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- EMDB-12040: Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 s... -

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Basic information

Entry
Database: EMDB / ID: EMD-12040
TitleUbiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2
Map data
Sample
  • Complex: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1
    • Complex: Cullin-1, E3 ubiquitin-protein ligase RBX1
      • Protein or peptide: Cullin-1
      • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Complex: ARIH1, SKP2, CKS1B, SKP1, UBC
      • Protein or peptide: E3 ubiquitin-protein ligase ARIH1
      • Protein or peptide: S-phase kinase-associated protein 2
      • Protein or peptide: Cyclin-dependent kinases regulatory subunit 1
      • Protein or peptide: S-phase kinase-associated protein 1
      • Protein or peptide: Polyubiquitin-C
    • Complex: Cyclin-dependent kinase inhibitor 1B
      • Protein or peptide: Cyclin-dependent kinase inhibitor 1B
  • Ligand: ZINC ION
Keywordsubiquitin / ubiquitin ligase / E3 ligase / F-box protein / RBR ligase / Cullin-RING-Ligase / CRL / SCF / NEDD8 / Post-translational modification / ubiquitylation / LIGASE
Function / homology
Function and homology information


PKR/eIFalpha signaling / cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / ubiquitin-like protein transferase activity / positive regulation of protein polyubiquitination / autophagic cell death / FOXO-mediated transcription of cell cycle genes / RBR-type E3 ubiquitin transferase / Parkin-FBXW7-Cul1 ubiquitin ligase complex ...PKR/eIFalpha signaling / cyclin-dependent protein kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / ubiquitin-like protein transferase activity / positive regulation of protein polyubiquitination / autophagic cell death / FOXO-mediated transcription of cell cycle genes / RBR-type E3 ubiquitin transferase / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of epithelial cell proliferation involved in prostate gland development / cellular response to cell-matrix adhesion / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of cell cycle G1/S phase transition / PcG protein complex / epithelial cell proliferation involved in prostate gland development / regulation of exit from mitosis / negative regulation of epithelial cell apoptotic process / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / cullin-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress / regulation of cyclin-dependent protein serine/threonine kinase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / RHO GTPases activate CIT / nuclear export / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of protein autoubiquitination / negative regulation of mitotic cell cycle / RNA polymerase II transcription initiation surveillance / epithelial cell apoptotic process / protein neddylation / Modulation of host responses by IFN-stimulated genes / AKT phosphorylates targets in the cytosol / ubiquitin ligase activator activity / NEDD8 ligase activity / ubiquitin conjugating enzyme binding / protein K27-linked ubiquitination / negative regulation of response to oxidative stress / VCB complex / molecular function inhibitor activity / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / cellular response to lithium ion / SCF ubiquitin ligase complex / positive regulation of intracellular estrogen receptor signaling pathway / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / p53-Dependent G1 DNA Damage Response / Lewy body / Cul4A-RING E3 ubiquitin ligase complex / PTK6 Regulates Cell Cycle / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Constitutive Signaling by AKT1 E17K in Cancer / RSV-host interactions / Cul4-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / Prolactin receptor signaling / Cul4B-RING E3 ubiquitin ligase complex / ciliary transition zone / cellular response to antibiotic / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / inner ear development / protein kinase inhibitor activity / ubiquitin ligase complex scaffold activity / regulation of G1/S transition of mitotic cell cycle / negative regulation of vascular associated smooth muscle cell proliferation / cullin family protein binding / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / protein monoubiquitination / ubiquitin ligase complex / protein K63-linked ubiquitination / Cyclin E associated events during G1/S transition / Cajal body / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of microtubule polymerization / positive regulation of double-strand break repair via homologous recombination / cyclin-dependent protein kinase holoenzyme complex / ubiquitin-like ligase-substrate adaptor activity / site of DNA damage / Notch signaling pathway / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / transcription-coupled nucleotide-excision repair / protein K48-linked ubiquitination / negative regulation of insulin receptor signaling pathway / Maturation of protein E / FLT3 Signaling / Maturation of protein E / regulation of cellular response to insulin stimulus / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora
Similarity search - Function
: / E3 ubiquitin-protein ligase ARIH1, UBA-like domain / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily ...: / E3 ubiquitin-protein ligase ARIH1, UBA-like domain / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / IBR domain, a half RING-finger domain / IBR domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin, N-terminal / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin alpha solenoid domain / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Ring finger / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Cyclin-dependent kinase inhibitor 1B / Cyclin-dependent kinases regulatory subunit 1 / E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / S-phase kinase-associated protein 2 / Cullin-1 / E3 ubiquitin-protein ligase ARIH1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsHorn-Ghetko D / Prabu JR / Schulman BA
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)H2020 789016-NEDD8Activate Germany
German Research Foundation (DFG)SCHU 3196/1-1 Germany
CitationJournal: Nature / Year: 2021
Title: Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly.
Authors: Daniel Horn-Ghetko / David T Krist / J Rajan Prabu / Kheewoong Baek / Monique P C Mulder / Maren Klügel / Daniel C Scott / Huib Ovaa / Gary Kleiger / Brenda A Schulman /
Abstract: E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates. However, rather ...E3 ligases are typically classified by hallmark domains such as RING and RBR, which are thought to specify unique catalytic mechanisms of ubiquitin transfer to recruited substrates. However, rather than functioning individually, many neddylated cullin-RING E3 ligases (CRLs) and RBR-type E3 ligases in the ARIH family-which together account for nearly half of all ubiquitin ligases in humans-form E3-E3 super-assemblies. Here, by studying CRLs in the SKP1-CUL1-F-box (SCF) family, we show how neddylated SCF ligases and ARIH1 (an RBR-type E3 ligase) co-evolved to ubiquitylate diverse substrates presented on various F-box proteins. We developed activity-based chemical probes that enabled cryo-electron microscopy visualization of steps in E3-E3 ubiquitylation, initiating with ubiquitin linked to the E2 enzyme UBE2L3, then transferred to the catalytic cysteine of ARIH1, and culminating in ubiquitin linkage to a substrate bound to the SCF E3 ligase. The E3-E3 mechanism places the ubiquitin-linked active site of ARIH1 adjacent to substrates bound to F-box proteins (for example, substrates with folded structures or limited length) that are incompatible with previously described conventional RING E3-only mechanisms. The versatile E3-E3 super-assembly may therefore underlie widespread ubiquitylation.
History
DepositionDec 5, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b5m
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12040.png

