2DZO: Crystal structure analysis of yeast Nas6p

Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3. Determined by X-ray diffraction at 3.0 Å resolution. Released 16 Oct 2007.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 4,763
Mol. weight: 69.71 kDa
Released: 16 Oct 2007

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

Secondary structure: helices and β-sheets

2DZO contains 42 α-helices and 6 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: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	5-11	7
α-helix	15-24	10
α-helix	26-28	3
α-helix	39-45	7
α-helix	49-57	9
α-helix	64-66	3
α-helix	75-82	8
α-helix	85-92	8
α-helix	97-99	3
α-helix	110-117	8
α-helix	120-128	9
α-helix	135-136	2
β-strand	137	1	1
β-strand	141	1	1
α-helix	143-150	8
α-helix	153-157	5
α-helix	158-162	5
α-helix	177-183	7
α-helix	187-196	10
α-helix	218-225	8

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	362	1	2
α-helix	368-373	6
α-helix	380-396	17
β-strand	402	1	2
α-helix	403	1
α-helix	404-412	9

Chain C: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	5-11	7
α-helix	18-23	6
α-helix	26-28	3
α-helix	39-45	7
α-helix	49-57	9
α-helix	64-66	3
α-helix	75-82	8
α-helix	85-92	8
α-helix	110-116	7
α-helix	120-128	9
α-helix	143-150	8
α-helix	153-160	8
α-helix	177-183	7
α-helix	187-195	9
α-helix	211-213	3
α-helix	218-225	8

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	351-359	9
β-strand	362	1	3
α-helix	368-372	5
α-helix	380-395	16
β-strand	402	1	3
α-helix	404-411	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable 26S proteasome regulatory subunit p28	A, C	protein	228	Saccharomyces cerevisiae	P50086 (AlphaFold model)
26S protease regulatory subunit 6B homolog	B, D	protein	82	Saccharomyces cerevisiae	P33298 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2DZO_1 Probable 26S proteasome regulatory subunit p28 (chains A, C)
MSNYPLHQACMENEFFKVQELLHSKPSLLLQKDQDGRIPLHWSVSFQAHEITSFLLSKME
NVNLDDYPDDSGWTPFHIACSVGNLEVVKSLYDRPLKPDLNKITNQGVTCLHLAVGKKWF
EVSQFLIENGASVRIKDKFNQIPLHRAASVGSLKLIELLCGLGKSAVNWQDKQGWTPLFH
ALAEGHGDAAVLLVEKYGAEYDLVDNKGAKAEDVALNEQVKKFFLNNV

Sequence of entity 2 (B, D), FASTA

>2DZO_2 26S protease regulatory subunit 6B homolog (chains B, D)
MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSD
LEEAYATQVKTDNTVDKFDFYK

Primary citation

Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3. Nakamura, Y., Padmanabhan, B., Yokoyama, S. To be published.

Other PDB entries of the same protein (UniProt P50086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2DZN 2.2 Å, Crystal structure analysis of yeast Nas6p complexed with the proteasome subunit, rpt3
1IXV 2.3 Å, Crystal Structure Analysis of homolog of oncoprotein gankyrin, an interactor of Rb and…
1WG0 2.53 Å, Structural comparison of Nas6p protein structures in two different crystal forms
35ZW 3.31 Å, yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2-Rpt3-Rpt4-Rpt5…
36BM 3.82 Å, yeast 26S proteasome base assembly intermediate, base-Hsm3-Nas6 with Rpt4-EQ
36BL 3.91 Å, yeast 26S proteasome base assembly intermediate, base-Rpn14-Hsm3-Nas6(2) with Rpt4-EQ
36BD 3.93 Å, yeast 26S proteasome base assembly intermediate, base-Rpn14-Hsm3-Nas6 with Rpt4-EQ
36AX 4.87 Å, yeast 26S proteasome base assembly intermediate, base-Nas2-Rpn14-Hsm3-Nas6 with Rpt4-EQ

Browse structure collections

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