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- EMDB-76283: Unknown entry -

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Basic information

Entry
Database: EMDB / ID: EMD-76283
TitleHuman 19S proteasome bound to TXNL1 PITH domain state 2
Map data
Sample
  • Complex: Human proteasome from HCT116 cells
    • Protein or peptide: x 19 types
  • Ligand: x 4 types
KeywordsProteasome / 19S / RP / TXNL1 / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsChen X / Negi H / Walters KJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIABC011490 United States
CitationJournal: To Be Published
Title: Structures of dynamic interactors at native proteasomes by PhIX-MS and cryo-electron microscopy
Authors: Lee K / Negi H / Chen X / Atallah-Yunes K / Truslow S / Castelino RE / Guest M / Ciancone AM / Tarasov SG / Chari R / Walters KJ / O'Reilly FJ
History
DepositionMar 25, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76283.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.123623006 - 0.26104233
Average (Standard dev.)-0.0002086809 (±0.011610329)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 349.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human proteasome from HCT116 cells

EntireName: Human proteasome from HCT116 cells
Components
  • Complex: Human proteasome from HCT116 cells
    • Protein or peptide: 26S proteasome regulatory subunit 7
    • Protein or peptide: 26S proteasome regulatory subunit 4
    • Protein or peptide: 26S protease regulatory subunit 8
    • Protein or peptide: 26S proteasome regulatory subunit 6B
    • Protein or peptide: 26S protease regulatory subunit 10B
    • Protein or peptide: 26S proteasome regulatory subunit 6A
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 1
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 3
    • Protein or peptide: RPN5
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 11
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 6
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 7
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 13
    • Protein or peptide: RPN10
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 14
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 8
    • Protein or peptide: 26S proteasome complex subunit SEM1
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 2
    • Protein or peptide: Thioredoxin-like protein 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Human proteasome from HCT116 cells

SupramoleculeName: Human proteasome from HCT116 cells / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: 26S proteasome regulatory subunit 7

MacromoleculeName: 26S proteasome regulatory subunit 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.700805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPDYLGADQR KTKEDEKDDK PIRALDEGDI ALLKTYGQST YSRQIKQVED DIQQLLKKIN ELTGIKESDT GLAPPALWDL AADKQTLQS EQPLQVARCT KIINADSEDP KYIINVKQFA KFVVDLSDQV APTDIEEGMR VGVDRNKYQI HIPLPPKIDP T VTMMQVEE ...String:
MPDYLGADQR KTKEDEKDDK PIRALDEGDI ALLKTYGQST YSRQIKQVED DIQQLLKKIN ELTGIKESDT GLAPPALWDL AADKQTLQS EQPLQVARCT KIINADSEDP KYIINVKQFA KFVVDLSDQV APTDIEEGMR VGVDRNKYQI HIPLPPKIDP T VTMMQVEE KPDVTYSDVG GCKEQIEKLR EVVETPLLHP ERFVNLGIEP PKGVLLFGPP GTGKTLCARA VANRTDACFI RV IGSELVQ KYVGEGARMV RELFEMARTK KACLIFFDEI DAIGGARFDD GAGGDNEVQR TMLELINQLD GFDPRGNIKV LMA TNRPDT LDPALMRPGR LDRKIEFSLP DLEGRTHIFK IHARSMSVER DIRFELLARL CPNSTGAEIR SVCTEAGMFA IRAR RKIAT EKDFLEAVNK VIKSYAKFSA TPRYMTYN

UniProtKB: 26S proteasome regulatory subunit 7

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Macromolecule #2: 26S proteasome regulatory subunit 4

