PDB entry 6wj3

View 6wj3 on RCSB PDB site
Description: cryoem structure of the slc38a9-raga-ragc-ragulator complex in the post-gap state
Deposited on 2020-04-11, released 2020-09-02
The last revision was dated 2020-11-18, with a file datestamp of 2020-11-13.
Experiment type: EM
Resolution: 3.9 Å
R-factor: N/A
AEROSPACI score: 0.11 (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-End)
      • 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: Ragulator complex protein LAMTOR5
    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: Sodium-coupled neutral amino acid transporter 9
    Species: Homo sapiens [TaxId:9606]
    Gene: SLC38A9, URLC11
    Database cross-references and differences (RAF-indexed):
  • Heterogens: GDP, U3J

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:
    >6wj3A (A:)
snaefmaccyssenedsdqdreerkllldpsspptkalngaepnyhslpsartdeqalls
silaktasniidvsaadsqgmeqheymdrarqystrlavlssslthwkklpplpsltsqp
hqvlasepipfsdlqqvsriaayaysalsqirvdakeelvvqfgip

    Sequence, based on observed residues (ATOM records):
    >6wj3A (A:)
deqallssilaktasniidvdrarqystrlavlssslthwkklpplpsltsqphqvlase
pipfsdlqqvsriaayaysalsqirvdakeelvvqf

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6wj3B (B:)
gamlrpkaltqvlsqantggvqstlllnnegsllaysgygdtdarvtaaiasniwaaydr
ngnqafnednlkfilmdcmegrvaitrvanlllcmyaketvgfgmlkakaqalvqyleep
ltqvaas

    Sequence, based on observed residues (ATOM records):
    >6wj3B (B:)
amlrpkaltqvlsqantggvqstlllnnegsllaysgygdtdarvtaaiasniwaaydrn
gnednlkfilmdcmegrvaitrvanlllcmyaketvgfgmlkakaqalvqyleepltqva

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6wj3C (C:)
maddlkrflykklpsveglhaivvsdrdgvpvikvandnapehalrpgflstfalatdqg
sklglsknksiicyyntyqvvqfnrlplvvsfiasssantglivslekelaplfeelrqv
vevs

    Sequence, based on observed residues (ATOM records):
    >6wj3C (C:)
ddlkrflykklpsveglhaivvsdrdgvpvikvandnapehalrpgflstfalatdqgsk
lglsknksiicyyntyqvvqfnrlplvvsfiasssantglivslekelaplfeelrqvv

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6wj3D (D:)
mtsaltqgleripdqlgylvlsegavlassgdlendeqaasaiselvstacgfrlhrgmn
vpfkrlsvvfgehtllvtvsgqrvfvvkrqnrgrepidv

    Sequence, based on observed residues (ATOM records):
    >6wj3D (D:)
saltqgleripdqlgylvlsegavlassgdlendeqaasaiselvstacgfrlhrgmnvp
fkrlsvvfgehtllvtvsgqrvfvvkrqnrgrep

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6wj3E (E:)
mepgaghldghragspslrqalcdgsavmfsskergrctvinfvpleaplrstprsrqvt
eacggegravplgsepewsvggmeatleqhledtmknpsivgvlctdsqglnlgcrgtls
dehagvisvlaqqaakltsdptdipvvclesdngnimiqkhdgitvavhkmas

    Sequence, based on observed residues (ATOM records):
    >6wj3E (E:)
ggmeatleqhledtmknpsivgvlctdsqglnlgcrgtlsdehagvisvlaqqaakltsd
ptdipvvclesdngnimiqkhdgitvavhkm

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6wj3F (F:)
mswshpqfekggfdidykddddkmpntamkkkvllmgksgsgktsmrsiifanyiardtr
rlgatidvehshvrflgnlvlnlwdcggqdtfmenyftsqrdnifrnvevliyvfdvesr
elekdmhyyqscleailqnspdakifclvhkmdlvqedqrdlifkereedlrrlsrplec
acfrtsiwdetlykawssivyqlipnvqqlemnlrnfaqiieadevllferatflvishy
qckeqrdvhrfekisniikqfklscsklaasfqsmevrnsnfaafidiftsntyvmvvms
dpsipsaatlinirnarkhfeklervdgpkhsllmr

    Sequence, based on observed residues (ATOM records):
    >6wj3F (F:)
mkkkvllmgksgsgktsmrsiifanyishvrflgnlvlnlwdcggqdtfmenyftsqrdn
ifrnvevliyvfdvesrelekdmhyyqscleailqnspdakifclvhkmdlvqedqrdli
fkereedlrrlsrplecacfrtsiwdetlykawssivyqlipnvqqlemnlrnfaqiiea
devllferatflvishyqckeqrdvhrfekisniikqfklscsklaasfqsmevrnsnfa
afidiftsntyvmvvmsdpsipsaatlinirnarkhfekle

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6wj3G (G:)
gadsrmslqygaeetplagsygaadsfpkdfgygveeeeeeaaaagggvgagagggcgpg
gadsskprillmglrrsgkssiqkvvfhkmspnetlflestnkiykddisnssfvnfqiw
dfpgqmdffdptfdyemifrgtgaliyvidaqddymealtrlhitvskaykvnpdmnfev
fihkvnglsddhkietqrdihqranddladagleklhlsfyltsiydhsifeafskvvqk
lipqlptlenllnifisnsgiekaflfdvvskiyiatdsspvdmqsyelccdmidvvidv
sciyglkedgsgsaydkesmaiiklnnttvlylkevtkflalvcilreesferkglidyn
fhcfrkaihevfevgvtshrscghqtsasslkalthngtprnai

    Sequence, based on observed residues (ATOM records):
    >6wj3G (G:)
prillmglrrsgkssiqkvvfhkmspnetlflestnkiykddisnssfvnfqiwdfpgqm
dffdptfdyemifrgtgaliyvidaqddymealtrlhitvskaykvnpdmnfevfihkvn
glsddhkietqrdihqranddladagleklhlsfyltsiydhsifeafskvvqklipqlp
tlenllnifisnsgiekaflfdvvskiyiatdsspvdmqsyelccdmidvvidvsciygl
kedgsgsaydkesmaiiklnnttvlylkevtkflalvcilreesferkglidynfhcfrk
aihevfev

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6wj3H (H:)
ggtmanmnsdsrhlgtsevdherdpgpmniqfepsdlrskrpfcieptnivnvnhviqrv
sdhasamnkrihyysrlttpadkaliapdhvvpapeecyvysplgsayklqsytegygkn
ts

    Sequence, based on observed residues (ATOM records):
    >6wj3H (H:)
pfcieptnivnvnhviqrvsdhasamnkrihyysrlttpadkaliapdhvvpapeecyv