7MNW: Nup358/RanBP2 Ran-binding domain 1

Crystal Structure of Nup358/RanBP2 Ran-binding domain 1 in complex with Ran-GPPNHP. Determined by X-ray diffraction at 2.4 Å resolution. Released 15 Jun 2022.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 8
Atoms: 11,711
Mol. weight: 165.33 kDa
Ligands: GNP, MG
Released: 15 Jun 2022

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

Secondary structure: helices and β-sheets

7MNW contains 53 α-helices and 58 β-strands across 8 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, 7 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	1
α-helix	23-32	10
β-strand	45-54	10	1
β-strand	57-66	10	1
α-helix	70-75	6
α-helix	76-79	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	138-141	4
β-strand	145-148	4	1
α-helix	159-169	11
β-strand	176	1	1
α-helix	178-180	3
α-helix	182-187	6
α-helix	194-206	13
α-helix	208-212	5

Chains B and F: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1179-1181	3
β-strand	1191-1205	15	2
β-strand	1210-1224	15	2
β-strand	1230-1235	6	2
β-strand	1242-1247	6	2
β-strand	1255-1256	2	2
β-strand	1263-1270	8	2
β-strand	1277-1284	8	2
α-helix	1288-1302	15

Chain C: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	3
α-helix	23-32	10
β-strand	45-54	10	3
β-strand	57-66	10	3
α-helix	70-75	6
α-helix	76-79	4
β-strand	85-91	7	3
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	3
α-helix	133-135	3
α-helix	138-142	5
β-strand	145-148	4	3
α-helix	159-169	11
β-strand	176	1	3
α-helix	178-180	3
α-helix	182-186	5
α-helix	191-206	16
α-helix	208-212	5

Chains D and H: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1179-1181	3
β-strand	1191-1205	15	4
β-strand	1210-1224	15	4
β-strand	1230-1235	6	4
β-strand	1242-1247	6	4
β-strand	1255-1256	2	4
β-strand	1263-1270	8	4
β-strand	1277-1284	8	4
α-helix	1288-1303	16

Chain E: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	5
α-helix	23-32	10
β-strand	45-54	10	5
β-strand	57-66	10	5
α-helix	70-75	6
α-helix	76-79	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	138-142	5
β-strand	145-148	4	5
α-helix	159-169	11
β-strand	176	1	5
α-helix	178-180	3
α-helix	182-187	6
α-helix	194-206	13
α-helix	208-212	5

Chain G: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	7
α-helix	23-32	10
β-strand	45-54	10	7
β-strand	57-66	10	7
α-helix	70-75	6
α-helix	76-79	4
β-strand	85-91	7	7
α-helix	95-99	5
α-helix	101-112	12
β-strand	117-122	6	7
α-helix	138-142	5
β-strand	145-148	4	7
β-strand	150	1	8
β-strand	155	1	8
α-helix	159-169	11
β-strand	176	1	7
α-helix	178-180	3
α-helix	182-187	6
α-helix	191-206	16
α-helix	208-212	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding nuclear protein Ran	A, C, E, G	protein	217	Homo sapiens	P62826 (AlphaFold model)
E3 SUMO-protein ligase RanBP2	B, D, F, H	protein	140	Homo sapiens	P49792

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

>7MNW_1 GTP-binding nuclear protein Ran (chains A, C, E, G)
SMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPI
KFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVL
CGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAM
PALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

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

>7MNW_2 E3 SUMO-protein ligase RanBP2 (chains B, D, F, H)
GPGSHFEPVVPLPDKIEVKTGEEDEEEFFCNRAKLFRFDVESKEWKERGIGNVKILRHKT
SGKIRLLMRREQVLKICANHYISPDMKLTPNAGSDRSFVWHALDYADELPKPEQLAIRFK
TPEEAALFKCKFEEAQSILK

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	4
MG	Magnesium ion	Mg	4

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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