MacromoleculeName: 26S proteasome regulatory subunit 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.260504 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQSQSGGHG PGGGKKDDKD KKKKYEPPVP TRVGKKKKKT KGPDAASKLP LVTPHTQCRL KLLKLERIKD YLLMEEEFIR NQEQMKPLE EKQEEERSKV DDLRGTPMSV GTLEEIIDDN HAIVSTSVGS EHYVSILSFV DKDLLEPGCS VLLNHKVHAV I GVLMDDTD ...String:
MGQSQSGGHG PGGGKKDDKD KKKKYEPPVP TRVGKKKKKT KGPDAASKLP LVTPHTQCRL KLLKLERIKD YLLMEEEFIR NQEQMKPLE EKQEEERSKV DDLRGTPMSV GTLEEIIDDN HAIVSTSVGS EHYVSILSFV DKDLLEPGCS VLLNHKVHAV I GVLMDDTD PLVTVMKVEK APQETYADIG GLDNQIQEIK ESVELPLTHP EYYEEMGIKP PKGVILYGPP GTGKTLLAKA VA NQTSATF LRVVGSELIQ KYLGDGPKLV RELFRVAEEH APSIVFIDEI DAIGTKRYDS NSGGEREIQR TMLELLNQLD GFD SRGDVK VIMATNRIET LDPALIRPGR IDRKIEFPLP DEKTKKRIFQ IHTSRMTLAD DVTLDDLIMA KDDLSGADIK AICT EAGLM ALRERRMKVT NEDFKKSKEN VLYKKQEGTP EGLYL

UniProtKB: 26S proteasome regulatory subunit 4

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Macromolecule #3: 26S protease regulatory subunit 8

MacromoleculeName: 26S protease regulatory subunit 8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.694047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALDGPEQME LEEGKAGSGL RQYYLSKIEE LQLIVNDKSQ NLRRLQAQRN ELNAKVRLLR EELQLLQEQG SYVGEVVRAM DKKKVLVKV HPEGKFVVDV DKNIDINDVT PNCRVALRND SYTLHKILPN KVDPLVSLMM VEKVPDSTYE MIGGLDKQIK E IKEVIELP ...String:
MALDGPEQME LEEGKAGSGL RQYYLSKIEE LQLIVNDKSQ NLRRLQAQRN ELNAKVRLLR EELQLLQEQG SYVGEVVRAM DKKKVLVKV HPEGKFVVDV DKNIDINDVT PNCRVALRND SYTLHKILPN KVDPLVSLMM VEKVPDSTYE MIGGLDKQIK E IKEVIELP VKHPELFEAL GIAQPKGVLL YGPPGTGKTL LARAVAHHTD CTFIRVSGSE LVQKFIGEGA RMVRELFVMA RE HAPSIIF MDEIDSIGSS RLEGGSGGDS EVQRTMLELL NQLDGFEATK NIKVIMATNR IDILDSALLR PGRIDRKIEF PPP NEEARL DILKIHSRKM NLTRGINLRK IAELMPGASG AEVKGVCTEA GMYALRERRV HVTQEDFEMA VAKVMQKDSE KNMS IKKLW K

UniProtKB: 26S proteasome regulatory subunit 8

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Macromolecule #4: 26S proteasome regulatory subunit 6B

MacromoleculeName: 26S proteasome regulatory subunit 6B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.426141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEIGILVEK AQDEIPALSV SRPQTGLSFL GPEPEDLEDL YSRYKKLQQE LEFLEVQEEY IKDEQKNLKK EFLHAQEEVK RIQSIPLVI GQFLEAVDQN TAIVGSTTGS NYYVRILSTI DRELLKPNAS VALHKHSNAL VDVLPPEADS SIMMLTSDQK P DVMYADIG ...String:
MEEIGILVEK AQDEIPALSV SRPQTGLSFL GPEPEDLEDL YSRYKKLQQE LEFLEVQEEY IKDEQKNLKK EFLHAQEEVK RIQSIPLVI GQFLEAVDQN TAIVGSTTGS NYYVRILSTI DRELLKPNAS VALHKHSNAL VDVLPPEADS SIMMLTSDQK P DVMYADIG GMDIQKQEVR EAVELPLTHF ELYKQIGIDP PRGVLMYGPP GCGKTMLAKA VAHHTTAAFI RVVGSEFVQK YL GEGPRMV RDVFRLAKEN APAIIFIDEI DAIATKRFDA QTGADREVQR ILLELLNQMD GFDQNVNVKV IMATNRADTL DPA LLRPGR LDRKIEFPLP DRRQKRLIFS TITSKMNLSE EVDLEDYVAR PDKISGADIN SICQESGMLA VRENRYIVLA KDFE KAYKT VIKKDEQEHE FYK

UniProtKB: 26S proteasome regulatory subunit 6B

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Macromolecule #5: 26S protease regulatory subunit 10B

