5YU6: Exportin-5:RANGTP complex

Crystal structure of exportin-5:RANGTP complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 29 Aug 2018.

Method
X-ray diffraction
Resolution
3.0 Å
Organisms
Homo sapiens, unidentified, Canis lupus familiaris
Chains
6
Atoms
20,096
Mol. weight
325.17 kDa
Ligands
MG, GTP
Released
29 Aug 2018

Explore 5YU6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YU6 contains 150 α-helices and 22 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: 67 helices, 4 β-strands

ElementResiduesLengthSheet
α-helix6-2015
α-helix27-4317
α-helix47-548
α-helix61-7717
α-helix84-10017
α-helix110-12718
α-helix135-1439
α-helix147-16115
α-helix162-1665
α-helix172-18413
α-helix186-20621
α-helix214-23118
α-helix240-2434
α-helix245-25612
α-helix257-2593
α-helix261-27515
α-helix281-2844
α-helix285-2917
α-helix293-30311
α-helix313-33826
α-helix349-36012
α-helix365-37915
α-helix388-40518
α-helix418-4258
α-helix429-45325
α-helix455-47016
α-helix498-52023
α-helix528-54013
α-helix546-55914
α-helix560-5645
α-helix567-5693
α-helix570-58112
α-helix592-5943
α-helix595-61420
α-helix616-6194
α-helix620-6223
α-helix623-63513
α-helix642-65615
α-helix657-6593
α-helix662-68019
α-helix683-6908
α-helix692-6998
α-helix712-73423
α-helix741-7466
β-strand750-75341
β-strand759-76131
α-helix766-78621
α-helix789-7924
α-helix807-8137
α-helix832-85726
α-helix859-8635
α-helix868-8758
α-helix885-8917
α-helix892-8965
α-helix897-9026
α-helix905-9073
α-helix908-9125
α-helix913-93624
α-helix953-97725
β-strand97812
β-strand101112
α-helix1013-10197
α-helix1022-103413
α-helix1035-10373
α-helix1041-10477
α-helix1048-10525
α-helix1053-10586
α-helix1068-108215
α-helix1087-110418
α-helix1110-11167
α-helix1123-113412
Chain B: 6 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand9-1793
α-helix23-3210
β-strand45-54103
β-strand57-66103
α-helix77-804
β-strand85-9173
α-helix95-11117
β-strand117-12263
α-helix133-1353
α-helix138-1414
β-strand145-14843
β-strand15014
β-strand15514
α-helix159-16911
Chain C: 69 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix6-2015
α-helix28-4114
α-helix47-548
α-helix61-7717
α-helix84-10017
α-helix110-13122
α-helix135-14511
α-helix147-16115
α-helix162-1665
α-helix172-18413
α-helix186-20621
α-helix214-23421
α-helix240-2434
α-helix245-25713
α-helix264-27512
α-helix281-2844
α-helix285-2917
α-helix293-30715
α-helix313-33927
α-helix349-36113
α-helix365-37915
α-helix388-40518
α-helix418-4258
α-helix429-45325
α-helix455-47117
α-helix498-52023
α-helix528-54013
α-helix546-55914
α-helix560-5645
α-helix567-5693
α-helix570-58112
α-helix592-5943
α-helix595-61420
α-helix616-6194
α-helix620-6223
α-helix623-63513
α-helix642-65615
α-helix657-6593
α-helix662-68019
α-helix683-6886
α-helix692-6998
α-helix713-73422
α-helix741-7466
β-strand750-75345
β-strand759-76135
α-helix766-78520
α-helix789-7924
α-helix800-8034
α-helix805-8062
α-helix807-8148
α-helix832-85726
α-helix860-8634
α-helix868-8758
α-helix880-8823
α-helix889-8913
α-helix892-8965
α-helix897-9015
α-helix905-9073
α-helix908-9125
α-helix913-93422
α-helix953-97725
β-strand97816
β-strand101116
α-helix1013-10197
α-helix1023-103412
α-helix1035-10373
α-helix1042-10476
α-helix1048-10525
α-helix1053-10586
α-helix1066-108217
α-helix1087-110418
α-helix1111-11155
α-helix1123-113412
Chain D: 6 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand9-1687
α-helix23-319
β-strand45-54107
β-strand57-66107
α-helix77-804
β-strand85-9177
α-helix95-11117
β-strand117-12267
α-helix133-1353
α-helix138-1414
β-strand145-14847
α-helix159-16911
Chains E and F: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix1306-131510

