6B4E: Nucleoporin GLE1

Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex. Determined by X-ray diffraction at 1.75 Å resolution. Released 20 Jun 2018.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 7,314
Mol. weight: 77.03 kDa
Ligands: PRO
Released: 20 Jun 2018

Explore 6B4E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B4E contains 57 α-helices and 8 β-strands across 4 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: 27 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	246-263	18
α-helix	264-268	5
α-helix	269-271	3
α-helix	276-289	14
α-helix	290-295	6
β-strand	299	1	3
α-helix	300-315	16
α-helix	321-338	18
α-helix	339-343	5
α-helix	344-345	2
α-helix	347-349	3
α-helix	350-363	14
α-helix	367-378	12
α-helix	380-383	4
α-helix	392-397	6
β-strand	402	1	4
α-helix	407	1
β-strand	408	1	4
α-helix	409-410	2
α-helix	411-430	20
α-helix	431-434	4
α-helix	435-438	4
α-helix	448-458	11
α-helix	462-464	3
α-helix	467-497	31
α-helix	498-503	6
α-helix	504-506	3
α-helix	508-510	3
α-helix	513-526	14
α-helix	533-536	4
β-strand	537	1	3

Chain B: 23 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	246-263	18
α-helix	264-268	5
α-helix	269-272	4
α-helix	276-293	18
β-strand	299	1	1
α-helix	300-315	16
α-helix	321-340	20
α-helix	342-345	4
α-helix	347-349	3
α-helix	350-363	14
α-helix	367-378	12
α-helix	380-383	4
α-helix	392-397	6
β-strand	402	1	2
β-strand	408	1	2
α-helix	409-410	2
α-helix	411-430	20
α-helix	432-434	3
α-helix	448-458	11
α-helix	462-464	3
α-helix	467-497	31
α-helix	498-503	6
α-helix	504-506	3
α-helix	508-510	3
α-helix	513-526	14
α-helix	533-536	4
β-strand	537	1	1

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	397-400	4
α-helix	403-410	8
α-helix	423-425	3
α-helix	426-428	3

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	403-410	8
α-helix	423-425	3
α-helix	426-428	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoporin GLE1	A, B	protein	296	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12315 (AlphaFold model)
Nucleoporin NUP42	C, D	protein	39	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P49686 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6B4E_1 Nucleoporin GLE1 (chains A, B)
MTNFDKISKMFWHYKDKIAQIKQDIVLPIKKADVNVRNLLSRHKRKINPKFGQLTNSNQQ
LFKIQNELTQLINDTKGDSLAYHWILNFIAKAVVHQAETEVRVKPESALPLGKLTLYLLV
QFPELQELFMARLVKKCPFVIGFTCEIDTEKGRQNMGWKRNNENKWEDNTSYDERMGGIL
SLFAIITRLQLPQEFITTTSHPFPIALSWHILARICNTPLNLITNTHFVILGSWWDAAAV
QFLQAYGNQASKLLILIGEELTSRMAEKKYVGAARLRILLEAWQNNNMESFPEMSP

Sequence of entity 2 (C, D), FASTA

>6B4E_2 Nucleoporin NUP42 (chains C, D)
GPSGSELADLAEETLKIFRANKFELGLVPDIPPPPALVA

Ligands and cofactors

ID	Name	Formula	Copies
PRO	Proline	C5 H9 N O2	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Lin, D.H., Correia, A.R., Cai, S.W. et al. Nat Commun (2018) 9:2319-2319. DOI 10.1038/s41467-018-04459-3 · PubMed

Other PDB entries of the same protein (UniProt Q12315 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PEV 2.5 Å, S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6
3PEU 2.6 Å, S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6
3RRM 2.9 Å, S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp
3RRN 4.0 Å, S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6
8ZZA Integrative structure and functional anatomy of a single spoke of a nuclear pore complex
8ZZB Integrative structure and functional anatomy of three spokes of a nuclear pore complex
8ZZC Integrative structure and functional anatomy of eight spokes of a nuclear pore complex

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