MacromoleculeName: 26S protease regulatory subunit 10B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.241008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADPRDKALQ DYRKKLLEHK EIDGRLKELR EQLKELTKQY EKSENDLKAL QSVGQIVGEV LKQLTEEKFI VKATNGPRYV VGCRRQLDK SKLKPGTRVA LDMTTLTIMR YLPREVDPLV YNMSHEDPGN VSYSEIGGLS EQIRELREVI ELPLTNPELF Q RVGIIPPK ...String:
MADPRDKALQ DYRKKLLEHK EIDGRLKELR EQLKELTKQY EKSENDLKAL QSVGQIVGEV LKQLTEEKFI VKATNGPRYV VGCRRQLDK SKLKPGTRVA LDMTTLTIMR YLPREVDPLV YNMSHEDPGN VSYSEIGGLS EQIRELREVI ELPLTNPELF Q RVGIIPPK GCLLYGPPGT GKTLLARAVA SQLDCNFLKV VSSSIVDKYI GESARLIREM FNYARDHQPC IIFMDEIDAI GG RRFSEGT SADREIQRTL MELLNQMDGF DTLHRVKMIM ATNRPDTLDP ALLRPGRLDR KIHIDLPNEQ ARLDILKIHA GPI TKHGEI DYEAIVKLSD GFNGADLRNV CTEAGMFAIR ADHDFVVQED FMKAVRKVAD SKKLESKLDY KPV

UniProtKB: 26S proteasome regulatory subunit 10B

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Macromolecule #6: 26S proteasome regulatory subunit 6A

MacromoleculeName: 26S proteasome regulatory subunit 6A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.266457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNLLPNIESP VTRQEKMATV WDEAEQDGIG EEVLKMSTEE IIQRTRLLDS EIKIMKSEVL RVTHELQAMK DKIKENSEKI KVNKTLPYL VSNVIELLDV DPNDQEEDGA NIDLDSQRKG KCAVIKTSTR QTYFLPVIGL VDAEKLKPGD LVGVNKDSYL I LETLPTEY ...String:
MNLLPNIESP VTRQEKMATV WDEAEQDGIG EEVLKMSTEE IIQRTRLLDS EIKIMKSEVL RVTHELQAMK DKIKENSEKI KVNKTLPYL VSNVIELLDV DPNDQEEDGA NIDLDSQRKG KCAVIKTSTR QTYFLPVIGL VDAEKLKPGD LVGVNKDSYL I LETLPTEY DSRVKAMEVD ERPTEQYSDI GGLDKQIQEL VEAIVLPMNH KEKFENLGIQ PPKGVLMYGP PGTGKTLLAR AC AAQTKAT FLKLAGPQLV QMFIGDGAKL VRDAFALAKE KAPSIIFIDE LDAIGTKRFD SEKAGDREVQ RTMLELLNQL DGF QPNTQV KVIAATNRVD ILDPALLRSG RLDRKIEFPM PNEEARARIM QIHSRKMNVS PDVNYEELAR CTDDFNGAQC KAVC VEAGM IALRRGATEL THEDYMEGIL EVQAKKKANL QYYA

UniProtKB: 26S proteasome regulatory subunit 6A

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Macromolecule #7: 26S proteasome non-ATPase regulatory subunit 1

