3GJ4: Human RanGDP-Nup153ZnF3 complex

Crystal structure of human RanGDP-Nup153ZnF3 complex. Determined by X-ray diffraction at 2.15 Å resolution. Released 4 Aug 2009.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 4
Atoms: 3,858
Mol. weight: 57.6 kDa
Ligands: MG, GDP, ZN
Released: 4 Aug 2009

Explore 3GJ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3GJ4 contains 31 α-helices and 32 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: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	1
α-helix	23-27	5
β-strand	30	1	2
α-helix	31-35	5
β-strand	38-40	3	1
α-helix	41-43	3
β-strand	45-54	10	1
β-strand	57-66	10	1
α-helix	69-71	3
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	176-178	3	1
α-helix	179-181	3
β-strand	182	1	2
α-helix	183-185	3
α-helix	191-205	15

Chain B: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	793-794	2	4
β-strand	801-802	2	4
β-strand	808	1	5
α-helix	814	1
β-strand	815	1	5
α-helix	816	1

Chain C: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	9-16	8	6
α-helix	23-27	5
β-strand	30	1	7
α-helix	31-35	5
β-strand	38-40	3	6
β-strand	45-54	10	6
β-strand	57-66	10	6
α-helix	69-72	4
α-helix	74-76	3
α-helix	77-80	4
β-strand	85-91	7	6
α-helix	95-99	5
α-helix	101-111	11
β-strand	117-122	6	6
α-helix	133-135	3
α-helix	138-140	3
β-strand	145-148	4	6
β-strand	150	1	8
α-helix	151-153	3
β-strand	155	1	8
α-helix	159-169	11
β-strand	176-178	3	6
α-helix	179-181	3
β-strand	182	1	7
α-helix	183-185	3
α-helix	191-206	16

Chain D: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	793-794	2	9
β-strand	801-802	2	9
β-strand	808	1	10
β-strand	815	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding nuclear protein Ran	A, C	protein	221	Homo sapiens	P62826 (AlphaFold model)
Nuclear pore complex protein Nup153	B, D	protein	33	Rattus norvegicus	P49791 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3GJ4_1 GTP-binding nuclear protein Ran (chains A, C)
GPHMASAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGESEKKYVATLGVEVHPLVFHTN
RGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENI
PIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLE
FVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 2 (B, D), FASTA

>3GJ4_2 Nuclear pore complex protein Nup153 (chains B, D)
GPLGSVGSWECPVCCVSNKAEDSRCVSCTSEKP

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
ZN	Zinc ion	Zn	2

Primary citation

Crystallographic and Biochemical Analysis of the Ran-binding Zinc Finger Domain. Partridge, J.R., Schwartz, T.U. J Mol Biol (2009) 391:375-389. DOI 10.1016/j.jmb.2009.06.011 · 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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