Downloads & links

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Map

FileDownload / File: emd_12040.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 312 pix.
= 340.08 Å		1.09 Å/pix.
x 312 pix.
= 340.08 Å		1.09 Å/pix.
x 312 pix.
= 340.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0185 / Movie #1: 0.0185
Minimum - Maximum-0.05181092 - 0.10555756
Average (Standard dev.)0.00016817033 (±0.002099611)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 340.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z340.080340.080340.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-0.0520.1060.000

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Supplemental data

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Mask #1

Fileemd_12040_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_12040_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12040_half_map_2.map
Projections & Slices
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Sample components

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Entire : CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1

EntireName: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1
Components
  • Complex: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1
    • Complex: Cullin-1, E3 ubiquitin-protein ligase RBX1
      • Protein or peptide: Cullin-1
      • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Complex: ARIH1, SKP2, CKS1B, SKP1, UBC
      • Protein or peptide: E3 ubiquitin-protein ligase ARIH1
      • Protein or peptide: S-phase kinase-associated protein 2
      • Protein or peptide: Cyclin-dependent kinases regulatory subunit 1
      • Protein or peptide: S-phase kinase-associated protein 1
      • Protein or peptide: Polyubiquitin-C
    • Complex: Cyclin-dependent kinase inhibitor 1B
      • Protein or peptide: Cyclin-dependent kinase inhibitor 1B
  • Ligand: ZINC ION

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Supramolecule #1: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1

SupramoleculeName: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 250 KDa

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Supramolecule #2: Cullin-1, E3 ubiquitin-protein ligase RBX1

SupramoleculeName: Cullin-1, E3 ubiquitin-protein ligase RBX1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: ARIH1, SKP2, CKS1B, SKP1, UBC

SupramoleculeName: ARIH1, SKP2, CKS1B, SKP1, UBC / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Cyclin-dependent kinase inhibitor 1B

SupramoleculeName: Cyclin-dependent kinase inhibitor 1B / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.800367 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR ...String:
MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR DCLFRPLNKQ VTNAVLKLIE KERNGETINT RLISGVVQSY VELGLNEDDA FAKGPTLTVY KESFESQFLA DT ERFYTRE STEFLQQNPV TEYMKKAEAR LLEEQRRVQV YLHESTQDEL ARKCEQVLIE KHLEIFHTEF QNLLDADKNE DLG RMYNLV SRIQDGLGEL KKLLETHIHN QGLAAIEKCG EAALNDPKMY VQTVLDVHKK YNALVMSAFN NDAGFVAALD KACG RFINN NAVTKMAQSS SKSPELLARY CDSLLKKSSK NPEEAELEDT LNQVMVVFKY IEDKDVFQKF YAKMLAKRLV HQNSA SDDA EASMISKLKQ ACGFEYTSKL QRMFQDIGVS KDLNEQFKKH LTNSEPLDLD FSIQVLSSGS WPFQQSCTFA LPSELE RSY QRFTAFYASR HSGRKLTWLY QLSKGELVTN CFKNRYTLQA STFQMAILLQ YNTEDAYTVQ QLTDSTQIKM DILAQVL QI LLKSKLLVLE DENANVDEVE LKPDTLIKLY LGYKNKKLRV NINVPMKTEQ KQEQETTHKN IEEDRKLLIQ AAIVRIMK M RKVLKHQQLL GEVLTQLSSR FKPRVPVIKK CIDILIEKEY LERVDGEKDT YSYLA

UniProtKB: Cullin-1

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Macromolecule #2: E3 ubiquitin-protein ligase ARIH1