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.958234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MITSAAGIIS LLDEDEPQLK EFALHKLNAV VNDFWAEISE SVDKIEVLYE DEGFRSRQFA ALVASKVFYH LGAFEESLNY ALGAGDLFN VNDNSEYVET IIAKCIDHYT KQCVENADLP EGEKKPIDQR LEGIVNKMFQ RCLDDHKYKQ AIGIALETRR L DVFEKTIL ...String:
MITSAAGIIS LLDEDEPQLK EFALHKLNAV VNDFWAEISE SVDKIEVLYE DEGFRSRQFA ALVASKVFYH LGAFEESLNY ALGAGDLFN VNDNSEYVET IIAKCIDHYT KQCVENADLP EGEKKPIDQR LEGIVNKMFQ RCLDDHKYKQ AIGIALETRR L DVFEKTIL ESNDVPGMLA YSLKLCMSLM QNKQFRNKVL RVLVKIYMNL EKPDFINVCQ CLIFLDDPQA VSDILEKLVK ED NLLMAYQ ICFDLYESAS QQFLSSVIQN LRTVGTPIAS VPGSTNTGTV PGSEKDSDSM ETEEKTSSAF VGKTPEASPE PKD QTLKMI KILSGEMAIE LHLQFLIRNN NTDLMILKNT KDAVRNSVCH TATVIANSFM HCGTTSDQFL RDNLEWLARA TNWA KFTAT ASLGVIHKGH EKEALQLMAT YLPKDTSPGS AYQEGGGLYA LGLIHANHGG DIIDYLLNQL KNASNDIVRH GGSLG LGLA AMGTARQDVY DLLKTNLYQD DAVTGEAAGL ALGLVMLGSK NAQAIEDMVG YAQETQHEKI LRGLAVGIAL VMYGRM EEA DALIESLCRD KDPILRRSGM YTVAMAYCGS GNNKAIRRLL HVAVSDVNDD VRRAAVESLG FILFRTPEQC PSVVSLL SE SYNPHVRYGA AMALGICCAG TGNKEAINLL EPMTNDPVNY VRQGALIASA LIMIQQTEIT CPKVNQFRQL YSKVINDK H DDVMAKFGAI LAQGILDAGG HNVTISLQSR TGHTHMPSVV GVLVFTQFWF WFPLSHFLSL AYTPTCVIGL NKDLKMPKV QYKSNCKPST FAYPAPLEVP KEKEKEKVST AVLSITAKAK KKEKEKEKKE EEKMEVDEAE KKEEKEKKKE PEPNFQLLDN PARVMPAQL KVLTMPETCR YQPFKPLSIG GIIILKDTSE DIEELVEPVA AHGPKIEEEE QEPEPPEPFE YIDD

UniProtKB: 26S proteasome non-ATPase regulatory subunit 1

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Macromolecule #8: 26S proteasome non-ATPase regulatory subunit 3

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.0665 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKQEGSARRR GADKAKPPPG GGEQEPPPPP APQDVEMKEE AATGGGSTGE ADGKTAAAAA EHSQRELDTV TLEDIKEHVK QLEKAVSGK EPRFVLRALR MLPSTSRRLN HYVLYKAVQG FFTSNNATRD FLLPFLEEPM DTEADLQFRP RTGKAASTPL L PEVEAYLQ ...String:
MKQEGSARRR GADKAKPPPG GGEQEPPPPP APQDVEMKEE AATGGGSTGE ADGKTAAAAA EHSQRELDTV TLEDIKEHVK QLEKAVSGK EPRFVLRALR MLPSTSRRLN HYVLYKAVQG FFTSNNATRD FLLPFLEEPM DTEADLQFRP RTGKAASTPL L PEVEAYLQ LLVVIFMMNS KRYKEAQKIS DDLMQKISTQ NRRALDLVAA KCYYYHARVY EFLDKLDVVR SFLHARLRTA TL RHDADGQ ATLLNLLLRN YLHYSLYDQA EKLVSKSVFP EQANNNEWAR YLYYTGRIKA IQLEYSEARR TMTNALRKAP QHT AVGFKQ TVHKLLIVVE LLLGEIPDRL QFRQPSLKRS LMPYFLLTQA VRTGNLAKFN QVLDQFGEKF QADGTYTLII RLRH NVIKT GVRMISLSYS RISLADIAQK LQLDSPEDAE FIVAKAIRDG VIEASINHEK GYVQSKEMID IYSTREPQLA FHQRI SFCL DIHNMSVKAM RFPPKSYNKD LESAEERRER EQQDLEFAKE MAEDDDDSFP

