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6nzdF (F:)
    mpntamkkkvllmgksgsgktsmrsiifanyiardtrrlgatidvehshvrflgnlvlnl
    wdcggqdtfmenyftsqrdnifrnvevliyvfdvesrelekdmhyyqscleailqnspda
    kifclvhkmdlvqedqrdlifkereedlrrlsrplecacfrtsiwdetlykawssivyql
    ipnvqqlemnlrnfaqiieadevllferatflvishyqckeqrdvhrfekisniikqfkl
    scsklaasfqsmevrnsnfaafidiftsntyvmvvmsdpsipsaatlinirnarkhfekl
    ervdgpkhsllmr
    

    Sequence, based on observed residues (ATOM records):
    >6nzdF (F:)
    vllmgksgsgktsmrsiifavlnlwdvliyvfdvesrelekdmhyyqscleailqnspda
    kifclvhkmdlvqedqrdlifkereedlrrlsrplecacfrtsiwdetlykawssivyql
    ipnvqqlemnlrnfaqiieadevllferatflvishyqrfekisniikqfklscsklaas
    fqsmevrnsnfaafidiftsntyvmvvmsdpsipsaatlinirnark
    

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6nzdG (G:)
    gadsrmslqygaeetplagsygaadsfpkdfgygveeeeeeaaaagggvgagagggcgpg
    gadsskprillmglrrsgkssiqkvvfhkmspnetlflestnkiykddisnssfvnfqiw
    dfpgqmdffdptfdyemifrgtgaliyvidaqddymealtrlhitvskaykvnpdmnfev
    fihkvnglsddhkietqrdihqranddladagleklhlsfyltsiydhsifeafskvvqk
    lipqlptlenllnifisnsgiekaflfdvvskiyiatdsspvdmqsyelccdmidvvidv
    sciyglkedgsgsaydkesmaiiklnnttvlylkevtkflalvcilreesferkglidyn
    fhcfrkaihevfevgvtshrscghqtsasslkalthngtprnai
    

    Sequence, based on observed residues (ATOM records):
    >6nzdG (G:)
    prillmglrrsgkssiqkvvfhkmspnetlflestnkiykddisnssfvnfqiwdfpgqm
    dffdptfdyemifrgtgaliyvidaqddymealtrlhitvskaykvnpdmnfevfihkvn
    glsddhkietqrdihqranddladagleklhlsfyltsiydhsifeafskvvqklipqlp
    tlenllnifisnsgiekaflfdvvskiyiatdsspvdmqsyelccdmidvvidvsciygl
    aydkesmaiiklnnttvlylkevtkflalvcilreesferkglidynfhcfrkaihevf
    

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6nzdH (H:)
    maswshpqfekgggarggsgggswshpqfekgfdykddddkgtmnaivalchfcelhgpr
    tlfctevlhaplpqgdgnedspgqgeqaeeeeggiqmnsrmrahspaegasvessspgpk
    ksdmcegcrslaaghpgyishdketsikyvshqhpshpqlfsivrqacvrslscevcpgr
    egpiffgdeqhgfvfshtffikdslargfqrwysiitimmdriylinswpfllgkvrgii
    delqgkalkvfeaeqfgcpqraqrmntaftpflhqrngnaarsltsltsddnlwaclhts
    fawllkacgsrltekllegaptedtlvqmekladleeeseswdnseaeeeekapvlpest
    egreltqgpaessslsgcgswqprklpvfkslrhmrqvlgapsfrmlawhvlmgnqviwk
    srdvdlvqsafevlrtmlpvgcvriipyssqyeeayrcnflglsphvqipphvlssefav
    ivevhaaarstlhpvgceddqslskyefvvtsgspvaadrvgptilnkieaaltnqnlsv
    dvvdqclvclkeewmnkvkvlfkftkvdsrpkedtqkllsilgaseednvkllkfwmtgl
    sktykshlmstvrsptasesrn
    

