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- EMDB-14083: 26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn... -

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Basic information

Entry
Database: EMDB / ID: EMD-14083
Title26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn1, Ubp6, and UbVS)
Map data
Sample
  • Complex: 26S proteasome WT-Ubp6-UbVS complex in the si state
    • Complex: yeast WT 26S proteasome body2 (ATPase, Rpn1)
      • Protein or peptide: x 7 types
    • Complex: Ubp6-UbVS
      • Protein or peptide: x 2 types
  • Ligand: x 3 types
Function / homology
Function and homology information


proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway ...proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / regulation of protein catabolic process / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / protein deubiquitination / Ub-specific processing proteases / enzyme regulator activity / Neutrophil degranulation / proteasome complex / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit P45-like / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / Ubiquitin carboxyl-terminal hydrolase 14-like / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain ...26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit P45-like / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / Ubiquitin carboxyl-terminal hydrolase 14-like / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Papain-like cysteine peptidase superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RPT1 isoform 1 / RPT6 isoform 1 / Ubiquitin carboxyl-terminal hydrolase / RPT3 isoform 1 / RPT2 isoform 1 / RPT5 isoform 1 / RPT4 isoform 1 / Ubiquitin B / 26S proteasome regulatory subunit RPN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsHung KYS / Klumpe S / Eisele MR / Elsasser S / Geng TT / Cheng C / Joshi T / Rudack T / Sakata E / Finley D
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
German Research Foundation (DFG)SFB1035/Project A01 Germany
German Research Foundation (DFG)CRC889/Project A11 Germany
Other governmentFoundation for the National Institutes of Health R01 GM043601
Other governmentMarie Curie Career Integration grant (PCIG14-GA-2013-631577)
CitationJournal: Nat Commun / Year: 2022
Title: Allosteric control of Ubp6 and the proteasome via a bidirectional switch.
Authors: Hung KYS / Klumpe S / Eisele MR / Elsasser S / Tian G / Sun S / Moroco JA / Cheng TC / Joshi T / Seibel T / Van Dalen D / Feng XH / Lu Y / Ovaa H / Engen JR / Lee BH / Rudack T / Sakata E / Finley D
History
DepositionDec 23, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateJun 1, 2022-
Current statusJun 1, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14083.png

Downloads & links

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Map

FileDownload / File: emd_14083.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 280 pix.
= 588. Å		2.1 Å/pix.
x 280 pix.
= 588. Å		2.1 Å/pix.
x 280 pix.
= 588. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.5
Minimum - Maximum-16.285027 - 33.914352
Average (Standard dev.)-0.023222981 (±0.7922115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 588.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 26S proteasome WT-Ubp6-UbVS complex in the si state

EntireName: 26S proteasome WT-Ubp6-UbVS complex in the si state
Components
  • Complex: 26S proteasome WT-Ubp6-UbVS complex in the si state
    • Complex: yeast WT 26S proteasome body2 (ATPase, Rpn1)
      • Protein or peptide: 26S proteasome regulatory subunit RPN1
      • Protein or peptide: RPT1 isoform 1
      • Protein or peptide: RPT2 isoform 1
      • Protein or peptide: RPT3 isoform 1
      • Protein or peptide: RPT4 isoform 1
      • Protein or peptide: RPT5 isoform 1
      • Protein or peptide: RPT6 isoform 1
    • Complex: Ubp6-UbVS
      • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase
      • Protein or peptide: Polyubiquitin-B
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: 26S proteasome WT-Ubp6-UbVS complex in the si state

SupramoleculeName: 26S proteasome WT-Ubp6-UbVS complex in the si state / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Molecular weightTheoretical: 2.5 MDa

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Supramolecule #2: yeast WT 26S proteasome body2 (ATPase, Rpn1)

SupramoleculeName: yeast WT 26S proteasome body2 (ATPase, Rpn1) / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: Ubp6-UbVS

SupramoleculeName: Ubp6-UbVS / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #8-#9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: 26S proteasome regulatory subunit RPN1

