8K0G: Human 26S RP

Cryo-EM structure of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub. Determined by electron microscopy at 3.8 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae
Chains: 30
Atoms: 68,848
Mol. weight: 1142.3 kDa
Ligands: ATP, MG, ADP
Released: 22 Jan 2025

Explore 8K0G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K0G contains 465 α-helices and 269 β-strands across 29 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: 21 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	21-31	11
α-helix	34-45	12
α-helix	54-68	15
α-helix	73-86	14
α-helix	90-103	14
α-helix	108-123	16
α-helix	131-143	13
α-helix	152-163	12
α-helix	166-168	3
α-helix	169-180	12
α-helix	190-205	16
α-helix	216-218	3
α-helix	220-224	5
α-helix	232-242	11
α-helix	249-256	8
α-helix	265-283	19
β-strand	290-292	3	50
α-helix	293-300	8
α-helix	304-306	3
α-helix	307-317	11
β-strand	323-325	3	50
β-strand	330-332	3	50
α-helix	343-375	33

Chain A: 23 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	27-33	7
α-helix	43-61	19
α-helix	72-74	3
α-helix	75-78	4
α-helix	81	1
α-helix	82-86	5
α-helix	87-90	4
β-strand	97-101	5	1
β-strand	111-114	4	1
β-strand	120-123	4	1
β-strand	125	1	1
β-strand	139-142	4	1
β-strand	149-152	4	1
α-helix	154-156	3
α-helix	159-162	4
β-strand	165	1	2
α-helix	174-176	3
α-helix	181-196	16
α-helix	200-204	5
β-strand	211-215	5	2
α-helix	222-229	8
β-strand	236-239	4	2
α-helix	253-266	14
β-strand	270-273	4	2
α-helix	277-280	4
α-helix	293-306	14
β-strand	315-320	6	2
α-helix	324-326	3
α-helix	329-332	4
β-strand	339-342	4	2
α-helix	349-358	10
β-strand	364	1	3
α-helix	371-375	5
α-helix	382-398	17
β-strand	404	1	3
α-helix	406-413	8
α-helix	414-418	5

Chain b: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	64
β-strand	13	1	65
α-helix	14-17	4
α-helix	25-42	18
β-strand	48-53	6	64
β-strand	59-65	7	64
α-helix	69-75	7
β-strand	82	1	65
α-helix	86-97	12
β-strand	106-113	8	64
α-helix	121-134	14
β-strand	137-142	6	64
α-helix	146-160	15
β-strand	170-171	2	64
α-helix	180-183	4

Chain B: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	59-84	26
α-helix	96-102	7
β-strand	108-117	10	1
β-strand	120-124	5	1
β-strand	130-131	2	1
β-strand	135	1	1
β-strand	149-152	4	1
β-strand	159-162	4	1
β-strand	175	1	6
α-helix	184-186	3
α-helix	191-197	7
α-helix	198-202	5
α-helix	203-206	4
α-helix	210-214	5
α-helix	217-219	3
β-strand	221-225	5	6
α-helix	232-241	10
β-strand	247-251	5	6
α-helix	262-276	15
β-strand	281-285	5	6
α-helix	287-289	3
α-helix	300-316	17
β-strand	326-330	5	6
α-helix	339-342	4
β-strand	349-352	4	6
α-helix	354-356	3
α-helix	358-368	11
α-helix	380-386	7
α-helix	392-408	17
α-helix	416-425	10
β-strand	439	1	7

Chain c: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	66
α-helix	35-47	13
β-strand	54-63	10	66
β-strand	66-74	9	66
β-strand	77	1	67
β-strand	80	1	68
β-strand	83	1	68
β-strand	84-85	2	69
β-strand	86	1	67
α-helix	90-100	11
β-strand	108-114	7	66
α-helix	124-136	13
β-strand	142-146	5	66
β-strand	156-162	7	66
α-helix	165-169	5
α-helix	186-188	3
α-helix	189-193	5
β-strand	196	1	66
β-strand	200-202	3	66
β-strand	205-206	2	66
α-helix	215-218	4
α-helix	226-229	4
α-helix	235-257	23
α-helix	267-273	7
α-helix	279	1
α-helix	280-284	5
α-helix	285-308	24

Chain C: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	29-66	38
β-strand	71-79	9	1
β-strand	85-89	5	1
β-strand	95-97	3	1
β-strand	98	1	18
α-helix	105-107	3
β-strand	113-117	5	1
β-strand	122	1	18
β-strand	123-127	5	1
α-helix	128-130	3
α-helix	155-165	11
α-helix	167-170	4
α-helix	172-176	5
α-helix	177-179	3
β-strand	186-189	4	19
α-helix	196-205	10
β-strand	210-211	2	20
α-helix	226-240	15
β-strand	244-247	4	20
α-helix	251-253	3
α-helix	268-281	14
α-helix	285-286	2
β-strand	289-292	4	20
β-strand	293-295	3	19
α-helix	298-300	3
β-strand	313-316	4	19
α-helix	318-320	3
α-helix	322-332	11
α-helix	344-349	6
α-helix	358-372	15
α-helix	380-390	11
α-helix	400-403	4
β-strand	405	1	21