UniProtKB: 26S proteasome non-ATPase regulatory subunit 3

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Macromolecule #9: RPN5

MacromoleculeName: RPN5 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.979359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADGGSERAD GRIVKMEVDY SATVDQRLPE CAKLAKEGRL QEVIETLLSL EKQTRTASDM VSTSRILVAV VKMCYEAKEW DLLNENIML LSKRRSQLKQ AVAKMVQQCC TYVEEITDLP IKLRLIDTLR MVTEGKIYVE IERARLTKTL ATIKEQNGDV K EAASILQE ...String:
MADGGSERAD GRIVKMEVDY SATVDQRLPE CAKLAKEGRL QEVIETLLSL EKQTRTASDM VSTSRILVAV VKMCYEAKEW DLLNENIML LSKRRSQLKQ AVAKMVQQCC TYVEEITDLP IKLRLIDTLR MVTEGKIYVE IERARLTKTL ATIKEQNGDV K EAASILQE LQVETYGSME KKERVEFILE QMRLCLAVKD YIRTQIISKK INTKFFQEEN TEKLKLKYYN LMIQLDQHEG SY LSICKHY RAIYDTPCIQ AESEKWQQAL KSVVLYVILA PFDNEQSDLV HRISGDKKLE EIPKYKDLLK LFTTMELMRW STL VEDYGM ELRKGSLESP ATDVFGSTEE GEKRWKDLKN RVVEHNIRIM AKYYTRITMK RMAQLLDLSV DESEAFLSNL VVNK TIFAK VDRLAGIINF QRPKDPNNLL NDWSQKLNSL MSLVNKTTHL IAKEEMIHNL Q

UniProtKB: 26S proteasome non-ATPase regulatory subunit 12

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Macromolecule #10: 26S proteasome non-ATPase regulatory subunit 11

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.526688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAAVVEFQ RAQSLLSTDR EASIDILHSI VKRDIQENDE EAVQVKEQSI LELGSLLAKT GQAAELGGLL KYVRPFLNSI SKAKAARLV RSLLDLFLDM EAATGQEVEL CLECIEWAKS EKRTFLRQAL EARLVSLYFD TKRYQEALHL GSQLLRELKK M DDKALLVE ...String:
MAAAAVVEFQ RAQSLLSTDR EASIDILHSI VKRDIQENDE EAVQVKEQSI LELGSLLAKT GQAAELGGLL KYVRPFLNSI SKAKAARLV RSLLDLFLDM EAATGQEVEL CLECIEWAKS EKRTFLRQAL EARLVSLYFD TKRYQEALHL GSQLLRELKK M DDKALLVE VQLLESKTYH ALSNLPKARA ALTSARTTAN AIYCPPKLQA TLDMQSGIIH AAEEKDWKTA YSYFYEAFEG YD SIDSPKA ITSLKYMLLC KIMLNTPEDV QALVSGKLAL RYAGRQTEAL KCVAQASKNR SLADFEKALT DYRAELRDDP IIS THLAKL YDNLLEQNLI RVIEPFSRVQ IEHISSLIKL SKADVERKLS QMILDKKFHG ILDQGEGVLI IFDEPPVDKT YEAA LETIQ NMSKVVDSLY NKAKKLT

UniProtKB: 26S proteasome non-ATPase regulatory subunit 11

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Macromolecule #11: 26S proteasome non-ATPase regulatory subunit 6

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 6 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.592285 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPLENLEEEG LPKNPDLRIA QLRFLLSLPE HRGDAAVRDE LMAAVRDNNM APYYEALCKS LDWQIDVDLL NKMKKANEDE LKRLDEELE DAEKNLGESE IRDAMMAKAE YLCRIGDKEG ALTAFRKTYD KTVALGHRLD IVFYLLRIGL FYMDNDLITR N TEKAKSLI ...String:
MPLENLEEEG LPKNPDLRIA QLRFLLSLPE HRGDAAVRDE LMAAVRDNNM APYYEALCKS LDWQIDVDLL NKMKKANEDE LKRLDEELE DAEKNLGESE IRDAMMAKAE YLCRIGDKEG ALTAFRKTYD KTVALGHRLD IVFYLLRIGL FYMDNDLITR N TEKAKSLI EEGGDWDRRN RLKVYQGLYC VAIRDFKQAA ELFLDTVSTF TSYELMDYKT FVTYTVYVSM IALERPDLRE KV IKGAEIL EVLHSLPAVR QYLFSLYECR YSVFFQSLAV VEQEMKKDWL FAPHYRYYVR EMRIHAYSQL LESYRSLTLG YMA EAFGVG VEFIDQELSR FIAAGRLHCK IDKVNEIVET NRPDSKNWQY QETIKKGDLL LNRVQKLSRV INM

UniProtKB: 26S proteasome non-ATPase regulatory subunit 6

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Macromolecule #12: 26S proteasome non-ATPase regulatory subunit 7

