6X07: Nic96 from S. cerevisiae bound by VHH-SAN12

Nic96 from S. cerevisiae bound by VHH-SAN12. Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Vicugna pacos
Chains: 2
Atoms: 5,802
Mol. weight: 91 kDa
Released: 9 Dec 2020

Explore 6X07 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X07 contains 47 α-helices and 17 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: 43 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	202-204	3
α-helix	206-228	23
α-helix	234-244	11
α-helix	248-263	16
α-helix	270-289	20
α-helix	301-312	12
β-strand	314	1	1
β-strand	320	1	1
β-strand	327-328	2	2
β-strand	331-332	2	2
α-helix	333-342	10
α-helix	346-355	10
α-helix	357-359	3
α-helix	365-375	11
α-helix	384-393	10
α-helix	394-398	5
α-helix	406-416	11
α-helix	426-428	3
α-helix	432-442	11
α-helix	446-448	3
α-helix	459-469	11
α-helix	471-473	3
α-helix	478-484	7
α-helix	488-496	9
α-helix	500-512	13
α-helix	534-541	8
α-helix	542-545	4
α-helix	550-557	8
α-helix	558-562	5
α-helix	568-583	16
α-helix	586-590	5
β-strand	591-593	3	3
α-helix	598	1
β-strand	599-601	3	3
α-helix	603-606	4
α-helix	608-611	4
α-helix	618-634	17
α-helix	637-646	10
α-helix	650-667	18
α-helix	685-696	12
α-helix	700-703	4
α-helix	708-728	21
α-helix	732-741	10
α-helix	750-760	11
α-helix	765-768	4
α-helix	771-789	19
α-helix	799-820	22
α-helix	821-823	3
α-helix	828-836	9

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-13	3	5
β-strand	18-25	8	4
β-strand	34-39	6	6
α-helix	44	1
β-strand	45-51	7	6
β-strand	57-59	3	6
α-helix	61-63	3
β-strand	67-72	6	4
β-strand	77-82	6	4
α-helix	87-89	3
β-strand	91-97	7	6
α-helix	102-104	3
β-strand	112-114	3	6
β-strand	115-117	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoporin NIC96	A	protein	669	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P34077 (AlphaFold model)
VHH-SAN12	B	protein	133	Vicugna pacos

Sequence of entity 1 (A), FASTA

>6X07_1 Nucleoporin NIC96 (chains A)
GPGSEFELGAPAGRQGNKGNNILNSNESRLNVNENNILREKFENYARIVFQFNNSRQANG
NFDIANEFISILSSANGTRNAQLLESWKILESMKSKDINIVEVGKQYLEQQFLQYTDNLY
KKNMNEGLATNVNKIKSFIDTKLKKADKSWKISNLTVINGVPIWALIFYLLRAGLIKEAL
QVLVENKANIKKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIKSSLDGDPYRLA
VYKLIGRCDLSRKNIPAVTLSIEDWLWMHLMLIKEKDAENDPVYERYSLEDFQNIIISYG
PSRFSNYYLQTLLLSGLYGLAIDYTYTFSEMDAVHLAIGLASLKLFKIDSSTRLTKKPKR
DIRFANILANYTKSFRYSDPRVAVEYLVLITLNEGPTDVELCHEALRELVLETKEFTVLL
GKIGRDGARIPGVIEERQPLLHVRDEKEFLHTITEQAARRADEDGRIYDSILLYQLAEEY
DIVITLVNSLLSDTLSASDLDQPLVGPDDNSETNPVLLARRMASIYFDNAGISRQIHVKN
KEICMLLLNISSIRELYFNKQWQETLSQMELLDLLPFSDELSARKKAQDFSNLDDNIVKN
IPNLLIITLSCISNMIHILNESKYQSSTKGQQIDSLKNVARQCMIYAGMIQYRMPRETYS
TLINIDVSL

Sequence of entity 2 (B), FASTA

>6X07_2 VHH-SAN12 (chains B)
MQVQLVETGGGLVQAGGSLRLSCATSGFNFRLRTMGWYRQAPGKERELVASITSGGSTDY
ADSVKGRFTISRDNAKNTISLEMNSLKPDDTAVYYCNIWAPTTAAITNWGQGTQVTVSSL
PETGGLEHHHHHH

Primary citation

A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure. Nordeen, S.A., Andersen, K.R., Knockenhauer, K.E. et al. Nat Commun (2020) 11:6179-6179. DOI 10.1038/s41467-020-19884-6 · PubMed

Other PDB entries of the same protein (UniProt P34077 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QX5 2.5 Å, Structure of nucleoporin Nic96
2RFO 2.6 Å, Crystral Structure of the nucleoporin Nic96
7WOO 3.71 Å, Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear…
7WOT 3.73 Å, Cryo-EM structure of the inner ring monomer of the Saccharomyces cerevisiae nuclear pore…
8TJ5 6.6 Å, Inner spoke ring of the yeast NPC
7N85 7.6 Å, Inner ring spoke from the isolated yeast NPC
7N9F 37.0 Å, Structure of the in situ yeast NPC
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
9A0F Integrative model of the wild type yeast nuclear pore complex
9A0G Integrative model of Nup116 knockout (at 25C) yeast nuclear pore complex

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