MacromoleculeName: 26S proteasome regulatory subunit RPN1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 109.601906 KDa
SequenceString: MVDESDKKQQ TIDEQSQISP EKQTPNKKDK KKEEEEQLSE EDAKLKTDLE LLVERLKEDD SSLYEASLNA LKESIKNSTS SMTAVPKPL KFLRPTYPDL CSIYDKWTDP NLKSSLADVL SILAMTYSEN GKHDSLRYRL LSDVSDFEGW GHEYIRHLAL E IGEVYNDQ ...String:
MVDESDKKQQ TIDEQSQISP EKQTPNKKDK KKEEEEQLSE EDAKLKTDLE LLVERLKEDD SSLYEASLNA LKESIKNSTS SMTAVPKPL KFLRPTYPDL CSIYDKWTDP NLKSSLADVL SILAMTYSEN GKHDSLRYRL LSDVSDFEGW GHEYIRHLAL E IGEVYNDQ VEKDAEDETS SDGSKSDGSA ATSGFEFSKE DTLRLCLDIV PYFLKHNGEE DAVDLLLEIE SIDKLPQFVD EN TFQRVCQ YMVACVPLLP PPEDVAFLKT AYSIYLSQNE LTDAIALAVR LGEEDMIRSV FDATSDPVMH KQLAYILAAQ KTS FEYEGV QDIIGNGKLS EHFLYLAKEL NLTGPKVPED IYKSHLDNSK SVFSSAGLDS AQQNLASSFV NGFLNLGYCN DKLI VDNDN WVYKTKGDGM TSAVASIGSI YQWNLDGLQQ LDKYLYVDEP EVKAGALLGI GISASGVHDG EVEPALLLLQ DYVTN PDTK ISSAAILGLG IAFAGSKNDE VLGLLLPIAA STDLPIETAA MASLALAHVF VGTCNGDITT SIMDNFLERT AIELKT DWV RFLALALGIL YMGQGEQVDD VLETISAIEH PMTSAIEVLV GSCAYTGTGD VLLIQDLLHR LTPKNVKGEE DADEEET AE GQTNSISDFL GEQVNEPTKN EEAEIEVDEM EVDAEGEEVE VKAEITEKKN GESLEGEEIK SEEKKGKSSD KDATTDGK N DDEEEEKEAG IVDELAYAVL GIALIALGED IGKEMSLRHF GHLMHYGNEH IRRMVPLAMG IVSVSDPQMK VFDTLTRFS HDADLEVSMN SIFAMGLCGA GTNNARLAQL LRQLASYYSR EQDALFITRL AQGLLHLGKG TMTMDVFNDA HVLNKVTLAS ILTTAVGLV SPSFMLKHHQ LFYMLNAGIR PKFILALNDE GEPIKVNVRV GQAVETVGQA GRPKKITGWI TQSTPVLLNH G ERAELETD EYISYTSHIE GVVILKKNPD YREEE

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Macromolecule #2: RPT1 isoform 1

MacromoleculeName: RPT1 isoform 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 52.054891 KDa
SequenceString: MPPKEDWEKY KAPLEDDDKK PDDDKIVPLT EGDIQVLKSY GAAPYAAKLK QTENDLKDIE ARIKEKAGVK ESDTGLAPSH LWDIMGDRQ RLGEEHPLQV ARCTKIIKGN GESDETTTDN NNSGNSNSNS NQQSTDADED DEDAKYVINL KQIAKFVVGL G ERVSPTDI ...String:
MPPKEDWEKY KAPLEDDDKK PDDDKIVPLT EGDIQVLKSY GAAPYAAKLK QTENDLKDIE ARIKEKAGVK ESDTGLAPSH LWDIMGDRQ RLGEEHPLQV ARCTKIIKGN GESDETTTDN NNSGNSNSNS NQQSTDADED DEDAKYVINL KQIAKFVVGL G ERVSPTDI EEGMRVGVDR SKYNIELPLP PRIDPSVTMM TVEEKPDVTY SDVGGCKDQI EKLREVVELP LLSPERFATL GI DPPKGIL LYGPPGTGKT LCARAVANRT DATFIRVIGS ELVQKYVGEG ARMVRELFEM ARTKKACIIF FDEIDAVGGA RFD DGAGGD NEVQRTMLEL ITQLDGFDPR GNIKVMFATN RPNTLDPALL RPGRIDRKVE FSLPDLEGRA NIFRIHSKSM SVER GIRWE LISRLCPNST GAELRSVCTE AGMFAIRARR KVATEKDFLK AVDKVISGYK KFSSTSRYMQ YN

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Macromolecule #3: RPT2 isoform 1

