6MSK: 26S proteasome non-ATPase regulatory subunit 1

Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Determined by electron microscopy at 3.2 Å resolution. Released 21 Nov 2018.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae RM11-1a
Chains: 47
Atoms: 105,222
Mol. weight: 1665.24 kDa
Ligands: ADP, MG, ATP, ZN
Released: 21 Nov 2018

Explore 6MSK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MSK contains 601 α-helices and 531 β-strands across 47 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: 23 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	18-28	11
α-helix	36-46	11
α-helix	52-54	3
α-helix	55-66	12
α-helix	73-87	15
α-helix	90-103	14
α-helix	111-120	10
α-helix	131-141	11
α-helix	150-160	11
α-helix	161-163	3
α-helix	170-182	13
α-helix	190-206	17
α-helix	220-223	4
α-helix	231-242	12
α-helix	249-256	8
α-helix	262-264	3
α-helix	265-275	11
α-helix	277-283	7
β-strand	291-292	2	16
α-helix	293-299	7
α-helix	304-306	3
α-helix	307-317	11
β-strand	323-324	2	16
β-strand	330-332	3	16
α-helix	344-370	27

Chain A: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	27-33	7
α-helix	42-63	22
α-helix	81-85	5
α-helix	86-88	3
β-strand	97-98	2	68
β-strand	100-103	4	69
β-strand	111-114	4	69
β-strand	121-123	3	69
β-strand	125	1	68
β-strand	140-142	3	68
β-strand	149-152	4	68
α-helix	154-158	5
α-helix	161-164	4
β-strand	165	1	70
α-helix	174-176	3
α-helix	183-190	8
α-helix	192-196	5
β-strand	211-215	5	70
α-helix	222-229	8
β-strand	236-239	4	70
α-helix	242-244	3
α-helix	252-266	15
β-strand	270-273	4	70
α-helix	293-304	12
β-strand	315-320	6	70
β-strand	339-342	4	70
α-helix	349-358	10
β-strand	364	1	71
α-helix	371-375	5
α-helix	382-398	17
β-strand	404	1	71
α-helix	406-416	11

Chain b: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	44
β-strand	13	1	45
α-helix	14-16	3
α-helix	25-43	19
β-strand	48-53	6	44
β-strand	62-65	4	44
α-helix	69-74	6
β-strand	82	1	45
α-helix	87-97	11
β-strand	106-113	8	44
α-helix	121-134	14
β-strand	137-142	6	44
α-helix	151-158	8
β-strand	171	1	44
α-helix	181-185	5

Chain B: 15 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
α-helix	59-82	24
α-helix	95-102	8
β-strand	107-114	8	75
β-strand	120-124	5	75
β-strand	131	1	68
β-strand	132-134	3	75
β-strand	135	1	76
β-strand	149-152	4	75
β-strand	159	1	76
β-strand	162	1	75
β-strand	175	1	77
α-helix	191-200	10
α-helix	202-206	5
α-helix	216-219	4
β-strand	221-225	5	77
α-helix	232-241	10
β-strand	247-251	5	77
α-helix	262-276	15
β-strand	281-285	5	77
α-helix	287-289	3
α-helix	301-317	17
β-strand	326-330	5	77
α-helix	339-342	4
β-strand	349-352	4	77
α-helix	361-367	7
β-strand	374	1	78
α-helix	381-386	6
α-helix	392-408	17
β-strand	414	1	78
α-helix	416-427	12
β-strand	439	1	79

Chain c: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	50
α-helix	35-47	13
β-strand	54-61	8	50
β-strand	66-74	9	50
α-helix	76-78	3
α-helix	84-86	3
α-helix	89-101	13
β-strand	108-114	7	50
α-helix	124-136	13
β-strand	141-145	5	50
β-strand	157-160	4	50
α-helix	189-192	4
β-strand	202	1	50
β-strand	205-207	3	50
α-helix	214-221	8
α-helix	226-229	4
α-helix	238-259	22
α-helix	267-272	6
α-helix	279-283	5
α-helix	286-308	23

