6Q84: RanGTP-Pdr6-eIF5A export complex

Crystal structure of RanGTP-Pdr6-eIF5A export complex. Determined by X-ray diffraction at 3.7 Å resolution. Released 1 May 2019.

Method
X-ray diffraction
Resolution
3.7 Å
Organisms
Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains
6
Atoms
21,207
Mol. weight
319.52 kDa
Ligands
GTP, MG
Released
1 May 2019

Explore 6Q84 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q84 contains 151 α-helices and 42 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 64 helices, 4 β-strands

ElementResiduesLengthSheet
α-helix4-1411
α-helix23-3311
α-helix39-4810
α-helix54-6512
α-helix80-10324
α-helix108-12518
α-helix145-1517
α-helix166-1727
α-helix177-1837
α-helix187-21024
α-helix217-2204
α-helix221-2255
α-helix226-23813
α-helix246-26116
α-helix273-28513
α-helix294-30916
α-helix311-3133
α-helix316-32611
α-helix345-35511
α-helix359-37315
α-helix374-3763
α-helix377-3859
β-strand38611
α-helix396-41318
β-strand41812
β-strand42212
α-helix424-44017
β-strand44711
α-helix451-46919
α-helix472-48110
α-helix486-51025
α-helix511-5155
α-helix516-5238
α-helix538-55619
α-helix565-5717
α-helix576-58813
α-helix595-61420
α-helix616-6216
α-helix623-6253
α-helix627-63913
α-helix650-67122
α-helix680-69011
α-helix699-71416
α-helix721-74323
α-helix750-76920
α-helix772-7732
α-helix787-7959
α-helix800-81213
α-helix815-8184
α-helix821-83111
α-helix837-8382
α-helix849-85911
α-helix865-88218
α-helix889-8957
α-helix896-9016
α-helix904-9085
α-helix912-92817
α-helix930-9345
α-helix939-9435
α-helix944-9496
α-helix956-97116
α-helix977-98913
α-helix991-100414
α-helix1010-102314
α-helix1025-103814
α-helix1045-10473
α-helix1048-10558
α-helix1064-107512
Chains B and E: 9 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand9-1793
α-helix23-319
α-helix34-363
α-helix41-433
β-strand46-5493
β-strand57-6593
α-helix78-803
β-strand85-9173
α-helix95-995
α-helix101-11111
β-strand117-12263
α-helix133-1353
α-helix138-1403
β-strand144-14853
β-strand15014
β-strand15514
α-helix159-16911
Chain C: 3 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand18-2255
α-helix23-253
β-strand31-3446
β-strand37-48126
β-strand55-6396
β-strand69-7576
β-strand79-8355
β-strand86-96117
β-strand99-10357
β-strand109-11467
α-helix115-1162
α-helix118-13013
β-strand135-14067
β-strand145-15177
Chain D: 63 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix4-1411
α-helix23-3311
α-helix39-4810
α-helix54-6512
α-helix80-9920
α-helix108-12518
α-helix145-1517
α-helix166-1727
α-helix177-1837
α-helix187-21024
α-helix217-2204
α-helix221-2255
α-helix226-23813
α-helix246-25813
α-helix273-28513
α-helix294-30916
α-helix311-3133
α-helix316-32611
α-helix345-35511
α-helix359-37315
α-helix374-3763
α-helix377-3859
α-helix396-41318
α-helix424-44017
α-helix451-46919
α-helix472-48110
α-helix486-51025
α-helix511-5155
α-helix516-5238
α-helix538-55619
α-helix565-5717
α-helix576-58813
α-helix595-61420
α-helix616-6216
α-helix623-6253
α-helix627-63913
α-helix651-67121
α-helix680-69011
α-helix699-71416
α-helix721-74323
α-helix750-76920
α-helix772-7732
α-helix786-79510
α-helix800-81213
α-helix815-8184
α-helix821-83111
α-helix837-8382
α-helix849-85911
α-helix865-88218
α-helix889-8957
α-helix896-9016
α-helix904-9085
α-helix912-92817
α-helix930-9345
α-helix939-9435
α-helix944-9496
α-helix956-97116
α-helix977-98913
α-helix991-100414
α-helix1010-102314
α-helix1025-103814
α-helix1048-10558
α-helix1064-107512
Chain F: 3 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand19-22410
α-helix23-253
β-strand31-34411
β-strand37-45911
β-strand58-63611
β-strand69-73511
β-strand79-82410
β-strand86-961112
β-strand99-103512
β-strand109-114612
α-helix115-1162
α-helix118-13013
β-strand134-140712
β-strand145-152812

