7MNV: ZnF8 of Nucleoporin NUP358/RanBP2

Crystal Structure of the ZnF8 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP. Determined by X-ray diffraction at 1.8 Å resolution. Released 15 Jun 2022.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,181
Mol. weight: 31.52 kDa
Ligands: ZN, MG, GDP
Released: 15 Jun 2022

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

Secondary structure: helices and β-sheets

7MNV contains 16 α-helices and 16 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: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	9-16	8	1
α-helix	23-27	5
β-strand	30	1	2
α-helix	31-35	5
β-strand	38-40	3	1
β-strand	45-54	10	1
β-strand	57-66	10	1
α-helix	69-72	4
α-helix	74-76	3
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
α-helix	133-135	3
α-helix	138-142	5
β-strand	145-148	4	1
β-strand	150	1	3
α-helix	151-153	3
β-strand	155	1	3
α-helix	159-169	11
β-strand	176	1	1
α-helix	179-181	3
β-strand	182	1	2
α-helix	183-185	3
α-helix	191-206	16

Chain B: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	1785-1786	2	4
β-strand	1793-1794	2	4
β-strand	1800	1	5
α-helix	1806	1
β-strand	1807	1	5
α-helix	1808	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding nuclear protein Ran	A	protein	236	Homo sapiens	P62826 (AlphaFold model)
E3 SUMO-protein ligase RanBP2	B	protein	41	Homo sapiens	P49792

Sequence of entity 1 (A), FASTA

>7MNV_1 GTP-binding nuclear protein Ran (chains A)
MGSSHHHHHHSSGLVPRGSHMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGESEKKYV
ATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKN
VPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKP
FLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 2 (B), FASTA

>7MNV_2 E3 SUMO-protein ligase RanBP2 (chains B)
GPLGSGFEGMFIRKGQWDCSVCCVQNESSSLKCVACDASKP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Water and common crystallization additives (GOL) 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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