3VLF: Yeast proteasome interacting protein

Crystal structure of yeast proteasome interacting protein. Determined by X-ray diffraction at 3.8 Å resolution. Released 22 Feb 2012.

Method: X-ray diffraction
Resolution: 3.8 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 8,594
Mol. weight: 137.09 kDa
Released: 22 Feb 2012

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

Secondary structure: helices and β-sheets

3VLF contains 78 α-helices and 4 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: 34 helices, 0 β-strands

Element	Residues	Length
α-helix	10-22	13
α-helix	29-42	14
α-helix	52-63	12
α-helix	73-81	9
α-helix	89-95	7
α-helix	98-106	9
α-helix	110-121	12
α-helix	129-131	3
α-helix	134-142	9
α-helix	150-163	14
α-helix	167-174	8
α-helix	178-187	10
α-helix	190-203	14
α-helix	221-227	7
α-helix	228-230	3
α-helix	231-250	20
α-helix	256-258	3
α-helix	264-272	9
α-helix	278-281	4
α-helix	285-295	11
α-helix	304-312	9
α-helix	320-329	10
α-helix	332-338	7
α-helix	340-344	5
α-helix	354-360	7
α-helix	364-370	7
α-helix	376-381	6
α-helix	384-394	11
α-helix	398-405	8
α-helix	409-413	5
α-helix	421-423	3
α-helix	427-441	15
α-helix	444-447	4
α-helix	452-464	13

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	384-393	10
β-strand	398	1	1
α-helix	404-409	6
α-helix	416-433	18
β-strand	438	1	1
α-helix	440-450	11

Chain C: 36 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	29-42	14
α-helix	52-63	12
α-helix	73-81	9
α-helix	93-96	4
α-helix	98-106	9
α-helix	110-121	12
α-helix	129-131	3
α-helix	133-142	10
α-helix	150-161	12
α-helix	167-171	5
α-helix	172-176	5
α-helix	178-186	9
α-helix	190-206	17
α-helix	221-227	7
α-helix	228-230	3
α-helix	231-249	19
α-helix	254-256	3
α-helix	258-261	4
α-helix	264-270	7
α-helix	278-283	6
α-helix	285-295	11
α-helix	301-303	3
α-helix	304-311	8
α-helix	323-329	7
α-helix	332-336	5
α-helix	340-346	7
α-helix	351-353	3
α-helix	354-360	7
α-helix	364-368	5
α-helix	378-381	4
α-helix	384-393	10
α-helix	398-405	8
α-helix	409-415	7
α-helix	427-441	15
α-helix	452-463	12

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	385-394	10
β-strand	398	1	2
α-helix	404-410	7
α-helix	416-433	18
β-strand	438	1	2
α-helix	440-450	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA mismatch repair protein HSM3	A, C	protein	500	Saccharomyces cerevisiae	P38348 (AlphaFold model)
26S protease regulatory subunit 7 homolog	B, D	protein	88	Saccharomyces cerevisiae	P33299 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3VLF_1 DNA mismatch repair protein HSM3 (chains A, C)
MGSSHHHHHHSSGLVPRGSHMSEKETNYVENLLTQLENELNEDNLPEDINTLLRKCSLNL
VTVVSLPDMDVKPLLATIKRFLTSNVSYDSLNYDYLLDVVDKLVPMADFDDVLEVYSAED
LVKALRSEIDPLKVAACRVIENSQPKGLFATSNIIDILLDILFDEKVENDKLITAIEKAL
ERLSTDELIRRRLFDNNLPYLVSVKGRMETVSFVRLIDFLTIEFQFISGPEFKDIIFCFT
KEEILKSVEDILVFIELVNYYTKFLLEIRNQDKYWALRHVKKILPVFAQLFEDTENYPDV
RAFSTNCLLQLFAEVSRIEEDEYSLFKTMDKDSLKIGSEAKLITEWLELINPQYLVKYHK
DVVENYFHVSGYSIGMLRNLSADEECFNAIRNKFSAEIVLRLPYLEQMQVVETLTRYEYT
SKFLLNEMPKVMGSLIGDGSAGAIIDLETVHYRNSALRNLLDKGEEKLSVWYEPLLREYS
KAVNGKNYSTGSETKIADCR

Sequence of entity 2 (B, D), FASTA

>3VLF_2 26S protease regulatory subunit 7 homolog (chains B, D)
MDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVAT
EKDFLKAVDKVISGYKKFSSTSRYMQYN

Primary citation

Structural basis for specific recognition of Rpt1, an ATPase subunit of the 26S proteasome, by a proteasome-dedicated chaperone Hsm3. Takagi, K., Kim, S., Yukii, H. et al. J Biol Chem (2012) 287:12172-12182. DOI 10.1074/jbc.M112.345876 · PubMed

Other PDB entries of the same protein (UniProt P38348 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VLD 2.05 Å, Crystal structure of yeast proteasome interacting protein
4A3T 2.1 Å, yeast regulatory particle proteasome assembly chaperone Hsm3
4FP7 2.2 Å, 2.2A resolution structure of Proteasome Assembly Chaperone Hsm3
3VLE 2.41 Å, Crystal structure of yeast proteasome interacting protein
35ZR 2.99 Å, yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (base-Hsm3-Nas6 with…
35ZW 3.31 Å, yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2-Rpt3-Rpt4-Rpt5…
4A3V 3.8 Å, yeast regulatory particle proteasome assembly chaperone Hsm3 in complex with Rpt1…
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
4JPO 5.0 Å, 5A resolution structure of Proteasome Assembly Chaperone Hsm3 in complex with a…

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