7UJD: PSMD2 Structure

PSMD2 Structure bound to MC1 and Fab8/14. Determined by electron microscopy at 2.5 Å resolution. Released 11 Jan 2023.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 5,269
Mol. weight: 168.9 kDa
Released: 11 Jan 2023

Explore 7UJD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UJD contains 38 α-helices and 24 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: 37 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	262-272	11
α-helix	275-282	8
α-helix	288-301	14
α-helix	314-321	8
α-helix	326-337	12
α-helix	345-348	4
α-helix	368-381	14
α-helix	396-399	4
α-helix	405-417	13
α-helix	422-429	8
α-helix	430-434	5
α-helix	438-450	13
α-helix	461-466	6
α-helix	475-488	14
α-helix	495-501	7
α-helix	502-505	4
α-helix	512-525	14
α-helix	532-544	13
α-helix	553-556	4
α-helix	557-565	9
α-helix	570-573	4
α-helix	574-579	6
α-helix	580-582	3
α-helix	585-599	15
α-helix	606-612	7
α-helix	650-661	12
α-helix	665-681	17
α-helix	686-689	4
α-helix	690-697	8
α-helix	704-713	10
α-helix	719-732	14
α-helix	739-751	13
α-helix	756-769	14
α-helix	771-774	4
β-strand	776-777	2	1
β-strand	781-782	2	2
β-strand	787-788	2	2
α-helix	790-803	14
α-helix	809-813	5
α-helix	815-824	10
β-strand	826-827	2	1
β-strand	829-830	2	3
β-strand	831-833	3	4
β-strand	839	1	4
β-strand	843-847	5	5
β-strand	866-869	4	5
β-strand	872-873	2	3
β-strand	879-882	4	5
β-strand	888-889	2	6
β-strand	897-899	3	4
β-strand	900-901	2	6

Chain D: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	7
β-strand	54-55	2	7
α-helix	56-58	3
β-strand	60-61	2	7

Chain E: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	8
β-strand	93	1	8

Chain F: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	9
β-strand	54-55	2	9
β-strand	60-61	2	9
β-strand	103	1	10
β-strand	106	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
26S proteasome non-ATPase regulatory subunit 2	A	protein	644	Homo sapiens	Q13200 (AlphaFold model)
Fab 14 LC CDRs	C	protein	217	Homo sapiens
Fab 14 HC CDRs	D	protein	231	Homo sapiens
Fab 8 LC CDRs	E	protein	217	Homo sapiens
Fab 8 HC CDRs	F	protein	229	Homo sapiens
Acy-phe-pro-asp-val-sar-leu-his-arg-tyr-trp-gly-trp-asp-cys-gly-NH2	Z	protein	17	synthetic construct

Sequence of entity 1 (A), FASTA

>7UJD_1 26S proteasome non-ATPase regulatory subunit 2 (chains A)
SRFPEALRLALMLNDMELVEDIFTSCKDVVVQKQMAFMLGRHGVFLELSEDVEEYEDLTE
IMSNVQLNSNFLALARELDIMEPKVPDDIYKTHLENNRFGGSGSQVDSARMNLASSFVNG
FVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILLWDVDGGLTQIDKYLYSSEDY
IKSGALLACGIVNSGVRNECDPALALLSDFVLHNSNTMRLGSIFGLGLAYAGSNREDVLT
LLLPVMGDSKSSMEVAGVTALACGMIAVGSCNGDVTSTILQTIMEKSETELKDTYARWLP
LGLGLNHLGKGEAIEAILAALEVVSEPFRSFANTLVDVCAYAGSGNVLKVQQLLHICSEH
FDSKEKEEDKDKKEKKDKDKKEAPADMGAHQGVAVLGIALIAMGEEIGAEMALRTFGHLL
RYGEPTLRRAVPLALALISVSNPRLNILDTLSKFSHDADPEVSYNSIFAMGMVGSGTNNA
RLAAMLRQLAQYHAKDPNNLFMVRLAQGLTHLGKGTLTLCPYHSDRQLMSQVAVAGLLTV
LVSFLDVRNIILGKSHYVLYGLVAAMQPRMLVTFDEELRPLPVSVRVGQAVDVVGQAGKP
KTITGFQTHTTPVLLAHGERAELATEEFLPVTPILEGFVILRKN

Sequence of entity 2 (C), FASTA

>7UJD_2 Fab 14 LC CDRs (chains C)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYYSYYYPVTFGQGTKVEIKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (D), FASTA

>7UJD_3 Fab 14 HC CDRs (chains D)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVYYYSIHWVRQAPGKGLEWVASIYPYYSY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYQSSSYGYGLDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 4 (E), FASTA

>7UJD_4 Fab 8 LC CDRs (chains E)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYYYSSSLVTFGQGTKVEIKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (F), FASTA

>7UJD_5 Fab 8 HC CDRs (chains F)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSSYSMHWVRQAPGKGLEWVAYIYPYSSY
TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARKYQWRGALDYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 6 (Z), FASTA

>7UJD_6 ACY-PHE-PRO-ASP-VAL-SAR-LEU-HIS-ARG-TYR-TRP-GLY-TRP-ASP-CYS-GLY-NH2 (chains Z)
XFPDVGLHRYWGWDCGX

Primary citation

Targeted degradation via direct 26S proteasome recruitment. Bashore, C., Prakash, S., Johnson, M.C. et al. Nat Chem Biol (2023) 19:55-63. DOI 10.1038/s41589-022-01218-w · PubMed

Other PDB entries of the same protein (UniProt Q13200 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9K53 2.5 Å, Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state ED2.1
8USD 2.7 Å, Rpn1/Nub1UBL-focused alignment of the non-substrate-engaged human 26S proteasome
8USB 2.73 Å, Non-substrate-engaged human 26S proteasome with Nub1/FAT10 bound to Rpn1
9MBP 2.75 Å, Substrate-engaged human 26S proteasome bound to midnolin with RPT1 at top of spiral…
9NKG 2.8 Å, Structure of substrate engaged MIDN-bound human 26S proteasome, EB-MIDN (Composite map)
9MBO 2.83 Å, Focused refinement of RPN1 and the C-terminal helix of midnolin in the substrate-engaged…
9E8I 2.87 Å, Human proteasome in resting state conformation bound to TXNL1 in Forward conformation
9BV3 2.9 Å, M1B Midnolin-Proteasome
9E8H 2.9 Å, Human proteasome in resting state conformation bound to TXNL1 in backward conformation
9K4J 2.9 Å, Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EA1.0
9NKF 2.9 Å, Structure of human substrate-free 26S proteasome in the presence of ATPgS and…
9U3L 2.91 Å, Substrate-engaged human 26S proteasome bound to midnolin with RPT2 at top of spiral…

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