6MSD: 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 5 Dec 2018.

Method
Electron microscopy
Resolution
3.2 Å
Organism
Homo sapiens
Chains
48
Atoms
105,426
Mol. weight
1681.81 kDa
Ligands
ZN, ATP, ADP, MG
Released
5 Dec 2018

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

Secondary structure: helices and β-sheets

6MSD contains 634 α-helices and 542 β-strands across 48 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, 4 β-strands

ElementResiduesLengthSheet
α-helix5-106
α-helix20-289
α-helix29-313
α-helix38-414
α-helix43-464
α-helix52-554
α-helix57-6610
α-helix74-8714
α-helix90-10314
α-helix111-12111
α-helix130-1356
α-helix149-16416
α-helix170-17910
α-helix190-20617
α-helix224-2263
α-helix231-24212
α-helix247-2504
α-helix265-28319
β-strand292141
α-helix293-2997
α-helix304-31714
β-strand320-325615
β-strand330141
β-strand331-336615
α-helix345-37026
Chain A: 18 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix42-6019
α-helix79-824
β-strand97-98270
β-strand100-103471
β-strand111-114471
β-strand122-123271
β-strand124172
β-strand140-142370
β-strand148172
β-strand149-152470
α-helix154-1563
α-helix162-1643
β-strand165173
α-helix174-1763
α-helix181-19111
α-helix193-1964
α-helix207-2093
β-strand212-215473
α-helix222-23211
β-strand236-241673
α-helix242-2443
α-helix252-26615
β-strand270-275673
α-helix293-30412
β-strand315-321773
α-helix324-3263
β-strand339-342473
α-helix349-35810
β-strand364174
α-helix371-3744
α-helix382-39817
β-strand404174
α-helix406-41611
α-helix427-4304
Chain b: 8 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand4-9646
α-helix14-163
α-helix25-4319
β-strand50-52346
β-strand55147
α-helix69-746
β-strand84147
α-helix89-979
β-strand106-113846
α-helix121-13414
β-strand137-142646
α-helix154-1585
β-strand170-171246
α-helix172-1743
α-helix185-1895
Chain B: 19 helices, 17 β-strands
ElementResiduesLengthSheet
α-helix59-8527
α-helix94-1029
β-strand107-112677
β-strand116178
β-strand120178
β-strand123-124277
β-strand130-131277
β-strand134178
β-strand135177
β-strand149-152477
β-strand159-162477
α-helix171-1744
β-strand175179
α-helix184-1863
α-helix194-1974
α-helix198-2025
α-helix203-2064
α-helix210-2145
β-strand221-225579
α-helix232-24211
β-strand246-251679
α-helix252-2554
α-helix262-27514
β-strand280-285679
α-helix288-2903
α-helix302-31615
β-strand325-330679
α-helix339-3424
β-strand349-352479
α-helix355-3573
α-helix360-3689
β-strand374180
α-helix380-3845
α-helix392-40615
β-strand414180
α-helix416-42611
Chain c: 14 helices, 10 β-strands
ElementResiduesLengthSheet
β-strand31-32251
α-helix37-4711
β-strand54-61851
β-strand67-74851
β-strand77-79352
β-strand84-86352
α-helix90-10112
β-strand107-113751
α-helix126-1338
α-helix1401
β-strand141-144451
β-strand160-162351
α-helix165-1706
α-helix186-1883
α-helix189-1935
β-strand200-202351
β-strand205-206251
α-helix215-2217
α-helix234-24310
α-helix245-25511
α-helix269-2724
α-helix273-2753
α-helix280-2845
α-helix286-30823
Chain C: 23 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix21-3111
α-helix32-343
α-helix35-5925
α-helix62-643
α-helix69-702
β-strand71-73383
β-strand75-80677
β-strand84-89677
β-strand92-98777
β-strand113-116483
β-strand123-127583
α-helix133-1419
α-helix148-1503
α-helix155-1617
α-helix162-1665
α-helix167-1704
α-helix173-1764
α-helix181-1833
β-strand185-189584
α-helix196-20611
β-strand210-214584
α-helix220-2234
α-helix232-2343
α-helix235-2384
β-strand244-248584
α-helix268-27912
β-strand289-294684
α-helix298-3003
β-strand313-316484
α-helix318-3203
α-helix322-33211
β-strand338185
α-helix344-3507
α-helix359-37214
β-strand378185
α-helix380-39415
Chain d: 11 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix19-3214
α-helix49-5810
α-helix71-8212
α-helix95-10814
α-helix113-1164
α-helix117-1204
α-helix131-14414
α-helix149-1535
α-helix164-18118
α-helix205-2106
β-strand217157
β-strand222157
α-helix236-25419
Chain D: 17 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix40-6223
α-helix64-7815
α-helix79-824
β-strand87-91589
β-strand92-97683
β-strand100-104583
β-strand110-114583
α-helix121-1233
β-strand129-132489
β-strand139-142489
α-helix171-18111
α-helix183-1864
α-helix188-1947
β-strand201-205590
α-helix212-22110
β-strand227-231590
α-helix242-25615
β-strand261-265590
α-helix267-2693
α-helix281-29515
β-strand306-310590
β-strand329-332490
α-helix334-3363
α-helix341-3488
α-helix361-3644
α-helix375-38713
α-helix396-40611
α-helix415-4173