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 7 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.086441 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPELAVQKVV VHPLVLLSVV DHFNRIGKVG NQKRVVGVLL GSWQKKVLDV SNSFAVPFDE DDKDDSVWFL DHDYLENMYG MFKKVNARE RIVGWYHTGP KLHKNDIAIN ELMKRYCPNS VLVIIDVKPK DLGLPTEAYI SVEEVHDDGT PTSKTFEHVT S EIGAEEAE ...String:
MPELAVQKVV VHPLVLLSVV DHFNRIGKVG NQKRVVGVLL GSWQKKVLDV SNSFAVPFDE DDKDDSVWFL DHDYLENMYG MFKKVNARE RIVGWYHTGP KLHKNDIAIN ELMKRYCPNS VLVIIDVKPK DLGLPTEAYI SVEEVHDDGT PTSKTFEHVT S EIGAEEAE EVGVEHLLRD IKDTTVGTLS QRITNQVHGL KGLNSKLLDI RSYLEKVATG KLPINHQIIY QLQDVFNLLP DV SLQEFVK AFYLKTNDQM VVVYLASLIR SVVALHNLIN NKIANRDAEK KEGQEKEESK KDRKEDKEKD KDKEKSDVKK EEK KEKK

UniProtKB: 26S proteasome non-ATPase regulatory subunit 7

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Macromolecule #13: 26S proteasome non-ATPase regulatory subunit 13

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.995359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKDVPGFLQQ SQNSGPGQPA VWHRLEELYT KKLWHQLTLQ VLDFVQDPCF AQGDGLIKLY ENFISEFEHR VNPLSLVEII LHVVRQMTD PNVALTFLEK TREKVKSSDE AVILCKTAIG ALKLNIGDLQ VTKETIEDVE EMLNNLPGVT SVHSRFYDLS S KYYQTIGN ...String:
MKDVPGFLQQ SQNSGPGQPA VWHRLEELYT KKLWHQLTLQ VLDFVQDPCF AQGDGLIKLY ENFISEFEHR VNPLSLVEII LHVVRQMTD PNVALTFLEK TREKVKSSDE AVILCKTAIG ALKLNIGDLQ VTKETIEDVE EMLNNLPGVT SVHSRFYDLS S KYYQTIGN HASYYKDALR FLGCVDIKDL PVSEQQERAF TLGLAGLLGE GVFNFGELLM HPVLESLRNT DRQWLIDTLY AF NSGNVER FQTLKTAWGQ QPDLAANEAQ LLRKIQLLCL MEMTFTRPAN HRQLTFEEIA KSAKITVNEV ELLVMKALSV GLV KGSIDE VDKRVHMTWV QPRVLDLQQI KGMKDRLEFW CTDVKSMEML VEHQAHDILT

UniProtKB: 26S proteasome non-ATPase regulatory subunit 13

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Macromolecule #14: RPN10

MacromoleculeName: RPN10 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.78159 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLESTMVCV DNSEYMRNGD FLPTRLQAQQ DAVNIVCHSK TRSNPENNVG LITLANDCEV LTTLTPDTGR ILSKLHTVQP KGKITFCTG IRVAHLALKH RQGKNHKMRI IAFVGSPVED NEKDLVKLAK RLKKEKVNVD IINFGEEEVN TEKLTAFVNT L NGKDGTGS ...String:
MVLESTMVCV DNSEYMRNGD FLPTRLQAQQ DAVNIVCHSK TRSNPENNVG LITLANDCEV LTTLTPDTGR ILSKLHTVQP KGKITFCTG IRVAHLALKH RQGKNHKMRI IAFVGSPVED NEKDLVKLAK RLKKEKVNVD IINFGEEEVN TEKLTAFVNT L NGKDGTGS HLVTVPPGPS LADALISSPI LAGEGGAMLG LGASDFEFGV DPSADPELAL ALRVSMEEQR QRQEEEARRA AA ASAAEAG IATTGTEDSD DALLKMTISQ QEFGRTGLPD LSSMTEEEQI AYAMQMSLQG AEFGQAESAD IDASSAMDTS EPA KEEDDY DVMQDPEFLQ SVLENLPGVD PNNEAIRNAM GSLASQATKD GKKDKKEEDK K

UniProtKB: 26S proteasome non-ATPase regulatory subunit 4

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Macromolecule #15: 26S proteasome non-ATPase regulatory subunit 14

