8CVT: Human 19S-20S proteasome, state SD2

Human 19S-20S proteasome, state SD2. Determined by electron microscopy at 3.0 Å resolution. Released 2 Nov 2022.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 46
Atoms: 101,640
Mol. weight: 1668 kDa
Ligands: ZN, LDZ, ATP
Released: 2 Nov 2022

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

Secondary structure: helices and β-sheets

8CVT contains 622 α-helices and 528 β-strands across 46 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: 28 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-6	2
α-helix	7-11	5
α-helix	18-31	14
α-helix	34-36	3
α-helix	37-41	5
α-helix	42-46	5
α-helix	52-68	17
α-helix	72-87	16
α-helix	93-103	11
α-helix	108-125	18
α-helix	130-142	13
α-helix	150-165	16
α-helix	169-182	14
α-helix	190-199	10
α-helix	200-204	5
α-helix	205-206	2
α-helix	220-226	7
α-helix	231-238	8
α-helix	239-243	5
α-helix	247-256	10
α-helix	258-261	4
α-helix	265-283	19
α-helix	287-289	3
α-helix	293-299	7
α-helix	304-317	14
β-strand	324	1	134
α-helix	347-351	5
α-helix	355-370	16
α-helix	372-375	4

Chain A: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	48-71	24
α-helix	81-83	3
α-helix	85-90	6
α-helix	94-95	2
β-strand	97-101	5	1
β-strand	112-114	3	1
β-strand	120-122	3	1
β-strand	124-125	2	1
α-helix	126	1
β-strand	139-143	5	1
β-strand	148-152	5	1
α-helix	154-156	3
α-helix	159-164	6
β-strand	165	1	2
α-helix	181-191	11
α-helix	193-196	4
α-helix	198-203	6
β-strand	211-215	5	2
α-helix	222-232	11
β-strand	236-239	4	2
α-helix	242-245	4
α-helix	252-266	15
β-strand	270-275	6	2
α-helix	277-279	3
α-helix	293-306	14
β-strand	315-321	7	2
α-helix	329-332	4
β-strand	339-342	4	2
α-helix	348-360	13
β-strand	364	1	3
α-helix	370-376	7
α-helix	382-398	17
β-strand	404	1	3
α-helix	406-413	8
α-helix	414-419	6
β-strand	432	1	4

Chain b: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	10
β-strand	13	1	11
α-helix	14-17	4
α-helix	25-43	19
β-strand	48-53	6	10
β-strand	55	1	12
β-strand	65	1	10
α-helix	69-75	7
β-strand	81	1	11
α-helix	83	1
β-strand	84	1	12
α-helix	86-99	14
β-strand	106-113	8	10
α-helix	121-134	14
β-strand	137-142	6	10
α-helix	148-150	3
α-helix	151-160	10
β-strand	171	1	10
α-helix	172-174	3
α-helix	180-189	10

Chain B: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	67-82	16
α-helix	95-102	8
β-strand	107-111	5	5
β-strand	112	1	6
β-strand	121-122	2	7
β-strand	123	1	6
β-strand	132-133	2	7
β-strand	135	1	5
β-strand	149-153	5	5
β-strand	159	1	5
α-helix	163-164	2
α-helix	169-174	6
β-strand	175-176	2	8
α-helix	191-200	10
α-helix	202-206	5
α-helix	208-214	7
α-helix	216-219	4
β-strand	221-225	5	8
α-helix	232-241	10
β-strand	246-249	4	8
α-helix	252-254	3
α-helix	263-276	14
β-strand	280-285	6	8
α-helix	305-317	13
β-strand	325-331	7	8
β-strand	349-352	4	8
α-helix	354-356	3
α-helix	359-369	11
β-strand	374	1	9
α-helix	380-386	7
α-helix	392-408	17
β-strand	414	1	9
α-helix	416-426	11

Chain c: 17 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	15
α-helix	34	1
α-helix	35-47	13
β-strand	54-60	7	15
β-strand	66-73	8	15
α-helix	74-77	4
α-helix	84-86	3
α-helix	89-101	13
β-strand	110-114	5	15
α-helix	124-136	13
β-strand	142-145	4	15
β-strand	159-162	4	15
α-helix	166-168	3
α-helix	178-185	8
α-helix	191-195	5
β-strand	200-207	8	15
α-helix	208-209	2
α-helix	212-220	9
α-helix	221-225	5
α-helix	249-263	15
α-helix	265-272	8
α-helix	288-299	12
α-helix	302-303	2
α-helix	304-308	5

Chain C: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	25-35	11
α-helix	36-38	3
α-helix	39-62	24
α-helix	63-67	5
α-helix	69-70	2
β-strand	71-80	10	5
β-strand	84-89	6	5
β-strand	94-99	6	5
α-helix	100	1
β-strand	112-116	5	5
β-strand	123-127	5	5
α-helix	135-138	4
α-helix	143-146	4
α-helix	155-164	10
α-helix	166-170	5
α-helix	172-178	7
α-helix	181-183	3
β-strand	185-189	5	13
α-helix	196-205	10
β-strand	210-213	4	13
α-helix	229-233	5
α-helix	234-240	7
β-strand	244-247	4	13
α-helix	270-280	11
β-strand	289-293	5	13
α-helix	298-300	3
α-helix	303-306	4
β-strand	313-316	4	13
α-helix	318-321	4
α-helix	322-332	11
β-strand	338	1	14
α-helix	339	1
α-helix	344-350	7
α-helix	357-372	16
β-strand	378	1	14
α-helix	380-390	11

