7MNZ: Nup358/RanBP2 Ran-binding domain 4

Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP. Determined by X-ray diffraction at 2.35 Å resolution. Released 15 Jun 2022.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 12
Atoms: 17,360
Mol. weight: 246.99 kDa
Ligands: MG, GNP
Released: 15 Jun 2022

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

Secondary structure: helices and β-sheets

7MNZ contains 73 α-helices and 96 β-strands across 12 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: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	1
α-helix	23-32	10
β-strand	40	1	2
β-strand	45-54	10	1
β-strand	57-66	10	1
α-helix	70-72	3
α-helix	76-80	5
β-strand	85-91	7	1
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	1
α-helix	138-142	5
β-strand	145-148	4	1
α-helix	159-169	11
β-strand	176	1	1
α-helix	178-180	3
α-helix	182-185	4
α-helix	187-189	3
α-helix	194-204	11
β-strand	207	1	3

Chain B: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2930-2944	15	4
β-strand	2949-2963	15	4
β-strand	2969-2975	7	4
β-strand	2981-2986	6	4
β-strand	2994-2995	2	4
β-strand	3002-3009	8	4
β-strand	3016-3024	9	4
α-helix	3027-3042	16

Chain C: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	5
α-helix	23-32	10
β-strand	45-54	10	5
β-strand	57-66	10	5
α-helix	70-72	3
α-helix	77-80	4
β-strand	85-91	7	5
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	5
α-helix	133-135	3
α-helix	138-141	4
β-strand	145-148	4	5
α-helix	159-169	11
β-strand	176	1	5
α-helix	178-180	3
α-helix	182-185	4
α-helix	194-204	11
α-helix	208-210	3

Chain D: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2909-2917	9	6
β-strand	2930-2944	15	7
β-strand	2949-2963	15	7
β-strand	2969-2974	6	7
β-strand	2981-2986	6	7
β-strand	2994-2995	2	7
β-strand	3002-3009	8	7
β-strand	3016-3024	9	7
α-helix	3027-3042	16

Chain E: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	8
α-helix	23-32	10
β-strand	40	1	3
β-strand	45-54	10	8
β-strand	57-66	10	8
α-helix	70-72	3
α-helix	76-80	5
β-strand	85-91	7	8
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	8
α-helix	138-142	5
β-strand	145-148	4	8
β-strand	150	1	9
β-strand	155	1	9
α-helix	159-169	11
β-strand	176	1	8
α-helix	178-180	3
α-helix	182-185	4
α-helix	191-205	15
β-strand	207	1	2

Chain F: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2930-2944	15	10
β-strand	2949-2963	15	10
β-strand	2969-2975	7	10
β-strand	2981-2986	6	10
β-strand	2994-2995	2	10
β-strand	3002-3009	8	10
β-strand	3016-3023	8	10
α-helix	3027-3042	16

Chain G: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	11
α-helix	23-32	10
β-strand	45-54	10	11
β-strand	57-66	10	11
α-helix	70-72	3
α-helix	76-80	5
β-strand	85-91	7	11
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	11
α-helix	138-142	5
β-strand	145-148	4	11
α-helix	159-169	11
β-strand	176	1	11
α-helix	178-180	3
α-helix	182-185	4
α-helix	187-189	3
α-helix	191-193	3
α-helix	194-206	13

Chain H: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2909-2917	9	6
β-strand	2930-2944	15	12
β-strand	2949-2963	15	12
β-strand	2969-2974	6	12
β-strand	2981-2986	6	12
β-strand	2994-2995	2	12
β-strand	3002-3009	8	12
β-strand	3016-3023	8	12
α-helix	3027-3042	16

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding nuclear protein Ran	A, C, E, G, I, K	protein	216	Homo sapiens	P62826 (AlphaFold model)
E3 SUMO-protein ligase RanBP2	B, D, F, H, J, L	protein	139	Homo sapiens	P49792

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>7MNZ_1 GTP-binding nuclear protein Ran (chains A, C, E, G, I, K)
SMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPI
KFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVL
CGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAM
PALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDD

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>7MNZ_2 E3 SUMO-protein ligase RanBP2 (chains B, D, F, H, J, L)
GPGSHFEPIVSLPEVEVKSGEEDEEILFKERAKLYRWDRDVSQWKERGVGDIKILQNYDN
KQVRILMRRDQVFKVCANHVITKTMELKPLNVSNNALVWTASDYADGEAKVEQLAVRFKT
KEVADCFKKTFEECQQNLM

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	6
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	6

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

Browse structure collections

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