MacromoleculeName: RPT2 isoform 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 48.89816 KDa
SequenceString: MGQGVSSGQD KKKKKGSNQK PKYEPPVQSK FGRKKRKGGP ATAEKLPNIY PSTRCKLKLL RMERIKDHLL LEEEFVSNSE ILKPFEKKQ EEEKKQLEEI RGNPLSIGTL EEIIDDDHAI VTSPTMPDYY VSILSFVDKE LLEPGCSVLL HHKTMSIVGV L QDDADPMV ...String:
MGQGVSSGQD KKKKKGSNQK PKYEPPVQSK FGRKKRKGGP ATAEKLPNIY PSTRCKLKLL RMERIKDHLL LEEEFVSNSE ILKPFEKKQ EEEKKQLEEI RGNPLSIGTL EEIIDDDHAI VTSPTMPDYY VSILSFVDKE LLEPGCSVLL HHKTMSIVGV L QDDADPMV SVMKMDKSPT ESYSDIGGLE SQIQEIKESV ELPLTHPELY EEMGIKPPKG VILYGAPGTG KTLLAKAVAN QT SATFLRI VGSELIQKYL GDGPRLCRQI FKVAGENAPS IVFIDEIDAI GTKRYDSNSG GEREIQRTML ELLNQLDGFD DRG DVKVIM ATNKIETLDP ALIRPGRIDR KILFENPDLS TKKKILGIHT SKMNLSEDVN LETLVTTKDD LSGADIQAMC TEAG LLALR ERRMQVTAED FKQAKERVMK NKVEENLEGL YL

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Macromolecule #4: RPT3 isoform 1

MacromoleculeName: RPT3 isoform 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 47.953676 KDa
SequenceString: MEELGIVTPV EKAVEEKPAV KSYASLLAQL NGTVNNNSAL SNVNSDIYFK LKKLEKEYEL LTLQEDYIKD EQRHLKRELK RAQEEVKRI QSVPLVIGQF LEPIDQNTGI VSSTTGMSYV VRILSTLDRE LLKPSMSVAL HRHSNALVDI LPPDSDSSIS V MGENEKPD ...String:
MEELGIVTPV EKAVEEKPAV KSYASLLAQL NGTVNNNSAL SNVNSDIYFK LKKLEKEYEL LTLQEDYIKD EQRHLKRELK RAQEEVKRI QSVPLVIGQF LEPIDQNTGI VSSTTGMSYV VRILSTLDRE LLKPSMSVAL HRHSNALVDI LPPDSDSSIS V MGENEKPD VTYADVGGLD MQKQEIREAV ELPLVQADLY EQIGIDPPRG VLLYGPPGTG KTMLVKAVAN STKAAFIRVN GS EFVHKYL GEGPRMVRDV FRLARENAPS IIFIDEVDSI ATKRFDAQTG SDREVQRILI ELLTQMDGFD QSTNVKVIMA TNR ADTLDP ALLRPGRLDR KIEFPSLRDR RERRLIFGTI ASKMSLAPEA DLDSLIIRND SLSGAVIAAI MQEAGLRAVR KNRY VILQS DLEEAYATQV KTDNTVDKFD FYK

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Macromolecule #5: RPT4 isoform 1

MacromoleculeName: RPT4 isoform 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 49.480137 KDa
SequenceString: MSEEQDPLLA GLGETSGDNH TQQSHEQQPE QPQETEEHHE EEPSRVDPEQ EAHNKALNQF KRKLLEHRRY DDQLKQRRQN IRDLEKLYD KTENDIKALQ SIGQLIGEVM KELSEEKYIV KASSGPRYIV GVRNSVDRSK LKKGVRVTLD ITTLTIMRIL P RETDPLVY ...String:
MSEEQDPLLA GLGETSGDNH TQQSHEQQPE QPQETEEHHE EEPSRVDPEQ EAHNKALNQF KRKLLEHRRY DDQLKQRRQN IRDLEKLYD KTENDIKALQ SIGQLIGEVM KELSEEKYIV KASSGPRYIV GVRNSVDRSK LKKGVRVTLD ITTLTIMRIL P RETDPLVY NMTSFEQGEI TFDGIGGLTE QIRELREVIE LPLKNPEIFQ RVGIKPPKGV LLYGPPGTGK TLLAKAVAAT IG ANFIFSP ASGIVDKYIG ESARIIREMF AYAKEHEPCI IFMDEVDAIG GRRFSEGTSA DREIQRTLME LLTQMDGFDN LGQ TKIIMA TNRPDTLDPA LLRPGRLDRK VEIPLPNEAG RLEIFKIHTA KVKKTGEFDF EAAVKMSDGF NGADIRNCAT EAGF FAIRD DRDHINPDDL MKAVRKVAEV KKLEGTIEYQ KL

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Macromolecule #6: RPT5 isoform 1

