5BXQ: NTF2:RanGDP complex

Structure of the NTF2:RanGDP complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 1 Jul 2015.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Rattus norvegicus, Canis familiaris
Chains: 5
Atoms: 7,174
Mol. weight: 103.85 kDa
Ligands: GDP, MG
Released: 1 Jul 2015

Explore 5BXQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5BXQ contains 47 α-helices and 48 β-strands across 5 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	26-32	7
β-strand	33-41	9	1
β-strand	44-47	4	1
α-helix	49-57	9
β-strand	64-75	12	1
β-strand	81-91	11	1
α-helix	94-96	3
β-strand	97-108	12	1
β-strand	111-121	11	1

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	26-32	7
β-strand	38-41	4	2
β-strand	44-47	4	2
α-helix	49-57	9
β-strand	64-75	12	2
β-strand	81-91	11	2
α-helix	95-96	2
β-strand	97-107	11	2
β-strand	112-121	10	2

Chain C: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	3
α-helix	23-28	6
β-strand	30	1	4
α-helix	31-35	5
β-strand	38-40	3	3
β-strand	45-54	10	3
β-strand	57-66	10	3
α-helix	69-71	3
α-helix	74-76	3
α-helix	77-80	4
β-strand	85-91	7	3
α-helix	95-99	5
α-helix	101-111	11
β-strand	117-122	6	3
α-helix	133-136	4
β-strand	144-148	5	3
β-strand	150	1	5
α-helix	151-153	3
β-strand	155	1	5
α-helix	159-169	11
β-strand	176	1	3
α-helix	179-181	3
β-strand	182	1	4
α-helix	183-185	3
α-helix	188-190	3
α-helix	191-202	12

Chain D: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	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	69-71	3
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	133-136	4
β-strand	144-148	5	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	191-207	17

Chain E: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	9
α-helix	23-27	5
β-strand	30	1	10
α-helix	31-35	5
β-strand	38-40	3	9
α-helix	41-43	3
β-strand	45-54	10	9
β-strand	57-66	10	9
α-helix	69-72	4
α-helix	77-80	4
β-strand	85-91	7	9
α-helix	95-99	5
α-helix	101-111	11
β-strand	117-122	6	9
β-strand	144-148	5	9
β-strand	150	1	11
α-helix	151-153	3
β-strand	155	1	11
α-helix	159-169	11
β-strand	176-178	3	9
β-strand	182	1	10
α-helix	183-185	3
α-helix	191-206	16
α-helix	208-211	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear transport factor 2	A, B	protein	127	Rattus norvegicus	P61972 (AlphaFold model)
GTP-binding nuclear protein Ran	C, D, E	protein	216	Canis familiaris	P62825 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5BXQ_1 Nuclear transport factor 2 (chains A, B)
MGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLP
FQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFR
LALHNFG

Sequence of entity 2 (C, D, E), FASTA

>5BXQ_2 GTP-binding nuclear protein Ran (chains C, D, E)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	3
MG	Magnesium ion	Mg	3

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

Primary citation

Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran. Stewart, M., Kent, H.M., McCoy, A.J. J Mol Biol (1998) 277:635-646. DOI 10.1006/jmbi.1997.1602 · PubMed

Other PDB entries of the same protein (UniProt P61972 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GY6 1.6 Å, NTF2 from rat, ammonium sulphate conditions
1JB2 2.0 Å, Crystal structure of NTF2 M84E mutant
1JB4 2.23 Å, Crystal structure of NTF2 M102E mutant
1AR0 2.3 Å, Nuclear transport factor 2 (NTF2) E42K mutant
1ASK 2.3 Å, Nuclear transport factor 2 (NTF2) H66A mutant
1JB5 2.3 Å, Crystal structure of NTF2 M118E mutant
1OUN 2.3 Å, Crystal structure of nuclear transport factor 2 (NTF2)
1QMA 2.5 Å, Nuclear Transport Factor 2 (NTF2) W7A mutant
1U5O 2.5 Å, Structure of the D23A mutant of the nuclear transport carrier NTF2

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