8OZB: Nup35-Nb complex

Crystal structure of Nup35-Nb complex. Determined by X-ray diffraction at 2.09 Å resolution. Released 28 Feb 2024.

Method: X-ray diffraction
Resolution: 2.09 Å
Organisms: Lama glama, Homo sapiens
Chains: 4
Atoms: 3,045
Mol. weight: 42.43 kDa
Released: 28 Feb 2024

Explore 8OZB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OZB contains 10 α-helices and 34 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-11	2	2
β-strand	18-24	7	1
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-100	10	2
β-strand	105-110	6	2
β-strand	114-117	4	2

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	10-12	3	4
β-strand	18-24	7	3
β-strand	33-39	7	4
β-strand	46-51	6	4
β-strand	57-59	3	4
α-helix	61-63	3
β-strand	67-72	6	3
β-strand	77-82	6	3
α-helix	87-89	3
β-strand	91-100	10	4
β-strand	105-110	6	4
β-strand	114-118	5	4

Chains E and F: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	175-179	5	4
α-helix	183-185	3
α-helix	186-194	9
β-strand	201-204	4	4
β-strand	210-214	5	4
α-helix	218-225	8
β-strand	230-232	3	5
β-strand	236-238	3	5
β-strand	239-242	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nup35 nanobody	A	protein	116	Lama glama
Nup35 nanobody	C	protein	117	Lama glama
Nucleoporin NUP35	E, F	protein	76	Homo sapiens	Q8NFH5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8OZB_1 Nup35 nanobody (chains A)
QLVESGGGLVQAGGSLRLSCVGTGNISSAYTMAWYRQAAGKEREVVAGILNGGSTHYADS
VKGRFTISRDNAKNTVYLQMNSLQPEDTGVYCCHVVIESTRFVYDHYWGQGTRVTV

Sequence of entity 2 (C), FASTA

>8OZB_2 Nup35 nanobody (chains C)
QLVESGGGLVQAGGSLRLSCVGTGNISSAYTMAWYRQAAGKEREVVAGILNGGSTHYADS
VKGRFTISRDNAKNTVYLQMNSLQPEDTGVYCCHVVIESTRFVYDHYWGQGTRVTVS

Sequence of entity 3 (E, F), FASTA

>8OZB_3 Nucleoporin NUP35 (chains E, F)
DSWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIF
GESIMIGVKPCIDKSV

Primary citation

A checkpoint function for Nup98 in nuclear pore formation suggested by novel inhibitory nanobodies. Sola Colom, M., Fu, Z., Gunkel, P. et al. EMBO J (2024) 43:2198-2232. DOI 10.1038/s44318-024-00081-w · PubMed

Other PDB entries of the same protein (UniProt Q8NFH5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LIR 2.46 Å, Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapiens at 2.46 A resolution
7MW1 3.4 Å, Crystal structure of the Homo sapiens NUP93-NUP53 complex (NUP93 residues 174-819; NUP53…
7R5K 12.0 Å, Human nuclear pore complex (constricted)
7R5J 50.0 Å, Human nuclear pore complex (dilated)

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