Chain d: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	17-29	13
α-helix	42-65	24
α-helix	68-82	15
α-helix	95-108	14
α-helix	113-116	4
α-helix	119-121	3
α-helix	131-144	14
α-helix	149-154	6
α-helix	164-181	18
α-helix	191-196	6
α-helix	206-212	7
α-helix	239-253	15

Chain D: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	40-80	41
β-strand	88-97	10	1
β-strand	100-105	6	1
β-strand	108-113	6	1
β-strand	115	1	1
β-strand	129-132	4	1
β-strand	139-142	4	1
α-helix	143-145	3
β-strand	153	1	10
α-helix	171-194	24
β-strand	201-205	5	10
α-helix	213-222	10
β-strand	226-230	5	10
α-helix	232-235	4
α-helix	242-256	15
β-strand	260-264	5	10
α-helix	282-296	15
β-strand	307-311	5	10
α-helix	319-322	4
β-strand	329-332	4	10
α-helix	338-350	13
α-helix	361-364	4
α-helix	372-388	17
α-helix	399-407	9
α-helix	412-414	3

21 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
26S protease regulatory subunit 7	A	protein	433	Homo sapiens	P35998 (AlphaFold model)
26S protease regulatory subunit 4	B	protein	440	Homo sapiens	P62191 (AlphaFold model)
26S protease regulatory subunit 6B	D	protein	418	Homo sapiens	P43686 (AlphaFold model)
26S protease regulatory subunit 6A	F	protein	439	Homo sapiens	P17980 (AlphaFold model)
26S protease regulatory subunit 8	C	protein	406	Homo sapiens	P62195
Proteasome subunit alpha type-6	G	protein	246	Homo sapiens	P60900
Proteasome subunit alpha type-2	H	protein	234	Homo sapiens	P25787
Proteasome subunit alpha type-4	I	protein	261	Homo sapiens	P25789
Proteasome subunit alpha type-7	J	protein	248	Homo sapiens	O14818
Proteasome subunit alpha type-5	K	protein	241	Homo sapiens	P28066
Proteasome subunit alpha type-1	L	protein	263	Homo sapiens	P25786
Proteasome subunit alpha type-3	M	protein	255	Homo sapiens	P25788

15 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8K0G_1 26S protease regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 2 (B), FASTA

>8K0G_2 26S protease regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Sequence of entity 3 (D), FASTA

>8K0G_3 26S protease regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 4 (F), FASTA

>8K0G_4 26S protease regulatory subunit 6A (chains F)
MNLLPNIESPVTRQEKMATVWDEAEQDGIGEEVLKMSTEEIIQRTRLLDSEIKIMKSEVL
RVTHELQAMKDKIKENSEKIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGK
CAVIKTSTRQTYFLPVIGLVDAEKLKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDER
PTEQYSDIGGLDKQIQELVEAIVLPMNHKEKFENLGIQPPKGVLMYGPPGTGKTLLARAC
AAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPSIIFIDELDAIGTKRFDSEK
AGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSGRLDRKIEFPMPNEE
ARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKAVCVEAGMIALRRGATELTHEDY
MEGILEVQAKKKANLQYYA

Sequence of entity 5 (C), FASTA

>8K0G_5 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 6 (G), FASTA

>8K0G_6 Proteasome subunit alpha type-6 (chains G)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 7 (H), FASTA

>8K0G_7 Proteasome subunit alpha type-2 (chains H)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 8 (I), FASTA

>8K0G_8 Proteasome subunit alpha type-4 (chains I)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 9 (J), FASTA

>8K0G_9 Proteasome subunit alpha type-7 (chains J)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 10 (K), FASTA

>8K0G_10 Proteasome subunit alpha type-5 (chains K)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 11 (L), FASTA

>8K0G_11 Proteasome subunit alpha type-1 (chains L)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 12 (M), FASTA

>8K0G_12 Proteasome subunit alpha type-3 (chains M)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3
MG	Magnesium ion	Mg	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

Primary citation

Structural basis of K11/K48-branched ubiquitin chain recognition by the human 26S proteasome. Draczkowski, P., Chen, S.N., Chen, T. et al. Nat Commun (2025) 16:9094-9094. DOI 10.1038/s41467-025-64719-x · PubMed

Other PDB entries of the same protein (UniProt P35998 (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…
9PDL 2.76 Å, Nub1/Fat10-processing human 26S proteasome with Rpt5 at top of spiral staircase (AAA+…
9NKG 2.8 Å, Structure of substrate engaged MIDN-bound human 26S proteasome, EB-MIDN (Composite map)
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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