7MO0: Nucleoporin NUP50 Ran-Binding Domain

Crystal Structure of Nucleoporin NUP50 Ran-Binding Domain in Complex with Ran-GPPNHP. Determined by X-ray diffraction at 2.45 Å resolution. Released 15 Jun 2022.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,503
Mol. weight: 81.09 kDa
Ligands: MG, GNP
Released: 15 Jun 2022

Explore 7MO0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MO0 contains 24 α-helices and 33 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: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	1
α-helix	23-31	9
β-strand	45-54	10	1
β-strand	57-66	10	1
α-helix	70-73	4
α-helix	77-80	4
β-strand	85-91	7	1
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	1
β-strand	144-148	5	1
β-strand	150	1	2
β-strand	155	1	2
α-helix	159-169	11
β-strand	176-177	2	1
α-helix	178-180	3
α-helix	191-203	13
α-helix	208-211	4

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	344-346	3
α-helix	351-353	3
β-strand	359-369	11	3
β-strand	372-385	14	3
β-strand	391-397	7	3
β-strand	404-409	6	3
β-strand	416-419	4	3
β-strand	423-428	6	3
β-strand	443-448	6	3
α-helix	452-467	16

Chain C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	4
α-helix	23-31	9
β-strand	45-52	8	4
β-strand	53-54	2	5
β-strand	59-66	8	4
α-helix	77-80	4
β-strand	85-91	7	4
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	4
α-helix	138-140	3
β-strand	144-148	5	4
β-strand	150	1	6
β-strand	155	1	6
α-helix	159-169	11
β-strand	176-177	2	5
α-helix	178-180	3
α-helix	182-186	5
α-helix	191-203	13
α-helix	208-212	5

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	351-353	3
β-strand	359-369	11	7
β-strand	372-385	14	7
β-strand	391-397	7	7
β-strand	404-409	6	7
β-strand	416-419	4	7
β-strand	423-428	6	7
β-strand	443-448	6	7
α-helix	452-467	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding nuclear protein Ran	A, C	protein	217	Homo sapiens	P62826 (AlphaFold model)
Nuclear pore complex protein Nup50	B, D	protein	134	Homo sapiens	Q9UKX7 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7MO0_1 GTP-binding nuclear protein Ran (chains A, C)
SMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPI
KFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVL
CGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAM
PALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 2 (B, D), FASTA

>7MO0_2 Nuclear pore complex protein Nup50 (chains B, D)
GSDEEENDEPPKVVVTEVKEEDAFYSKKCKLFYKKDNEFKEKGIGTLHLKPTANQKTQLL
VRADTNLGNILLNVLIPPNMPCTRTGKNNVLIVCVPNPPIDEKNATMPVTMLIRVKTSED
ADELHKILLEKKDA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Architecture of the cytoplasmic face of the nuclear pore. Bley, C.J., Nie, S., Mobbs, G.W. et al. Science (2022) 376:eabm9129-eabm9129. DOI 10.1126/science.abm9129 · PubMed

Other PDB entries of the same protein (UniProt P62826 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GJ0 1.48 Å, Crystal structure of human RanGDP
7MO5 1.55 Å, Crystal Structure of the ZnF4 of Nucleoporin NUP153 in complex with Ran-GDP
7MO1 1.6 Å, Crystal Structure of the ZnF1 of Nucleoporin NUP153 in complex with Ran-GDP
5CIQ 1.65 Å, Ran GDP wild type tetragonal crystal form
7MO2 1.65 Å, Crystal Structure of the ZnF2 of Nucleoporin NUP153 in complex with Ran-GDP
5CIT 1.75 Å, Ran GDP wild type monoclinic crystal form
5CIW 1.75 Å, Ran GDP Y39A mutant monoclinic crystal form
5CJ2 1.75 Å, Ran GDP Y39A mutant triclinic crystal form
1I2M 1.76 Å, Ran-RCC1-SO4 complex
4HAT 1.78 Å, Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1-Ran-RanBP1
3GJ3 1.79 Å, Crystal structure of human RanGDP-Nup153ZnF2 complex
3GJ5 1.79 Å, Crystal structure of human RanGDP-Nup153ZnF4 complex

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