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
26S proteasome non-ATPase regulatory subunit 1Uprotein953Homo sapiensQ99460 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 3Vprotein534Homo sapiensO43242 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 12Wprotein456Homo sapiensO00232 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 11Xprotein422Homo sapiensO00231 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 6Yprotein389Homo sapiensQ15008
26S proteasome non-ATPase regulatory subunit 7Zprotein324Homo sapiensP51665
26S proteasome non-ATPase regulatory subunit 13aprotein376Homo sapiensQ9UNM6
26S proteasome non-ATPase regulatory subunit 4bprotein377Homo sapiensP55036
26S proteasome non-ATPase regulatory subunit 14cprotein309Homo sapiensO00487
26S proteasome non-ATPase regulatory subunit 8dprotein349Homo sapiensP48556
26S proteasome complex subunit SEM1eprotein70Homo sapiensP60896
26S proteasome non-ATPase regulatory subunit 2fprotein908Homo sapiensQ13200

21 more molecules are not listed.

Sequence of entity 1 (U), FASTA
>6MSD_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
>6MSD_2 26S proteasome non-ATPase regulatory subunit 3 (chains V)
MKQEGSARRRGADKAKPPPGGGEQEPPPPPAPQDVEMKEEAATGGGSTGEADGKTAAAAA
EHSQRELDTVTLEDIKEHVKQLEKAVSGKEPRFVLRALRMLPSTSRRLNHYVLYKAVQGF
FTSNNATRDFLLPFLEEPMDTEADLQFRPRTGKAASTPLLPEVEAYLQLLVVIFMMNSKR
YKEAQKISDDLMQKISTQNRRALDLVAAKCYYYHARVYEFLDKLDVVRSFLHARLRTATL
RHDADGQATLLNLLLRNYLHYSLYDQAEKLVSKSVFPEQANNNEWARYLYYTGRIKAIQL
EYSEARRTMTNALRKAPQHTAVGFKQTVHKLLIVVELLLGEIPDRLQFRQPSLKRSLMPY
FLLTQAVRTGNLAKFNQVLDQFGEKFQADGTYTLIIRLRHNVIKTGVRMISLSYSRISLA
DIAQKLQLDSPEDAEFIVAKAIRDGVIEASINHEKGYVQSKEMIDIYSTREPQLAFHQRI
SFCLDIHNMSVKAMRFPPKSYNKDLESAEERREREQQDLEFAKEMAEDDDDSFP
Sequence of entity 3 (W), FASTA
>6MSD_3 26S proteasome non-ATPase regulatory subunit 12 (chains W)
MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDM
VSTSRILVAVVKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPI
KLRLIDTLRMVTEGKIYVEIERARLTKTLATIKEQNGDVKEAASILQELQVETYGSMEKK
ERVEFILEQMRLCLAVKDYIRTQIISKKINTKFFQEENTEKLKLKYYNLMIQLDQHEGSY
LSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPFDNEQSDLVHRISGDKKLEEIP
KYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEKRWKDLKNRVVE
HNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPKD
PNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
Sequence of entity 4 (X), FASTA
>6MSD_4 26S proteasome non-ATPase regulatory subunit 11 (chains X)
MAAAAVVEFQRAQSLLSTDREASIDILHSIVKRDIQENDEEAVQVKEQSILELGSLLAKT
GQAAELGGLLKYVRPFLNSISKAKAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSE
KRTFLRQALEARLVSLYFDTKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHAL
SNLPKARAALTSARTTANAIYCPPKLQATLDMQSGIIHAAEEKDWKTAYSYFYEAFEGYD
SIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRYAGRQTEALKCVAQASKNRSLA
DFEKALTDYRAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEHISSLIKLSKAD
VERKLSQMILDKKFHGILDQGEGVLIIFDEPPVDKTYEAALETIQNMSKVVDSLYNKAKK
LT
Sequence of entity 5 (Y), FASTA
>6MSD_5 26S proteasome non-ATPase regulatory subunit 6 (chains Y)
MPLENLEEEGLPKNPDLRIAQLRFLLSLPEHRGDAAVRDELMAAVRDNNMAPYYEALCKS
LDWQIDVDLLNKMKKANEDELKRLDEELEDAEKNLGESEIRDAMMAKAEYLCRIGDKEGA
LTAFRKTYDKTVALGHRLDIVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRL
