6GX9: TNPO3 - CPSF6 RSLD complex

Crystal structure of the TNPO3 - CPSF6 RSLD complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 13 Mar 2019.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,667
Mol. weight: 227.92 kDa
Ligands: MG, BCN, BEN
Released: 13 Mar 2019

Explore 6GX9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GX9 contains 127 α-helices and 0 β-strands across 2 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, 0 β-strands

Element	Residues	Length
α-helix	8-20	13
α-helix	24-38	15
α-helix	43-53	11
α-helix	57-73	17
α-helix	75-77	3
α-helix	80-82	3
α-helix	83-96	14
α-helix	102-117	16
α-helix	125-133	9
α-helix	140-154	15
α-helix	163-175	13
α-helix	177-189	13
α-helix	195-210	16
α-helix	216-220	5
α-helix	223-231	9
α-helix	239-254	16
α-helix	263-274	12
α-helix	277-285	9
α-helix	289-305	17
α-helix	307-312	6
α-helix	317-319	3
α-helix	322-331	10
α-helix	336-339	4
α-helix	340-342	3
α-helix	343-355	13
α-helix	359-379	21
α-helix	381-383	3
α-helix	390-391	2
α-helix	395-410	16
α-helix	411-413	3
α-helix	416-428	13
α-helix	434-447	14
α-helix	448-450	3
α-helix	456-467	12
α-helix	475-487	13
α-helix	489-494	6
α-helix	496-498	3
α-helix	499-510	12
α-helix	516-529	14
α-helix	532-534	3
α-helix	538-546	9
α-helix	555-570	16
α-helix	574-594	21
α-helix	609-620	12
α-helix	630-632	3
α-helix	633-651	19
α-helix	656-673	18
α-helix	678-680	3
α-helix	681-694	14
α-helix	699-711	13
α-helix	715-717	3
α-helix	718-736	19
α-helix	741-744	4
α-helix	746-762	17
α-helix	764-768	5
α-helix	773-783	11
α-helix	789-804	16
α-helix	815-839	25
α-helix	840-844	5
α-helix	847-849	3
α-helix	850-863	14
α-helix	865-877	13
α-helix	892-903	12
α-helix	908-920	13

Chain B: 63 helices, 0 β-strands

Element	Residues	Length
α-helix	8-20	13
α-helix	24-38	15
α-helix	43-53	11
α-helix	57-73	17
α-helix	75-77	3
α-helix	80-82	3
α-helix	83-96	14
α-helix	102-117	16
α-helix	125-133	9
α-helix	140-154	15
α-helix	163-175	13
α-helix	177-189	13
α-helix	195-211	17
α-helix	216-220	5
α-helix	223-231	9
α-helix	239-254	16
α-helix	263-274	12
α-helix	277-285	9
α-helix	289-305	17
α-helix	307-312	6
α-helix	317-319	3
α-helix	322-331	10
α-helix	336-339	4
α-helix	340-342	3
α-helix	343-355	13
α-helix	359-379	21
α-helix	381-383	3
α-helix	390-391	2
α-helix	395-410	16
α-helix	411-413	3
α-helix	416-428	13
α-helix	434-447	14
α-helix	448-450	3
α-helix	456-467	12
α-helix	475-487	13
α-helix	489-494	6
α-helix	496-498	3
α-helix	499-510	12
α-helix	516-529	14
α-helix	532-534	3
α-helix	538-546	9
α-helix	555-570	16
α-helix	574-594	21
α-helix	609-620	12
α-helix	630-632	3
α-helix	633-651	19
α-helix	656-673	18
α-helix	678-680	3
α-helix	681-694	14
α-helix	699-711	13
α-helix	715-736	22
α-helix	741-744	4
α-helix	746-762	17
α-helix	764-768	5
α-helix	773-783	11
α-helix	789-804	16
α-helix	815-839	25
α-helix	840-844	5
α-helix	847-849	3
α-helix	850-863	14
α-helix	865-877	13
α-helix	892-903	12
α-helix	908-920	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transportin-3	A, B	protein	923	Homo sapiens	Q9Y5L0 (AlphaFold model)
Cleavage and polyadenylation specificity factor subunit 6	C, D	protein	70	Homo sapiens	Q16630 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6GX9_1 Transportin-3 (chains A, B)
MEGAKPTLQLVYQAVQALYHDPDPSGKERASFWLGELQRSVHAWEISDQLLQIRQDVESC
YFAAQTMKMKIQTSFYELPTDSHASLRDSLLTHIQNLKDLSPVIVTQLALAIADLALQMP
SWKGCVQTLVEKYSNDVTSLPFLLEILTVLPEEVHSRSLRIGANRRTEIIEDLAFYSSTV
VSLLMTCVEKAGTDEKMLMKVFRCLGSWFNLGVLDSNFMANNKLLALLFEVLQQDKTSSN
LHEAASDCVCSALYAIENVETNLPLAMQLFQGVLTLETAYHMAVAREDLDKVLNYCRIFT
ELCETFLEKIVCTPGQGLGDLRTLELLLICAGHPQYEVVEISFNFWYRLGEHLYKTNDEV
IHGIFKAYIQRLLHALARHCQLEPDHEGVPEETDDFGEFRMRVSDLVKDLIFLIGSMECF
AQLYSTLKEGNPPWEVTEAVLFIMAAIAKSVDPENNPTLVEVLEGVVRLPETVHTAVRYT
SIELVGEMSEVVDRNPQFLDPVLGYLMKGLCEKPLASAAAKAIHNICSVCRDHMAQHFNG
LLEIARSLDSFLLSPEAAVGLLKGTALVLARLPLDKITECLSELCSVQVMALKKLLSQEP
SNGISSDPTVFLDRLAVIFRHTNPIVENGQTHPCQKVIQEIWPVLSETLNKHRADNRIVE
RCCRCLRFAVRCVGKGSAALLQPLVTQMVNVYHVHQHSCFLYLGSILVDEYGMEEGCRQG
LLDMLQALCIPTFQLLEQQNGLQNHPDTVDDLFRLATRFIQRSPVTLLRSQVVIPILQWA
IASTTLDHRDANCSVMRFLRDLIHTGVANDHEEDFELRKELIGQVMNQLGQQLVSQLLHT
CCFCLPPYTLPDVAEVLWEIMQVDRPTFCRWLENSLKGLPKETTVGAVTVTHKQLTDFHK
QVTSAEECKQVCWALRDFTRLFR

Sequence of entity 2 (C, D), FASTA

>6GX9_2 Cleavage and polyadenylation specificity factor subunit 6 (chains C, D)
ESKSYGSGSRRERSRERDHSRSREKSRRHKSRSRDRHDDYYRERSRERERHRDRDRDRDR
ERDREREYRH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
BCN	Bicine	C6 H13 N O4	2
BEN	Benzamidine	C7 H8 N2	2

Primary citation

Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6. Jang, S., Cook, N.J., Pye, V.E. et al. Nucleic Acids Res (2019) 47:4663-4683. DOI 10.1093/nar/gkz206 · PubMed

Other PDB entries of the same protein (UniProt Q9Y5L0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4C0O 2.56 Å, Transportin 3 in complex with phosphorylated ASF/SF2
4OL0 2.9 Å, Crystal structure of transportin-SR2, a karyopherin involved in human disease, in…
8CMK 2.94 Å, Transportin-3 TNPO3 in complex with RSY region of CIRBP
4C0P 2.95 Å, Unliganded Transportin 3
4C0Q 3.42 Å, Transportin 3 in complex with Ran(Q69L)GTP

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