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 14 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.620023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDRLLRLGGG MPGLGQGPPT DAPAVDTAEQ VYISSLALLK MLKHGRAGVP MEVMGLMLGE FVDDYTVRVI DVFAMPQSGT GVSVEAVDP VFQAKMLDML KQTGRPEMVV GWYHSHPGFG CWLSGVDINT QQSFEALSER AVAVVVDPIQ SVKGKVVIDA F RLINANMM ...String:
MDRLLRLGGG MPGLGQGPPT DAPAVDTAEQ VYISSLALLK MLKHGRAGVP MEVMGLMLGE FVDDYTVRVI DVFAMPQSGT GVSVEAVDP VFQAKMLDML KQTGRPEMVV GWYHSHPGFG CWLSGVDINT QQSFEALSER AVAVVVDPIQ SVKGKVVIDA F RLINANMM VLGHEPRQTT SNLGHLNKPS IQALIHGLNR HYYSITINYR KNELEQKMLL NLHKKSWMEG LTLQDYSEHC KH NESVVKE MLELAKNYNK AVEEEDKMTP EQLAIKNVGK QDPKRHLEEH VDVLMTSNIV QCLAAMLDTV VFK

UniProtKB: Ubiquitin C-terminal hydrolase PSMD14

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Macromolecule #16: 26S proteasome non-ATPase regulatory subunit 8

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 8 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.667871 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFIKGRAPRA PPRERRRATR GGLRQVVAPP RALGSTSRPH FRRASVCRRR CRKSGGLLAA SRKMAAAAVN GAAGFSSSGP AATSGAVLQ AATGMYEQLK GEWNRKSPNL SKCGEELGRL KLVLLELNFL PTTGTKLTKQ QLILARDILE IGAQWSILRK D IPSFERYM ...String:
MFIKGRAPRA PPRERRRATR GGLRQVVAPP RALGSTSRPH FRRASVCRRR CRKSGGLLAA SRKMAAAAVN GAAGFSSSGP AATSGAVLQ AATGMYEQLK GEWNRKSPNL SKCGEELGRL KLVLLELNFL PTTGTKLTKQ QLILARDILE IGAQWSILRK D IPSFERYM AQLKCYYFDY KEQLPESAYM HQLLGLNLLF LLSQNRVAEF HTELERLPAK DIQTNVYIKH PVSLEQYLME GS YNKVFLA KGNIPAESYT FFIDILLDTI RDEIAGCIEK AYEKILFTEA TRILFFNTPK KMTDYAKKRG WVLGPNNYYS FAS QQQKPE DTTIPSTELA KQVIEYARQL EMIV

UniProtKB: 26S proteasome non-ATPase regulatory subunit 8

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Macromolecule #17: 26S proteasome complex subunit SEM1

MacromoleculeName: 26S proteasome complex subunit SEM1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.284611 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSEKKQPVDL GLLEEDDEFE EFPAEDWAGL DEDEDAHVWE DNWDDDNVED DFSNQLRAEL EKHGYKMETS

UniProtKB: 26S proteasome complex subunit SEM1

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Macromolecule #18: 26S proteasome non-ATPase regulatory subunit 2

