3A6P: Exportin-5:RanGTP:pre-miRNA complex

Crystal structure of Exportin-5:RanGTP:pre-miRNA complex. Determined by X-ray diffraction at 2.92 Å resolution. Released 8 Dec 2009.

Method
X-ray diffraction
Resolution
2.92 Å
Organisms
Homo sapiens, Canis lupus familiaris
Chains
10
Atoms
22,052
Mol. weight
355.86 kDa
Ligands
MG, GTP
Released
8 Dec 2009

Explore 3A6P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3A6P contains 155 α-helices and 20 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-helix6-2116
α-helix27-4317
α-helix47-548
α-helix61-7717
α-helix79-813
α-helix84-10017
α-helix110-12718
α-helix135-14410
α-helix147-16115
α-helix162-1665
α-helix172-18413
α-helix186-20722
α-helix214-23219
α-helix240-2445
α-helix249-2568
α-helix257-2593
α-helix264-27512
α-helix281-2844
α-helix285-2917
α-helix293-30412
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-helix570-58213
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-helix713-73422
α-helix741-7466
β-strand750-75341
β-strand759-76131
α-helix766-78520
α-helix789-7924
α-helix797-7993
α-helix805-8062
α-helix807-8137
α-helix832-85827
α-helix868-8758
α-helix885-8917
α-helix892-8965
α-helix897-9015
α-helix905-9073
α-helix908-9125
α-helix913-93523
α-helix953-97725
β-strand97812
β-strand101112
α-helix1013-10197
α-helix1022-103514
α-helix1041-10477
α-helix1048-10525
α-helix1053-10564
α-helix1066-108217
α-helix1087-110317
α-helix1111-11155
α-helix1123-113210
Chains B and G: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix1307-13159
Chain C: 8 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand11-1773
α-helix23-319
α-helix40-423
β-strand45-54103
β-strand57-66103
α-helix70-723
α-helix76-805
β-strand85-9173
α-helix95-995
α-helix101-11111
β-strand117-12263
α-helix138-1414
β-strand145-14843
α-helix159-16810
Chain F: 72 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix6-2116
α-helix27-4216
α-helix47-548
α-helix61-7313
α-helix74-785
α-helix84-9613
α-helix97-1015
α-helix110-12718
α-helix135-14410
α-helix147-16115
α-helix162-1665
α-helix172-18413
α-helix186-20722
α-helix214-23219
α-helix240-2423
α-helix249-2568
α-helix257-2593
α-helix264-27512
α-helix281-2833
α-helix285-2917
α-helix293-30412
α-helix313-33725
α-helix344-3463
α-helix349-36012
α-helix365-37915
α-helix388-3914
α-helix394-40512
α-helix418-4258
α-helix429-45325
α-helix455-46915
α-helix498-52023
α-helix528-53912
α-helix546-55914
α-helix560-5645
α-helix567-5693
α-helix570-58213
α-helix595-61420
α-helix616-6194
α-helix623-63513
α-helix642-65615
α-helix657-6593
α-helix662-67211
α-helix674-6807
α-helix683-6908
α-helix692-6998
α-helix713-73422
α-helix741-7477
β-strand750-75344
β-strand759-76134
α-helix766-78520
α-helix791-7933
α-helix797-7993
α-helix807-8148
α-helix829-8313
α-helix832-85827
α-helix860-8634
α-helix868-8736
α-helix880-8823
α-helix885-8917
α-helix892-8965
α-helix897-9015
α-helix905-9073
α-helix908-9125
α-helix913-93523
α-helix953-97725
β-strand97815
β-strand101115
α-helix1013-10197
α-helix1022-103716
α-helix1041-10477
α-helix1048-10525
α-helix1053-10564
α-helix1066-108217
α-helix1087-110317
α-helix1111-11155
α-helix1123-113311
Chain H: 6 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand11-1776
α-helix23-3210
β-strand45-54106
β-strand57-66106
α-helix76-794
β-strand85-9176
α-helix95-995
α-helix101-11111
β-strand117-12266
α-helix138-1414
β-strand145-14846
α-helix159-16911

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Exportin-5A, Fprotein1204Homo sapiensQ9HAV4 (AlphaFold model)
13-mer peptideB, Gprotein13Homo sapiens
GTP-binding nuclear protein RanC, Hprotein216Canis lupus familiarisP62825 (AlphaFold model)
pre-microRNAD, IRNA24
pre-microRNAE, JRNA24
Sequence of entity 1 (A, F), FASTA
>3A6P_1 Exportin-5 (chains A, F)
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 (B, G), FASTA
>3A6P_2 13-mer peptide (chains B, G)
XXXXXXXXXXXXX
Sequence of entity 3 (C, H), FASTA
>3A6P_3 GTP-binding nuclear protein Ran (chains C, H)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL
Sequence of entity 4 (D, I), FASTA
>3A6P_4 pre-microRNA (chains D, I)
GGUAAACAUCCUCGACUGGAAGCU
Sequence of entity 5 (E, J), FASTA
>3A6P_5 pre-microRNA (chains E, J)
GGCUUUCAGUCGGAUGUUUGCCGC

Ligands and cofactors

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

Primary citation

A high-resolution structure of the pre-microRNA nuclear export machinery. Okada, C., Yamashita, E., Lee, S.J. et al. Science (2009) 326:1275-1279. DOI 10.1126/science.1178705 · 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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