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Importin beta-like protein KAP122A, Dprotein1080Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P32767 (AlphaFold model)
GTP-binding nuclear protein RanB, Eprotein176Homo sapiensP62826 (AlphaFold model)
Eukaryotic translation initiation factor 5A-1C, Fprotein142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P23301 (AlphaFold model)
Sequence of entity 1 (A, D), FASTA
>6Q84_1 Importin beta-like protein KAP122 (chains A, D)
SSIHEVVALIEELYSPHPKHDVNQIQQSLQSIQKSEQGFHLANELLSDDKYSANVKYFGA
LTLTVQLNTRGENDYETLWNVFRSNLLYLTKFSTLYVSNPNMYGQSLIIIKKLMSNLSLI
FTKINDPQLNNAGNENMIKQWNNPINTFIQLMSVQNQNINADQLLLDSINCSLTYEQLSQ
FVSLSQKHNELALTFTEVIVEDLTKFQTKRHSMSQIHEVVHEHLYISTMALINLNLTAQA
VFNPTVFDCITAWINYISLTRSVSSSGRMDLSEIFQNLIDLMYQSTEGSDGYENAEKILT
IFGNVFANDPLLMSYDLRQQIECIFLGVVRPDSGITDISNKNSWMLQYMNYLVTNDFFSE
LKELAICIVDFLQINTLSVCNKLFTNIQAADNGQVQDEYIQEYIKVLLQMTNFPLTPVLQ
EFFSVRMVDFWLDLSDAYTNLASETLRPNSIELSTQIFQQLINIYLPKISLSVKQRIIEE
EGESTSVNEFEDFRNAVSDLAQSLWSILGNDNLTNVLIDGMGQMPAASDETLIIKDTDVL
FRIETMCFVLNTILVDMTLSESPWIKNIVDANKFFNQNVISVFQTGFQTSASTKVSQILK
LDFVRTSTTLIGTLAGYFKQEPFQLNPYVEALFQGLHTCTNFTSKNEQEKISNDKLEVMV
IKTVSTLCETCREELTPYLMHFISFLNTVIMPDSNVSHFTRTKLVRSIGYVVQCQVSNGP
EEQAKYILQLTNLLSGSIEHCLASSVQLQEQQDYINCLLYCISELATSLIQPTEIIENDA
LLQRLSEFQSFWSSDPLQIRSKIMCTIDKVLDNSIYCKNSAFVEIGCLIVGKGLNLPDGE
PYFLKYNMSEVMNFVLRHVPNCELATCLPYFVYLLEKLISEFRKELTPQEFDFMFEKILL
VYYDAYIINDPDLLQMTIGFVNNVLDVKPGLAIGSKHWTSFILPQFLKLIPSREKFTIVA
VAKFWTKLINNKKYNQEELTTVRQQVSSIGGDLVYQIMYGLFHTQRSDLNSYTDLLRALV
AKFPIEAREWLVAVLPQICNNPAGHEKFINKLLITRGSRAAGNVILQWWLDCTTLPNYQG
Sequence of entity 2 (B, E), FASTA
>6Q84_2 GTP-binding nuclear protein Ran (chains B, E)
GEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVW
DTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKV
DIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
Sequence of entity 3 (C, F), FASTA
>6Q84_3 Eukaryotic translation initiation factor 5A-1 (chains C, F)
SATYPMQCSALRKNGFVVIKSRPCKIVDMSTSKTGKHGHAKVHLVAIDIFTGKKLEDLSP
STHNMEVPVVKRNEYQLLDIDDGFLSLMNMDGDTKDDVKAPEGELGDSLQTAFDEGKDLM
VTIISAMGEEAAISFKEAARTD

Ligands and cofactors

IDNameFormulaCopies
GTPGuanosine-5'-triphosphateC10 H16 N5 O14 P32
MGMagnesium ionMg2

Primary citation

Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122. Aksu, M., Trakhanov, S., Vera Rodriguez, A. et al. J Cell Biol (2019) 218:1839-1852. DOI 10.1083/jcb.201812093 · PubMed

Other PDB entries of the same protein (UniProt P32767 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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