MacromoleculeName: E3 ubiquitin-protein ligase ARIH1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RBR-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.005605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDSDEGYNYE FDEDEECSEE DSGAEEEEDE DDDEPDDDTL DLGEVELVEP GLGVGGERDG LLCGETGGGG GSALGPGGGG GGGGGGGGG GPGHEQEEDY RYEVLTAEQI LQHMVECIRE VNEVIQNPAT ITRILLSHFN WDKEKLMERY FDGNLEKLFA E CHVINPSK ...String:
MDSDEGYNYE FDEDEECSEE DSGAEEEEDE DDDEPDDDTL DLGEVELVEP GLGVGGERDG LLCGETGGGG GSALGPGGGG GGGGGGGGG GPGHEQEEDY RYEVLTAEQI LQHMVECIRE VNEVIQNPAT ITRILLSHFN WDKEKLMERY FDGNLEKLFA E CHVINPSK KSRTRQMNTR SSAQDMPCQI CYLNYPNSYF TGLECGHKFC MQCWSEYLTT KIMEEGMGQT ISCPAHGCDI LV DDNTVMR LITDSKVKLK YQHLITNSFV ECNRLLKWCP APDCHHVVKV QYPDAKPVRC KCGRQFCFNC GENWHDPVKC KWL KKWIKK CDDDSETSNW IAANTKECPK CHVTIEKDGG CNHMVCRNQN CKAEFCWVCL GPWEPHGSAW YNCNRYNEDD AKAA RDAQE RSRAALQRYL FYCNRYMNHM QSLRAAHKLY AQVKQKMEEM QQHNMSWIEV QFLKKAVDVL CQCRATLMYT YVFAF YLKK NNQSIIFENN QADLENATAV LSGYLERDIS QDSLQDIKQK VQDKYRYCES RRRVLLQHVH EGYEKDLWEY IED

UniProtKB: E3 ubiquitin-protein ligase ARIH1

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Macromolecule #3: S-phase kinase-associated protein 2

MacromoleculeName: S-phase kinase-associated protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.817785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHRKHLQEIP DLSSNVATSF TWGWDSSKTS ELLSGMGVSA LEKEEPDSEN IPQELLSNLG HPESPPRKRL KSKGSDKDFV IVRRPKLNR ENFPGVSWDS LPDELLLGIF SCLCLPELLK VSGVCKRWYR LASDESLWQT LDLTGKNLHP DVTGRLLSQG V IAFRCPRS ...String:
MHRKHLQEIP DLSSNVATSF TWGWDSSKTS ELLSGMGVSA LEKEEPDSEN IPQELLSNLG HPESPPRKRL KSKGSDKDFV IVRRPKLNR ENFPGVSWDS LPDELLLGIF SCLCLPELLK VSGVCKRWYR LASDESLWQT LDLTGKNLHP DVTGRLLSQG V IAFRCPRS FMDQPLAEHF SPFRVQHMDL SNSVIEVSTL HGILSQCSKL QNLSLEGLRL SDPIVNTLAK NSNLVRLNLS GC SGFSEFA LQTLLSSCSR LDELNLSWCF DFTEKHVQVA VAHVSETITQ LNLSGYRKNL QKSDLSTLVR RCPNLVHLDL SDS VMLKND CFQEFFQLNY LQHLSLSRCY DIIPETLLEL GEIPTLKTLQ VFGIVPDGTL QLLKEALPHL QINCSHFTTI ARPT IGNKK NQEIWGIKCR LTLQKPSCL

UniProtKB: S-phase kinase-associated protein 2

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Macromolecule #4: Cyclin-dependent kinases regulatory subunit 1

MacromoleculeName: Cyclin-dependent kinases regulatory subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.679211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSHKQIYYSD KYDDEEFEYR HVMLPKDIAK LVPKTHLMSE SEWRNLGVQQ SQGWVHYMIH EPEPHILLFR RPLPKKPKK

UniProtKB: Cyclin-dependent kinases regulatory subunit 1

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Macromolecule #5: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #6: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.519778 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG

UniProtKB: Polyubiquitin-C

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Macromolecule #7: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #8: Cyclin-dependent kinase inhibitor 1B

MacromoleculeName: Cyclin-dependent kinase inhibitor 1B / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.185262 KDa
Recombinant expressionOrganism: synthetic construct (others)
SequenceString: MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW NFDFQNHKPL EGKYEWQEVE KGSLPEFYY RPPRPPKGAC KVPAQESQDV SGSRPAAPLI GAPANSEDTH LVDPKTDPSD SQTGLAEQCA GIRKRPATDD S ST(DHA)NKRAN ...String:
MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW NFDFQNHKPL EGKYEWQEVE KGSLPEFYY RPPRPPKGAC KVPAQESQDV SGSRPAAPLI GAPANSEDTH LVDPKTDPSD SQTGLAEQCA GIRKRPATDD S ST(DHA)NKRAN RTEENVSDGS PNAGSVEQ(TPO)P RRPGLRRRQT

UniProtKB: Cyclin-dependent kinase inhibitor 1B

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 5 / 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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 759489
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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