Chain C: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
α-helix	22-66	45
α-helix	69-70	2
β-strand	71-76	6	75
β-strand	84	1	83
β-strand	87-88	2	75
β-strand	94-96	3	75
β-strand	98	1	83
β-strand	112-117	6	75
β-strand	122	1	83
β-strand	123-127	5	75
α-helix	155-161	7
α-helix	162-166	5
α-helix	167-170	4
α-helix	173-178	6
α-helix	181-183	3
β-strand	185-188	4	84
α-helix	198-206	9
β-strand	210-215	6	84
β-strand	223	1	85
α-helix	226-237	12
β-strand	244-249	6	84
α-helix	267-279	13
β-strand	289-294	6	84
α-helix	298-300	3
β-strand	313-315	3	84
α-helix	318-321	4
α-helix	322-332	11
β-strand	338	1	86
α-helix	344-348	5
α-helix	359-371	13
β-strand	378	1	86
α-helix	380-390	11
α-helix	400-404	5

Chain d: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	17-29	13
α-helix	46-65	20
α-helix	68-81	14
α-helix	95-108	14
α-helix	112-118	7
α-helix	119-121	3
α-helix	125-128	4
α-helix	131-144	14
α-helix	149-153	5
α-helix	164-182	19
α-helix	191-193	3
α-helix	194-198	5
α-helix	205-211	7
α-helix	239-253	15

Chain D: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	40-79	40
β-strand	88-97	10	90
β-strand	100-105	6	90
β-strand	111-112	2	75
β-strand	113-114	2	90
β-strand	129-132	4	90
β-strand	139-142	4	90
α-helix	143-145	3
β-strand	153-154	2	91
α-helix	164-166	3
α-helix	171-180	10
α-helix	182-186	5
α-helix	189-194	6
β-strand	201-205	5	91
α-helix	213-221	9
β-strand	226-230	5	91
α-helix	242-255	14
β-strand	260-264	5	91
α-helix	283-294	12
β-strand	305-311	7	91
β-strand	329-332	4	91
α-helix	341-350	10
α-helix	372-387	16
α-helix	399-406	8
α-helix	413-415	3

32 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 non-ATPase regulatory subunit 1	U	protein	953	Homo sapiens	Q99460 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 3	V	protein	533	Homo sapiens	O43242 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 12	W	protein	456	Homo sapiens	O00232 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 11	X	protein	422	Homo sapiens	O00231 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 6	Y	protein	389	Homo sapiens	Q15008
26S proteasome non-ATPase regulatory subunit 7	Z	protein	324	Homo sapiens	P51665
26S proteasome non-ATPase regulatory subunit 13	a	protein	376	Homo sapiens	Q9UNM6
26S proteasome non-ATPase regulatory subunit 4	b	protein	377	Homo sapiens	P55036
26S proteasome non-ATPase regulatory subunit 14	c	protein	309	Homo sapiens	O00487
26S proteasome non-ATPase regulatory subunit 8	d	protein	349	Homo sapiens	P48556
26S proteasome complex subunit SEM1	e	protein	70	Homo sapiens	P60896
26S proteasome non-ATPase regulatory subunit 2	f	protein	892	Homo sapiens	Q13200

21 more molecules are not listed.

Sequence of entity 1 (U), FASTA

>6MSK_1 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 2 (V), FASTA

>6MSK_2 26S proteasome non-ATPase regulatory subunit 3 (chains V)
KQEGSARRRGADKAKPPPGGGEQEPPPPPAPQDVEMKEEAATGGGSTGEADGKTAAAAAE
HSQRELDTVTLEDIKEHVKQLEKAVSGKEPRFVLRALRMLPSTSRRLNHYVLYKAVQGFF
TSNNATRDFLLPFLEEPMDTEADLQFRPRTGKAASTPLLPEVEAYLQLLVVIFMMNSKRY
KEAQKISDDLMQKISTQNRRALDLVAAKCYYYHARVYEFLDKLDVVRSFLHARLRTATLR
HDADGQATLLNLLLRNYLHYSLYDQAEKLVSKSVFPEQANNNEWARYLYYTGRIKAIQLE
YSEARRTMTNALRKAPQHTAVGFKQTVHKLLIVVELLLGEIPDRLQFRQPSLKRSLMPYF
LLTQAVRTGNLAKFNQVLDQFGEKFQADGTYTLIIRLRHNVIKTGVRMISLSYSRISLAD
IAQKLQLDSPEDAEFIVAKAIRDGVIEASINHEKGYVQSKEMIDIYSTREPQLAFHQRIS
FCLDIHNMSVKAMRFPPKSYNKDLESAEERREREQQDLEFAKEMAEDDDDSFP