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 2 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.313625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEGGRDKAP VQPQQSPAAA PGGTDEKPSG KERRDAGDKD KEQELSEEDK QLQDELEMLV ERLGEKDTSL YRPALEELRR QIRSSTTSM TSVPKPLKFL RPHYGKLKEI YENMAPGENK RFAADIISVL AMTMSGEREC LKYRLVGSQE ELASWGHEYV R HLAGEVAK ...String:
MEEGGRDKAP VQPQQSPAAA PGGTDEKPSG KERRDAGDKD KEQELSEEDK QLQDELEMLV ERLGEKDTSL YRPALEELRR QIRSSTTSM TSVPKPLKFL RPHYGKLKEI YENMAPGENK RFAADIISVL AMTMSGEREC LKYRLVGSQE ELASWGHEYV R HLAGEVAK EWQELDDAEK VQREPLLTLV KEIVPYNMAH NAEHEACDLL MEIEQVDMLE KDIDENAYAK VCLYLTSCVN YV PEPENSA LLRCALGVFR KFSRFPEALR LALMLNDMEL VEDIFTSCKD VVVQKQMAFM LGRHGVFLEL SEDVEEYEDL TEI MSNVQL NSNFLALARE LDIMEPKVPD DIYKTHLENN RFGGSGSQVD SARMNLASSF VNGFVNAAFG QDKLLTDDGN KWLY KNKDH GMLSAAASLG MILLWDVDGG LTQIDKYLYS SEDYIKSGAL LACGIVNSGV RNECDPALAL LSDYVLHNSN TMRLG SIFG LGLAYAGSNR EDVLTLLLPV MGDSKSSMEV AGVTALACGM IAVGSCNGDV TSTILQTIME KSETELKDTY ARWLPL GLG LNHLGKGEAI EAILAALEVV SEPFRSFANT LVDVCAYAGS GNVLKVQQLL HICSEHFDSK EKEEDKDKKE KKDKDKK EA PADMGAHQGV AVLGIALIAM GEEIGAEMAL RTFGHLLRYG EPTLRRAVPL ALALISVSNP RLNILDTLSK FSHDADPE V SYNSIFAMGM VGSGTNNARL AAMLRQLAQY HAKDPNNLFM VRLAQGLTHL GKGTLTLCPY HSDRQLMSQV AVAGLLTVL VSFLDVRNII LGKSHYVLYG LVAAMQPRML VTFDEELRPL PVSVRVGQAV DVVGQAGKPK TITGFQTHTT PVLLAHGERA ELATEEFLP VTPILEGFVI LRKNPNYDL

UniProtKB: 26S proteasome non-ATPase regulatory subunit 2

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Macromolecule #19: Thioredoxin-like protein 1

MacromoleculeName: Thioredoxin-like protein 1 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.284229 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVGVKPVGSD PDFQPELSGA GSRLAVVKFT MRGCGPCLRI APAFSSMSNK YPQAVFLEVD VHQCQGTAAT NNISATPTFL FFRNKVRID QYQGADAVGL EEKIKQHLEN DPGSNEDTDI PKGYMDLMPF INKAGCECLN ESDEHGFDNC LRKDTTFLES D CDEQLLIT ...String:
MVGVKPVGSD PDFQPELSGA GSRLAVVKFT MRGCGPCLRI APAFSSMSNK YPQAVFLEVD VHQCQGTAAT NNISATPTFL FFRNKVRID QYQGADAVGL EEKIKQHLEN DPGSNEDTDI PKGYMDLMPF INKAGCECLN ESDEHGFDNC LRKDTTFLES D CDEQLLIT VAFNQPVKLY SMKFQGPDNG QGPKYVKIFI NLPRSMDFEE AERSEPTQAL ELTEDDIKED GIVPLRYVKF QN VNSVTIF VQSNQGEEET TRISYFTFIG TPVQATNMND FKRVVGKKGE SH

UniProtKB: Thioredoxin-like protein 1

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Macromolecule #20: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 20 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #21: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 21 / Number of copies: 3 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #22: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 22 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #23: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H12NO3ClTris(hydroxymethyl)aminomethane hydrochloride
50.0 mMNaClSodium Chloride
1.5 mMC10H12N5O12P3SATP-gamma-S
5.0 mMMgCl2Magnesium chloride
2.0 mM(CH(OH)CH2SH)2Dithiothreitol

Details: 50 mM Tris [pH7.5], 50 mM NaCl, 1.5 mM ATP-gamma-S, 5 mM MgCl2 and 2 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295.15 K / Instrument: LEICA EM GP
DetailsQuantifoil copper R 1.2/1.3 holey carbon 300 mesh grids (#Q3100CR1.3; Electron Microscopy Sciences).

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 40 / Average exposure time: 2.5 sec. / Average electron dose: 55.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1504498
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7wsi

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 21325
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7wsi

chain_id: A, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: B, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: C, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: D, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: E, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: F, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: U, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: V, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: W, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: X, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: Y, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: Z, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: a, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: b, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: c, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: d, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: e, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: f, source_name: PDB, initial_model_type: experimental model

1wwy

chain_id: g, source_name: PDB, initial_model_type: experimental model
chain_id: f, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 51 / Target criteria: Cross-correlation coefficient
Output model

PDB-12bm:
Human 19S proteasome bound to TXNL1 PITH domain state 2

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