    Sequence, based on observed residues (ATOM records):
    >6nzdH (H:)
    naivalchfcelhgprtlfctevikyvshqhpshpqlfsivrqacvrslscevcpgregp
    iffgdeqhgfvfshtffikdslargfqrwysiitimmdriylinswpfllgkvrgiidel
    qgkalkvfeaeqfgcpqraqrmntaftpflhqrngnaarsltsltsddnlwaclhtsfaw
    llkacgsrlpvfkslrhmrqvlgapsfrmlawhvlmgnqviwksrdvdlvqsafevlrtm
    lpvgcvriipyssqyeeayrcnflglsphvqipphvlssefavivevhaqslskyefvvt
    sgspvaadrvgptilnkieaaltnqnlsvdvvdqclvclkeewmnkvkvlfkftkrpked
    tqkllsilgaseednvkllkfwmtgls
    

  • Chain 'I':
    Sequence, based on SEQRES records:
    >6nzdI (I:)
    ggtmaptllqklfnkrgssgssaaasaqgrapkegpafswscsefdlneirlivyqdcdr
    rgrqvlfdskavqkieevtaqktedvpikisakccqgsssvsssssssisshsssggssh
    hakeqlpkyqytrpasdvnmlgemmfgsvamsykgstlkihyirsppqlmiskvfsarmg
    sfcgstnnlqdsfeyinqdpnlgklntnqnslgpcrtgsnlahstpvdmpsrgqnedrds
    giarsaslssllitpfpspssstsssssyqrrwlrsqttslengiiprrstdetfslaee
    tcssnpamvrrkkiaisiifslcekeeaqrnfqdfffshfplfeshmnrlksaiekamis
    crkiaesslrvqfyvsrlmealgefrgtiwnlysvpriaepvwltmmsgtleknqlcqrf
    lkeftllieqinknqffaalltavltyhlawvptvmpvdhppikafsekrtsqsvnmlak
    thpynplwaqlgdlygaigspvrltrtvvvgkqkdlvqrilyvltyflrcselqenqltw
    sgnhgegdqvlngskiitalekgeveeseyvvitvrnepalvppilpptaaerhnpwptg
    fpecpegtdsrdlglkpdkeanrrpeqgseacsagclgpasdaswkpqnafcgdeknkea
    pqdgssrlpscevlgagmkmdqqavcellkvemptrlpdrsvawpcpdrhlrekpslekv
    tfqigsfaspesdfesrmkkmeervkacgpsleaseaadvaqdpqvsrspfkpgfqenvc
    cpqnrlsegdegesdkgfaedrgsrndmaadiagqlshaadlgtashgaggtggrrleat
    rglyvkaaegpvlepvaprcvqrgpglvaganipcgddnkkanfrtegdiprnessdsal
    gdsddeacasamldlghggdrtggslevelplprsqsistqnvrnfgrsllagycptymp
    dlvlhgtgsdeklkqclvadlvhtvhhpvldepiaeavciiadtdkwsvqvatsqrkvtd
    nmklgqdvlvssqvssllqsilqlyklhlpadfcimhledrlqemylkskmlseylrght
    rvhvkelgvvlgiesndlplltaiasthspyvaqill
    

    Sequence, based on observed residues (ATOM records):
    >6nzdI (I:)
    lneirlivyqdcdrrgrqvlfdytrpasdvnmlgemmfgsvamsykgstlkihyirsppq
    lmiskvfsakiaisiifslcekeeaqrnfqdfffshfplfeshmnrlksaiekaqfyvsr
    lmealgefrgtiwnlysvpriaepvwltmmsgtleknqlcqrflkeftllieqinknqff
    aalltavltyhlawvptvmnplwaqlgdlygaigspvrltrtvvkqkdlvqrilyvltyf
    lrcsrnfgrsllagycptympdlvlhgtgsdeklkqclvadlvhtvhhpvldepiaeavc
    iiadtdkwsvqvatssqvssllqsilqlyklhlpadfcimhledrlqemylkskmlseyl
    rghtrvhvkelgvvndlplltaiasths