Sequence of entity 3 (W), FASTA

>6MSK_3 26S proteasome non-ATPase regulatory subunit 12 (chains W)
MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDM
VSTSRILVAVVKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPI
KLRLIDTLRMVTEGKIYVEIERARLTKTLATIKEQNGDVKEAASILQELQVETYGSMEKK
ERVEFILEQMRLCLAVKDYIRTQIISKKINTKFFQEENTEKLKLKYYNLMIQLDQHEGSY
LSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPFDNEQSDLVHRISGDKKLEEIP
KYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEKRWKDLKNRVVE
HNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPKD
PNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ

Sequence of entity 4 (X), FASTA

>6MSK_4 26S proteasome non-ATPase regulatory subunit 11 (chains X)
MAAAAVVEFQRAQSLLSTDREASIDILHSIVKRDIQENDEEAVQVKEQSILELGSLLAKT
GQAAELGGLLKYVRPFLNSISKAKAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSE
KRTFLRQALEARLVSLYFDTKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHAL
SNLPKARAALTSARTTANAIYCPPKLQATLDMQSGIIHAAEEKDWKTAYSYFYEAFEGYD
SIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRYAGRQTEALKCVAQASKNRSLA
DFEKALTDYRAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEHISSLIKLSKAD
VERKLSQMILDKKFHGILDQGEGVLIIFDEPPVDKTYEAALETIQNMSKVVDSLYNKAKK
LT

Sequence of entity 5 (Y), FASTA

>6MSK_5 26S proteasome non-ATPase regulatory subunit 6 (chains Y)
MPLENLEEEGLPKNPDLRIAQLRFLLSLPEHRGDAAVRDELMAAVRDNNMAPYYEALCKS
LDWQIDVDLLNKMKKANEDELKRLDEELEDAEKNLGESEIRDAMMAKAEYLCRIGDKEGA
LTAFRKTYDKTVALGHRLDIVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRL
KVYQGLYCVAIRDFKQAAELFLDTVSTFTSYELMDYKTFVTYTVYVSMIALERPDLREKV
IKGAEILEVLHSLPAVRQYLFSLYECRYSVFFQSLAVVEQEMKKDWLFAPHYRYYVREMR
IHAYSQLLESYRSLTLGYMAEAFGVGVEFIDQELSRFIAAGRLHCKIDKVNEIVETNRPD
SKNWQYQETIKKGDLLLNRVQKLSRVINM

Sequence of entity 6 (Z), FASTA

>6MSK_6 26S proteasome non-ATPase regulatory subunit 7 (chains Z)
MPELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDE
DDKDDSVWFLDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSV
LVIIDVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIK
DTTVGTLSQRITNQVHGLKGLNSKLLDIRSYLEKVATGKLPINHQIIYQLQDVFNLLPDV
SLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLINNKIANRDAEKKEGQEKEESKKDR
KEDKEKDKDKEKSDVKKEEKKEKK

Sequence of entity 7 (a), FASTA

>6MSK_7 26S proteasome non-ATPase regulatory subunit 13 (chains a)
MKDVPGFLQQSQNSGPGQPAVWHRLEELYTKKLWHQLTLQVLDFVQDPCFAQGDGLIKLY
ENFISEFEHRVNPLSLVEIILHVVRQMTDPNVALTFLEKTREKVKSSDEAVILCKTAIGA
LKLNIGDLQVTKETIEDVEEMLNNLPGVTSVHSRFYDLSSKYYQTIGNHASYYKDALRFL
GCVDIKDLPVSEQQERAFTLGLAGLLGEGVFNFGELLMHPVLESLRNTDRQWLIDTLYAF
NSGNVERFQTLKTAWGQQPDLAANEAQLLRKIQLLCLMEMTFTRPANHRQLTFEEIAKSA
KITVNEVELLVMKALSVGLVKGSIDEVDKRVHMTWVQPRVLDLQQIKGMKDRLEFWCTDV
KSMEMLVEHQAHDILT