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Exportin-5A, Cprotein1204Homo sapiensQ9HAV4 (AlphaFold model)
13-mer peptideE, Fprotein13unidentified
GTP-binding nuclear protein RanB, Dprotein216Canis lupus familiarisP62825 (AlphaFold model)
Sequence of entity 1 (A, C), FASTA
>5YU6_1 Exportin-5 (chains A, C)
MAMDQVNALCEQLVKAVTVMMDPNSTQRYRLEALKFCEEFKEKCPICVPCGLRLAEKTQV
AIVRHFGLQILEHVVKFRWNGMSRLEKVYLKNSVMELIANGTLNILEEENHIKDALSRIV
VEMIKREWPQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTFQTLPPQRRRDIQQ
TLTQNMERIFSFLLNTLQENVNKYQQVKTDTSQESKAQANCRVGVAALNTLAGYIDWVSM
SHITAENCKLLEILCLLLNEQELQLGAAECLLIAVSRKGKLEDRKPLMVLFGDVAMHYIL
SAAQTADGGGLVEKHYVFLKRLCQVLCALGNQLCALLGADSDVETPSNFGKYLESFLAFT
THPSQFLRSSTQMTWGALFRHEILSRDPLLLAIIPKYLRASMTNLVKMGFPSKTDSPSCE
YSRFDFDSDEDFNAFFNSSRAQQGEVMRLACRLDPKTSFQMAGEWLKYQLSTFLDAGSVN
SCSAVGTGEGSLCSVFSPSFVQWEAMTLFLESVITQMFRTLNREEIPVNDGIELLQMVLN
FDTKDPLILSCVLTNVSALFPFVTYRPEFLPQVFSKLFSSVTFETVEESKAPRTRAVRNV
RRHACSSIIKMCRDYPQLVLPNFDMLYNHVKQLLSNELLLTQMEKCALMEALVLISNQFK
NYERQKVFLEELMAPVASIWLSQDMHRVLSDVDAFIAYVGTDQKSCDPGLEDPCGLNRAR
MSFCVYSILGVVKRTCWPTDLEEAKAGGFVVGYTSSGNPIFRNPCTEQILKLLDNLLALI
RTHNTLYAPEMLAKMAEPFTKALDMLDAEKSAILGLPQPLLELNDSPVFKTVLERMQRFF
STLYENCFHILGKAGPSMQQDFYTVEDLATQLLSSAFVNLNNIPDYRLRPMLRVFVKPLV
LFCPPEHYEALVSPILGPLFTYLHMRLSQKWQVINQRSLLCGEDEAADENPESQEMLEEQ
LVRMLTREVMDLITVCCVSKKGADHSSAPPADGDDEEMMATEVTPSAMAELTDLGKCLMK
HEDVCTALLITAFNSLAWKDTLSCQRTTSQLCWPLLKQVLSGTLLADAVTWLFTSVLKGL
QMHGQHDGCMASLVHLAFQIYEALRPRYLEIRAVMEQIPEIQKDSLDQFDCKLLNPSLQK
VADKRRKDQFKRLIAGCIGKPLGEQFRKEVHIKNLPSLFKKTKPMLETEVLDNDGGGLAT
IFEP
Sequence of entity 2 (E, F), FASTA
>5YU6_2 13-mer peptide (chains E, F)
XXXXXXXXXXXXX
Sequence of entity 3 (B, D), FASTA
>5YU6_3 GTP-binding nuclear protein Ran (chains B, D)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Ligands and cofactors

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

Primary citation

Structural Basis for Selective Binding of Export Cargoes by Exportin-5. Yamazawa, R., Jiko, C., Choi, S. et al. Structure (2018) 26:1393-1398.e2. DOI 10.1016/j.str.2018.06.014 · PubMed

Other PDB entries of the same protein (UniProt Q9HAV4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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