8USD: 26S proteasome non-ATPase regulatory subunit 2

Rpn1/Nub1UBL-focused alignment of the non-substrate-engaged human 26S proteasome. Determined by electron microscopy at 2.7 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,882
Mol. weight: 333.81 kDa
Released: 6 Nov 2024

Explore 8USD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8USD contains 57 α-helices and 19 β-strands across 5 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	42-63	22

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	45-47	3
α-helix	59-83	25

Chain f: 49 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	156-171	16
α-helix	183-197	15
α-helix	201-211	11
α-helix	218-220	3
α-helix	226-235	10
α-helix	237-239	3
α-helix	244-258	15
α-helix	262-272	11
α-helix	275-284	10
α-helix	288-301	14
α-helix	314-322	9
α-helix	326-336	11
α-helix	345-349	5
α-helix	351-353	3
α-helix	368-381	14
α-helix	396-401	6
α-helix	406-417	12
α-helix	424-429	6
α-helix	432-434	3
α-helix	438-451	14
α-helix	461-465	5
α-helix	467-469	3
α-helix	475-488	14
α-helix	495-501	7
α-helix	503-506	4
α-helix	512-525	14
α-helix	532-544	13
α-helix	547-550	4
α-helix	553-556	4
α-helix	557-565	9
α-helix	571-573	3
α-helix	574-579	6
α-helix	584	1
α-helix	587-599	13
α-helix	606-617	12
α-helix	648-661	14
α-helix	665-681	17
α-helix	684-687	4
α-helix	690-697	8
α-helix	704-712	9
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	790-802	13
α-helix	803-805	3
α-helix	809-813	5
α-helix	815-824	10
β-strand	826-827	2	1
β-strand	830-833	4	3
β-strand	839	1	3
β-strand	843-849	7	4
β-strand	862-869	8	4
α-helix	873-875	3
β-strand	878-882	5	4
β-strand	887-889	3	5
β-strand	896-899	4	3
β-strand	900-902	3	5

Chain g: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	83-88	6	6
β-strand	98-103	6	6
β-strand	108	1	7
α-helix	109-119	11
α-helix	124-126	3
β-strand	127-131	5	6
β-strand	134-135	2	6
β-strand	141	1	7
α-helix	143-145	3
β-strand	152-157	6	6
α-helix	164-171	8

Chain U: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	835-837	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
26S proteasome non-ATPase regulatory subunit 2	f	protein	908	Homo sapiens	Q13200 (AlphaFold model)
NEDD8 ultimate buster 1	g	protein	254	Homo sapiens	Q9Y5A7 (AlphaFold model)
26S proteasome regulatory subunit 7	A	protein	433	Homo sapiens	P35998 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 1	U	protein	953	Homo sapiens	Q99460 (AlphaFold model)
26S proteasome regulatory subunit 4	B	protein	440	Homo sapiens	P62191

Sequence of entity 1 (f), FASTA

>8USD_1 26S proteasome non-ATPase regulatory subunit 2 (chains f)
MEEGGRDKAPVQPQQSPAAAPGGTDEKPSGKERRDAGDKDKEQELSEEDKQLQDELEMLV
ERLGEKDTSLYRPALEELRRQIRSSTTSMTSVPKPLKFLRPHYGKLKEIYENMAPGENKR
FAADIISVLAMTMSGERECLKYRLVGSQEELASWGHEYVRHLAGEVAKEWQELDDAEKVQ
REPLLTLVKEIVPYNMAHNAEHEACDLLMEIEQVDMLEKDIDENAYAKVCLYLTSCVNYV
PEPENSALLRCALGVFRKFSRFPEALRLALMLNDMELVEDIFTSCKDVVVQKQMAFMLGR
HGVFLELSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPKVPDDIYKTHLENNRFGG
SGSQVDSARMNLASSFVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILLW
DVDGGLTQIDKYLYSSEDYIKSGALLACGIVNSGVRNECDPALALLSDYVLHNSNTMRLG
SIFGLGLAYAGSNREDVLTLLLPVMGDSKSSMEVAGVTALACGMIAVGSCNGDVTSTILQ
TIMEKSETELKDTYARWLPLGLGLNHLGKGEAIEAILAALEVVSEPFRSFANTLVDVCAY
AGSGNVLKVQQLLHICSEHFDSKEKEEDKDKKEKKDKDKKEAPADMGAHQGVAVLGIALI
AMGEEIGAEMALRTFGHLLRYGEPTLRRAVPLALALISVSNPRLNILDTLSKFSHDADPE
VSYNSIFAMGMVGSGTNNARLAAMLRQLAQYHAKDPNNLFMVRLAQGLTHLGKGTLTLCP
YHSDRQLMSQVAVAGLLTVLVSFLDVRNIILGKSHYVLYGLVAAMQPRMLVTFDEELRPL
PVSVRVGQAVDVVGQAGKPKTITGFQTHTTPVLLAHGERAELATEEFLPVTPILEGFVIL
RKNPNYDL