KVYQGLYCVAIRDFKQAAELFLDTVSTFTSYELMDYKTFVTYTVYVSMIALERPDLREKV
IKGAEILEVLHSLPAVRQYLFSLYECRYSVFFQSLAVVEQEMKKDWLFAPHYRYYVREMR
IHAYSQLLESYRSLTLGYMAEAFGVGVEFIDQELSRFIAAGRLHCKIDKVNEIVETNRPD
SKNWQYQETIKKGDLLLNRVQKLSRVINM
Sequence of entity 6 (Z), FASTA
>6MSD_6 26S proteasome non-ATPase regulatory subunit 7 (chains Z)
MPELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDE
DDKDDSVWFLDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSV
LVIIDVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIK
DTTVGTLSQRITNQVHGLKGLNSKLLDIRSYLEKVATGKLPINHQIIYQLQDVFNLLPDV
SLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLINNKIANRDAEKKEGQEKEESKKDR
KEDKEKDKDKEKSDVKKEEKKEKK
Sequence of entity 7 (a), FASTA
>6MSD_7 26S proteasome non-ATPase regulatory subunit 13 (chains a)
MKDVPGFLQQSQNSGPGQPAVWHRLEELYTKKLWHQLTLQVLDFVQDPCFAQGDGLIKLY
ENFISEFEHRVNPLSLVEIILHVVRQMTDPNVALTFLEKTREKVKSSDEAVILCKTAIGA
LKLNIGDLQVTKETIEDVEEMLNNLPGVTSVHSRFYDLSSKYYQTIGNHASYYKDALRFL
GCVDIKDLPVSEQQERAFTLGLAGLLGEGVFNFGELLMHPVLESLRNTDRQWLIDTLYAF
NSGNVERFQTLKTAWGQQPDLAANEAQLLRKIQLLCLMEMTFTRPANHRQLTFEEIAKSA
KITVNEVELLVMKALSVGLVKGSIDEVDKRVHMTWVQPRVLDLQQIKGMKDRLEFWCTDV
KSMEMLVEHQAHDILT
Sequence of entity 8 (b), FASTA
>6MSD_8 26S proteasome non-ATPase regulatory subunit 4 (chains b)
MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEV
LTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDN
EKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLA
DALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALRVSMEEQRQRQEEEARRAAA
ASAAEAGIATTGTEDSDDALLKMTISQQEFGRTGLPDLSSMTEEEQIAYAMQMSLQGAEF
GQAESADIDASSAMDTSEPAKEEDDYDVMQDPEFLQSVLENLPGVDPNNEAIRNAMGSLA
SQATKDGKKDKKEEDKK
Sequence of entity 9 (c), FASTA
>6MSD_9 26S proteasome non-ATPase regulatory subunit 14 (chains c)
DRLLRLGGGMPGLGQGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEF
VDDYTVRVIDVFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCW
LSGVDINTQQSFEALSERAVAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSNL
GHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLLNLHKKSWMEGLTLQDYSEHCKHN
ESVVKEMLELAKNYNKAVEEEDKMTPEQLAIKNVGKQDPKRHLEEHVDVLMTSNIVQCLA
AMLDTVVFK
Sequence of entity 10 (d), FASTA
>6MSD_10 26S proteasome non-ATPase regulatory subunit 8 (chains d)
FIKGRAPRAPPRERRRATRGGLRQVVAPPRALGSTSRPHFRRASVCRRRCRKSGGLLAAS
RKMAAAAVNGAAGFSSSGPAATSGAVLQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKL
VLLELNFLPTTGTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQ
LPESAYMHQLLGLNLLFLLSQNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSY
NKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTD
YAKKRGWVLGPNNYYSFASQQQKPEDTTIPSTELAKQVIEYARQLEMIV
Sequence of entity 11 (e), FASTA
>6MSD_11 26S proteasome complex subunit SEM1 (chains e)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS
Sequence of entity 12 (f), FASTA
>6MSD_12 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

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P34
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P22
MGMagnesium ionMg5

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:

Browse structure collections

About this viewer

MolViewer shows 6MSD 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.