MacromoleculeName: RPT5 isoform 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 48.315727 KDa
SequenceString: MATLEELDAQ TLPGDDELDQ EILNLSTQEL QTRAKLLDNE IRIFRSELQR LSHENNVMLE KIKDNKEKIK NNRQLPYLVA NVVEVMDMN EIEDKENSES TTQGGNVNLD NTAVGKAAVV KTSSRQTVFL PMVGLVDPDK LKPNDLVGVN KDSYLILDTL P SEFDSRVK ...String:
MATLEELDAQ TLPGDDELDQ EILNLSTQEL QTRAKLLDNE IRIFRSELQR LSHENNVMLE KIKDNKEKIK NNRQLPYLVA NVVEVMDMN EIEDKENSES TTQGGNVNLD NTAVGKAAVV KTSSRQTVFL PMVGLVDPDK LKPNDLVGVN KDSYLILDTL P SEFDSRVK AMEVDEKPTE TYSDVGGLDK QIEELVEAIV LPMKRADKFK DMGIRAPKGA LMYGPPGTGK TLLARACAAQ TN ATFLKLA APQLVQMYIG EGAKLVRDAF ALAKEKAPTI IFIDELDAIG TKRFDSEKSG DREVQRTMLE LLNQLDGFSS DDR VKVLAA TNRVDVLDPA LLRSGRLDRK IEFPLPSEDS RAQILQIHSR KMTTDDDINW QELARSTDEF NGAQLKAVTV EAGM IALRN GQSSVKHEDF VEGISEVQAR KSKSVSFYA

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Macromolecule #7: RPT6 isoform 1

MacromoleculeName: RPT6 isoform 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 45.342742 KDa
SequenceString: MTAAVTSSNI VLETHESGIK PYFEQKIQET ELKIRSKTEN VRRLEAQRNA LNDKVRFIKD ELRLLQEPGS YVGEVIKIVS DKKVLVKVQ PEGKYIVDVA KDINVKDLKA SQRVCLRSDS YMLHKVLENK ADPLVSLMMV EKVPDSTYDM VGGLTKQIKE I KEVIELPV ...String:
MTAAVTSSNI VLETHESGIK PYFEQKIQET ELKIRSKTEN VRRLEAQRNA LNDKVRFIKD ELRLLQEPGS YVGEVIKIVS DKKVLVKVQ PEGKYIVDVA KDINVKDLKA SQRVCLRSDS YMLHKVLENK ADPLVSLMMV EKVPDSTYDM VGGLTKQIKE I KEVIELPV KHPELFESLG IAQPKGVILY GPPGTGKTLL ARAVAHHTDC KFIRVSGAEL VQKYIGEGSR MVRELFVMAR EH APSIIFM DEIDSIGSTR VEGSGGGDSE VQRTMLELLN QLDGFETSKN IKIIMATNRL DILDPALLRP GRIDRKIEFP PPS VAARAE ILRIHSRKMN LTRGINLRKV AEKMNGCSGA DVKGVCTEAG MYALRERRIH VTQEDFELAV GKVMNKNQET AISV AKLFK

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Macromolecule #8: Ubiquitin carboxyl-terminal hydrolase

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 57.188648 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGETFEFNI RHSGKVYPIT LSTDATSADL KSKAEELTQV PSARQKYMVK GGLSGEESIK IYPLIKPGST VMLLGTPDAN LISKPAKKN NFIEDLAPEQ QVQQFAQLPV GFKNMGNTCY LNATLQALYR VNDLRDMILN YNPSQGVSNS GAQDEEIHKQ I VIEMKRCF ...String:
MSGETFEFNI RHSGKVYPIT LSTDATSADL KSKAEELTQV PSARQKYMVK GGLSGEESIK IYPLIKPGST VMLLGTPDAN LISKPAKKN NFIEDLAPEQ QVQQFAQLPV GFKNMGNTCY LNATLQALYR VNDLRDMILN YNPSQGVSNS GAQDEEIHKQ I VIEMKRCF ENLQNKSFKS VLPIVLLNTL RKCYPQFAER DSQGGFYKQQ DAEELFTQLF HSMSIVFGDK FSEDFRIQFK TT IKDTAND NDITVKENES DSKLQCHISG TTNFMRNGLL EGLNEKIEKR SDLTGANSIY SVEKKISRLP KFLTVQYVRF FWK RSTNKK SKILRKVVFP FQLDVADMLT PEYAAEKVKV RDELRKVEKE KNEKEREIKR RKFDPSSSEN VMTPREQYET QVAL NESEK DQWLEEYKKH FPPNLEKGEN PSCVYNLIGV ITHQGANSES GHYQAFIRDE LDENKWYKFN DDKVSVVEKE KIESL AGGG ESDSALILMY KGFGL

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Macromolecule #9: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.560831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG(GLZ)

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Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 5 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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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

Concentration1.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88243
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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