Sequence of entity 2 (g), FASTA

>8USD_2 NEDD8 ultimate buster 1 (chains g)
MAQNKYLQAKLTQFLREDRIQLWKPPYTDENKKVGLALKDLAKQYSDRLECCENEVEKVI
EEIRCKAIERGTGNDNYRTTGIATIEVFLPPRLKKDRKNLLETRLHITGRELRSKIAETF
GLQENYIKIVINKKQLQLGKTLEEQGVAHNVKAMVLELKQSEEDARKNFQLEEEEQNEAK
LKEKQIQRTKRGLEILAKRAAETVVDPEMTPYLDIANQTGRSIRIPPSERKALMLAMGYH
EKGRAFLKRKEYGI

Sequence of entity 3 (A), FASTA

>8USD_3 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 4 (U), FASTA

>8USD_4 26S proteasome non-ATPase regulatory subunit 1 (chains U)
MITSAAGIISLLDEDEPQLKEFALHKLNAVVNDFWAEISESVDKIEVLYEDEGFRSRQFA
ALVASKVFYHLGAFEESLNYALGAGDLFNVNDNSEYVETIIAKCIDHYTKQCVENADLPE
GEKKPIDQRLEGIVNKMFQRCLDDHKYKQAIGIALETRRLDVFEKTILESNDVPGMLAYS
LKLCMSLMQNKQFRNKVLRVLVKIYMNLEKPDFINVCQCLIFLDDPQAVSDILEKLVKED
NLLMAYQICFDLYESASQQFLSSVIQNLRTVGTPIASVPGSTNTGTVPGSEKDSDSMETE
EKTSSAFVGKTPEASPEPKDQTLKMIKILSGEMAIELHLQFLIRNNNTDLMILKNTKDAV
RNSVCHTATVIANSFMHCGTTSDQFLRDNLEWLARATNWAKFTATASLGVIHKGHEKEAL
QLMATYLPKDTSPGSAYQEGGGLYALGLIHANHGGDIIDYLLNQLKNASNDIVRHGGSLG
LGLAAMGTARQDVYDLLKTNLYQDDAVTGEAAGLALGLVMLGSKNAQAIEDMVGYAQETQ
HEKILRGLAVGIALVMYGRMEEADALIESLCRDKDPILRRSGMYTVAMAYCGSGNNKAIR
RLLHVAVSDVNDDVRRAAVESLGFILFRTPEQCPSVVSLLSESYNPHVRYGAAMALGICC
AGTGNKEAINLLEPMTNDPVNYVRQGALIASALIMIQQTEITCPKVNQFRQLYSKVINDK
HDDVMAKFGAILAQGILDAGGHNVTISLQSRTGHTHMPSVVGVLVFTQFWFWFPLSHFLS
LAYTPTCVIGLNKDLKMPKVQYKSNCKPSTFAYPAPLEVPKEKEKEKVSTAVLSITAKAK
KKEKEKEKKEEEKMEVDEAEKKEEKEKKKEPEPNFQLLDNPARVMPAQLKVLTMPETCRY
QPFKPLSIGGIIILKDTSEDIEELVEPVAAHGPKIEEEEQEPEPPEPFEYIDD

Sequence of entity 5 (B), FASTA

>8USD_5 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Primary citation

NUB1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome. Arkinson, C., Dong, K.C., Gee, C.L. et al. Nat Struct Mol Biol (2025) 32:1752-1765. DOI 10.1038/s41594-025-01527-3 · PubMed

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

7UJD 2.5 Å, PSMD2 Structure bound to MC1 and Fab8/14
9K53 2.5 Å, Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state ED2.1
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…

Browse structure collections

About this viewer

MolViewer shows 8USD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.