2NBW: Rpn1 T1 site with the Rad23 UBL domain

Solution structure of the Rpn1 T1 site with the Rad23 UBL domain. Determined by solution NMR. Released 20 Jul 2016.

Method: Solution NMR
Organism: Saccharomyces cerevisiae S288c
Chains: 2
Atoms: 1,561
Mol. weight: 22.35 kDa
Released: 20 Jul 2016

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

Secondary structure: helices and β-sheets

2NBW contains 9 α-helices and 6 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	485-497	13
α-helix	503-513	11
α-helix	520-533	14
α-helix	541-552	12
α-helix	563-572	10
α-helix	580-590	11
α-helix	597-605	9

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	13-18	6	1
β-strand	23	1	2
α-helix	24-35	12
β-strand	43-45	3	1
β-strand	56	1	2
α-helix	57-60	4
β-strand	67-71	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
26S proteasome regulatory subunit RPN1	A	protein	131	Saccharomyces cerevisiae S288c	P38764 (AlphaFold model)
UV excision repair protein RAD23	B	protein	78	Saccharomyces cerevisiae S288c	P32628 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2NBW_1 26S proteasome regulatory subunit RPN1 (chains A)
DTKISSAAILGLGIAFAGSKNDEVLGLLLPIAASTDLPIETAAMASLALAHVFVGTCNGD
ITTSIMDNFLERTAIELKTDWVRFLALALGILYMGQGEQVDDVLETISAIEHPMTSAIEV
LVGSCAYTGTG

Sequence of entity 2 (B), FASTA

>2NBW_2 UV excision repair protein RAD23 (chains B)
MVSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKLIYSGKVLQDSKTVSEC
GLKDGDQVVFMVSQKKST

Primary citation

Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome. Chen, X., Randles, L., Shi, K. et al. Structure (2016) 24:1257-1270. DOI 10.1016/j.str.2016.05.018 · PubMed

Other PDB entries of the same protein (UniProt P38764 (AlphaFold model), which also has an AlphaFold model), best resolution first:

35ZV 3.11 Å, yeast 26S proteasome base assembly intermediate, Rpn14-Rpt6 (base-Rpn14-Hsm3-Nas6(2)…
9CGC 3.61 Å, Yeast 26S proteasome non-substrate-engaged (S1 state)
6J2Q 3.8 Å, Yeast proteasome in Ub-accepted state (C1-b)
6J2X 3.8 Å, Yeast proteasome in resting state (C1-a)
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
5MPD 4.1 Å, 26S proteasome in presence of ATP (s1)
6FVT 4.1 Å, 26S proteasome, s1 state
5WVK 4.2 Å, Yeast proteasome-ADP-AlFx
5MPE 4.5 Å, 26S proteasome in presence of ATP (s2)
6FVU 4.5 Å, 26S proteasome, s2 state

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