Chain d: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-32	17
α-helix	42-64	23
α-helix	69-83	15
α-helix	89-91	3
α-helix	93-108	16
α-helix	112-121	10
α-helix	123-126	4
α-helix	131-157	27
α-helix	164-172	9
α-helix	177-179	3
α-helix	191-193	3
α-helix	204-210	7
α-helix	212-214	3
α-helix	223-225	3
β-strand	227	1	17
β-strand	229	1	17
α-helix	239-256	18

Chain D: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	40-84	45
β-strand	87-94	8	5
β-strand	101-105	5	5
β-strand	110-113	4	5
β-strand	115	1	5
α-helix	121-124	4
β-strand	130-133	4	5
β-strand	139-142	4	5
α-helix	143-145	3
α-helix	171-180	10
α-helix	182-186	5
α-helix	188-194	7
β-strand	202-205	4	16
α-helix	212-222	11
α-helix	243-256	14
β-strand	261-264	4	16
α-helix	282-296	15
α-helix	301-303	3
β-strand	306-309	4	16
α-helix	319-322	4
β-strand	329-332	4	16
α-helix	334-336	3
α-helix	340-351	12
α-helix	360-365	6
α-helix	372-388	17
α-helix	396-406	11

38 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 proteasome regulatory subunit 7	A	protein	433	Homo sapiens	P35998 (AlphaFold model)
26S proteasome regulatory subunit 4	B	protein	440	Homo sapiens	P62191 (AlphaFold model)
26S protease regulatory subunit 8	C	protein	406	Homo sapiens	P62195 (AlphaFold model)
26S proteasome regulatory subunit 6B	D	protein	418	Homo sapiens	P43686 (AlphaFold model)
26S protease regulatory subunit 10B	E	protein	389	Homo sapiens	P62333
26S proteasome regulatory subunit 6A	F	protein	439	Homo sapiens	P17980
Proteasome subunit alpha type-6	G, g	protein	246	Homo sapiens	P60900
Proteasome subunit alpha type-2	H, h	protein	234	Homo sapiens	P25787
Proteasome subunit alpha type-4	I, i	protein	261	Homo sapiens	P25789
Proteasome subunit alpha type-7	J, j	protein	248	Homo sapiens	O14818
Proteasome subunit alpha type-5	K, k	protein	241	Homo sapiens	P28066
Proteasome subunit alpha type-1	L, l	protein	263	Homo sapiens	P25786

20 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8CVT_1 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 2 (B), FASTA

>8CVT_2 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Sequence of entity 3 (C), FASTA

>8CVT_3 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 4 (D), FASTA

>8CVT_4 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 5 (E), FASTA

>8CVT_5 26S protease regulatory subunit 10B (chains E)
MADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEV
LKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVY
NMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGK
TLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYARDHQPCIIFMDEIDAIGG
RRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLDPALLRPGRLDRKIH
IDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVCTEAGMFAIRADHD
FVVQEDFMKAVRKVADSKKLESKLDYKPV

Sequence of entity 6 (F), FASTA

>8CVT_6 26S proteasome regulatory subunit 6A (chains F)
MNLLPNIESPVTRQEKMATVWDEAEQDGIGEEVLKMSTEEIIQRTRLLDSEIKIMKSEVL
RVTHELQAMKDKIKENSEKIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGK
CAVIKTSTRQTYFLPVIGLVDAEKLKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDER
PTEQYSDIGGLDKQIQELVEAIVLPMNHKEKFENLGIQPPKGVLMYGPPGTGKTLLARAC
AAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPSIIFIDELDAIGTKRFDSEK
AGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSGRLDRKIEFPMPNEE
ARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKAVCVEAGMIALRRGATELTHEDY
MEGILEVQAKKKANLQYYA

Sequence of entity 7 (G, g), FASTA

>8CVT_7 Proteasome subunit alpha type-6 (chains G, g)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 8 (H, h), FASTA

>8CVT_8 Proteasome subunit alpha type-2 (chains H, h)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 9 (I, i), FASTA

>8CVT_9 Proteasome subunit alpha type-4 (chains I, i)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 10 (J, j), FASTA

>8CVT_10 Proteasome subunit alpha type-7 (chains J, j)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 11 (K, k), FASTA

>8CVT_11 Proteasome subunit alpha type-5 (chains K, k)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 12 (L, l), FASTA

>8CVT_12 Proteasome subunit alpha type-1 (chains L, l)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
LDZ	N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinami…	C26 H41 N3 O5	6
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4

Primary citation

Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins. Zhao, J., Makhija, S., Zhou, C. et al. Proc Natl Acad Sci U S A (2022) 119:e2207200119-e2207200119. DOI 10.1073/pnas.2207200119 · 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…

Browse structure collections

About this viewer

MolViewer shows 8CVT 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.