2VTX: Npm-a protein

Activation of nucleoplasmin, an oligomeric histone chaperone, challenges its stability. Determined by X-ray diffraction at 2.5 Å resolution. Released 16 Dec 2008.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: XENOPUS LAEVIS
Chains: 10
Atoms: 7,259
Mol. weight: 133.85 kDa
Released: 16 Dec 2008

Explore 2VTX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VTX contains 13 α-helices and 116 β-strands across 10 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	1
β-strand	29-32	4	2
α-helix	44	1
β-strand	45-52	8	1
β-strand	61-66	6	2
β-strand	75-81	7	2
β-strand	82	1	3
β-strand	86	1	3
β-strand	88-90	3	1
β-strand	95-96	2	1
α-helix	97	1
β-strand	100-106	7	2
β-strand	111-117	7	1

Chain B: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	4
β-strand	29-32	4	5
β-strand	44-52	9	4
β-strand	61-67	7	5
β-strand	74-81	8	5
β-strand	82	1	6
β-strand	86	1	6
β-strand	88-90	3	4
β-strand	95-96	2	4
β-strand	100-106	7	5
β-strand	111-118	8	4

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	7
β-strand	24	1	8
β-strand	27	1	8
β-strand	29-32	4	9
β-strand	45-52	8	7
β-strand	61-66	6	9
β-strand	75-81	7	9
β-strand	82	1	10
β-strand	86	1	10
β-strand	88-90	3	7
β-strand	95-96	2	7
α-helix	97	1
α-helix	99	1
β-strand	100-106	7	9
β-strand	111-117	7	7

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	11
β-strand	29-32	4	12
β-strand	45-52	8	11
β-strand	61-66	6	12
β-strand	75-81	7	12
β-strand	82	1	13
β-strand	86	1	13
β-strand	88-90	3	11
β-strand	95-96	2	11
α-helix	97	1
α-helix	99	1
β-strand	100-106	7	12
β-strand	111-117	7	11

Chain E: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	14
β-strand	24	1	15
β-strand	27	1	15
β-strand	29-32	4	16
β-strand	45-52	8	14
β-strand	61-66	6	16
β-strand	75-81	7	16
β-strand	82	1	17
β-strand	86	1	17
β-strand	88-90	3	14
β-strand	95-96	2	14
α-helix	97	1
β-strand	100-106	7	16
β-strand	111-117	7	14

Chain G: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	18
β-strand	29-32	4	19
β-strand	44-52	9	18
β-strand	61-67	7	19
β-strand	74-81	8	19
β-strand	82	1	20
β-strand	86	1	20
β-strand	88-90	3	18
β-strand	95-96	2	18
α-helix	97	1
β-strand	100-106	7	19
β-strand	111-118	8	18

Chain H: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	21
β-strand	24	1	22
β-strand	27	1	22
β-strand	29-32	4	23
α-helix	43-44	2
β-strand	45-52	8	21
β-strand	61-67	7	23
β-strand	74-81	8	23
β-strand	82	1	24
β-strand	86	1	24
β-strand	88-90	3	21
β-strand	95-96	2	21
α-helix	97	1
β-strand	100-106	7	23
β-strand	111-116	6	21

Chains I and J: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	25
β-strand	29-32	4	26
β-strand	45-52	8	25
β-strand	61-69	9	26
β-strand	72-81	10	26
β-strand	82	1	27
β-strand	86	1	27
β-strand	88-90	3	25
β-strand	95-96	2	25
α-helix	97	1
β-strand	100-106	7	26
β-strand	111-117	7	25

1 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
Npm-a protein	A, B, C, D, E, G, H, I, K	protein	120	XENOPUS LAEVIS	P05221 (AlphaFold model)
Npm-a protein	J	protein	120	XENOPUS LAEVIS	P05221 (AlphaFold model)

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

>2VTX_1 NPM-A PROTEIN (chains A, B, C, D, E, G, H, I, K)
MADDVDNDDKLEKPVDLIWGCELNEQNKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEF
HIVEIVDQEEGAEKSVPIATLKPSILPMATMVGIELDPPVTFRLKAGSGPLYISGQHVAM

Sequence of entity 2 (J), FASTA

>2VTX_2 NPM-A PROTEIN (chains J)
MADDVDNDDKLEKPVDLIWGCELNEQNKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEF
HIVEIVDQEEGAEKVVPIATLKPSILPMATMVGIELDPPVTFRLKAGSGPLYISGQHVAM

Primary citation

Activation of Nucleoplasmin, an Oligomeric Histone Chaperone, Challenges its Stability. Taneva, S.G., Munoz, I.G., Franco, G. et al. Biochemistry (2008) 47:13897. DOI 10.1021/BI800975R · PubMed

Other PDB entries of the same protein (UniProt P05221 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3UL1 1.9 Å, Mouse importin alpha: nucleoplasmin cNLS peptide complex
1K5J 2.3 Å, The Crystal Structure of Nucleoplasmin-Core
4BPL 2.3 Å, rice importin_alpha in complex with nucleoplasmin NLS
1EE5 2.4 Å, Yeast karyopherin (importin) alpha in a complex with a nucleoplasmin nls peptide
1EJY 2.9 Å, Mouse importin alpha-nucleoplasmin nls peptide complex
8VHI 5.0 Å, NPM2-H1.8 isolated from Xenopus egg extract
8VHK 5.16 Å, NPM2-H1.8 isolated from Xenopus egg extract (Stretched form)
8VHJ 5.9 Å, NPM2-H1.8 isolated from Xenopus egg extract (Bent form)

Browse structure collections

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