Sequence of entity 8 (b), FASTA

>6MSK_8 26S proteasome non-ATPase regulatory subunit 4 (chains b)
MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEV
LTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDN
EKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLA
DALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALRVSMEEQRQRQEEEARRAAA
ASAAEAGIATTGTEDSDDALLKMTISQQEFGRTGLPDLSSMTEEEQIAYAMQMSLQGAEF
GQAESADIDASSAMDTSEPAKEEDDYDVMQDPEFLQSVLENLPGVDPNNEAIRNAMGSLA
SQATKDGKKDKKEEDKK

Sequence of entity 9 (c), FASTA

>6MSK_9 26S proteasome non-ATPase regulatory subunit 14 (chains c)
DRLLRLGGGMPGLGQGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEF
VDDYTVRVIDVFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCW
LSGVDINTQQSFEALSERAVAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSNL
GHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLLNLHKKSWMEGLTLQDYSEHCKHN
ESVVKEMLELAKNYNKAVEEEDKMTPEQLAIKNVGKQDPKRHLEEHVDVLMTSNIVQCLA
AMLDTVVFK

Sequence of entity 10 (d), FASTA

>6MSK_10 26S proteasome non-ATPase regulatory subunit 8 (chains d)
FIKGRAPRAPPRERRRATRGGLRQVVAPPRALGSTSRPHFRRASVCRRRCRKSGGLLAAS
RKMAAAAVNGAAGFSSSGPAATSGAVLQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKL
VLLELNFLPTTGTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQ
LPESAYMHQLLGLNLLFLLSQNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSY
NKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTD
YAKKRGWVLGPNNYYSFASQQQKPEDTTIPSTELAKQVIEYARQLEMIV

Sequence of entity 11 (e), FASTA

>6MSK_11 26S proteasome complex subunit SEM1 (chains e)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS

Sequence of entity 12 (f), FASTA

>6MSK_12 26S proteasome non-ATPase regulatory subunit 2 (chains f)
MEEGGRDKAPVQPQQSPAAAPGGTDEKPSGKERRDAGDKDKEQELSEEDKQLQDELEMLV
ERLGEKDTSLYRPALEELRRQIRSSTTSMTSVPKPLKFLRPHYGKLKEIYENMAPGENKR
FAADIISVLAMTMSGERECLKYRLVGSQEELASWGHEYVRHLAGEVAKEWQELDDAEKVQ
REPLLTLVKEIVPYNMAHNAEHEACDLLMEIEQVDMLEKDIDENAYAKVCLYLTSCVNYV
PEPENSALLRCALGVFRKFSRFPEALRLALMLNDMELVEDIFTSCKDVVVQKQMAFMLGR
HGVFLELSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPKVPDDIYKTHLENNRFGG
SGSQVDSARMNLASSFVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILLW
DVDGGLTQIDKYLYSSEDYIKSGALLACGIVNSGVRNECDPALALLSDYVLHNSNTMRLG
SIFGLGLAYAGSNREDVLTLLLPVMGDSKSSMEVAGVTALACGMIAVGSCNGDVTSTILQ
TIMEKSETELKDTYARWLPLGLGLNHLGKGEAIEAILAALEVVSEPFRSFANTLVDVCAY
AGSGNVLKVQQLLHICSEHFDSKEKEEDKDKKEKKDKDKKEAPADMGAHQGVAVLGIALI
AMGEEIGAEMALRTFGHLLRYGEPTLRRAVPLALALISVSNPRLNILDTLSKFSHDADPE
VSYNSIFAMGMVGSGTNNARLAAMLRQLAQYHAKDPNNLFMVRLAQGLTHLGKGTLTLCP
YHSDRQLMSQVAVAGLLTVLVSFLDVRNIILGKSHYVLYGLVAAMQPRMLVTFDEELRPL
PVSVRVGQAVDVVGQAGKPKTITGFQTHTTPVLLAHGERAELATEEFLPVTP

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	5
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
ZN	Zinc ion	Zn	1

Primary citation

Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Dong, Y., Zhang, S., Wu, Z. et al. Nature (2019) 565:49-55. DOI 10.1038/s41586-018-0736-4 · PubMed

Other PDB entries of the same protein (UniProt Q99460 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex
6OI4 1.76 Å, RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex
5V1Z 2.0 Å, Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex
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)
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

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