3CH5: RanGDP-Nup153ZnF2 complex

The crystal structure of the RanGDP-Nup153ZnF2 complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 1 Jul 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 2
Atoms: 1,989
Mol. weight: 30.46 kDa
Ligands: ZN, GDP, MG
Released: 1 Jul 2008

Explore 3CH5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3CH5 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: 13 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
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	101-111	11
β-strand	117-122	6	1
α-helix	133-135	3
β-strand	145-148	4	1
β-strand	150	1	3
α-helix	151-153	3
β-strand	155	1	3
α-helix	158-169	12
β-strand	176-178	3	1
α-helix	179-181	3
β-strand	182	1	2
α-helix	183-185	3
α-helix	191-202	12

Chain B: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	720-721	2
β-strand	725-726	2	4
β-strand	733-734	2	4
β-strand	740	1	5
α-helix	746	1
β-strand	747	1	5
α-helix	748	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding nuclear protein Ran	A	protein	216	Homo sapiens	P62826 (AlphaFold model)
Fragment of Nuclear pore complex protein Nup153	B	protein	52	Rattus norvegicus	P49791 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3CH5_1 GTP-binding nuclear protein Ran (chains A)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 2 (B), FASTA

>3CH5_2 Fragment of Nuclear pore complex protein Nup153 (chains B)
SDKPASTSGTGFGDKFKPAIGTWDCDTCLVQNKPEAVKCVACETPKPGTGVK

Ligands and cofactors

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

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

Primary citation

The Crystal Structure of the Ran-Nup153ZnF2 Complex: a General Ran Docking Site at the Nuclear Pore Complex. Schrader, N., Koerner, C., Koessmeier, K. et al. Structure (2008) 16:1116-1125. DOI 10.1016/j.str.2008.03.014 · 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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