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- EMDB-18230: Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc3... -

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Basic information

Entry
Database: EMDB / ID: EMD-18230
TitleUbiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide
Map dataMap sharpened in deepEMhancer
Sample
  • Complex: Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide
    • Complex: RING E3 ligase (RBX1) and Cullin-2 (CUL2)
      • Protein or peptide: Cullin-2
      • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Complex: CDC34, NEDD8, ELOB, ELOC, FEM1C with UBE2R2-donor UB-Sil1 peptide
      • Protein or peptide: Protein fem-1 homolog C
      • Protein or peptide: Ubiquitin
      • Protein or peptide: Nucleotide exchange factor SIL1
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 R2
      • Protein or peptide: Elongin-C
      • Protein or peptide: Elongin-B
  • Ligand: 5-azanyl-1-oxidanyl-pentan-2-one
  • Ligand: ZINC ION
KeywordsCUL2 / FEM1C / ELOBC / SIL1 / Ubiquitin / Ubiquitin Ligase / Ubiquitylation / monoubiquitylation / LIGASE / Elongin B / Elongin C
Function / homology
Function and homology information


adenyl-nucleotide exchange factor activity / cotranslational protein targeting to membrane / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex ...adenyl-nucleotide exchange factor activity / cotranslational protein targeting to membrane / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / target-directed miRNA degradation / elongin complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / VCB complex / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / Prolactin receptor signaling / protein monoubiquitination / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / ubiquitin conjugating enzyme activity / cullin family protein binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / protein K48-linked ubiquitination / RNA Polymerase II Transcription Elongation / Nuclear events stimulated by ALK signaling in cancer / Formation of RNA Pol II elongation complex / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / RNA Polymerase II Pre-transcription Events / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / positive regulation of TORC1 signaling / post-translational protein modification / Downregulation of ERBB4 signaling / intrinsic apoptotic signaling pathway / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / regulation of cellular response to insulin stimulus / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / transcription corepressor binding / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / T cell activation / Gap-filling DNA repair synthesis and ligation in GG-NER
Similarity search - Function
Nucleotide exchange factor Fes1 / : / Nucleotide exchange factor Fes1 / : / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Elongin B / Elongin-C / : ...Nucleotide exchange factor Fes1 / : / Nucleotide exchange factor Fes1 / : / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Elongin B / Elongin-C / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / : / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / SKP1/BTB/POZ domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / 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 / E3 ubiquitin-protein ligase RBX1 / Cullin-2 / Elongin-C / Elongin-B / Ubiquitin-conjugating enzyme E2 R2 / Protein fem-1 homolog C / Nucleotide exchange factor SIL1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsLiwocha J / Prabu JR / Kleiger G / Schulman BA
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2024
Title: Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting.
Authors: Jerry Li / Nicholas Purser / Joanna Liwocha / Daniel C Scott / Holly A Byers / Barbara Steigenberger / Spencer Hill / Ishita Tripathi-Giesgen / Trent Hinkle / Fynn M Hansen / J Rajan Prabu / ...Authors: Jerry Li / Nicholas Purser / Joanna Liwocha / Daniel C Scott / Holly A Byers / Barbara Steigenberger / Spencer Hill / Ishita Tripathi-Giesgen / Trent Hinkle / Fynn M Hansen / J Rajan Prabu / Senthil K Radhakrishnan / Donald S Kirkpatrick / Kurt M Reichermeier / Brenda A Schulman / Gary Kleiger /
Abstract: Cullin-RING ligases (CRLs) ubiquitylate specific substrates selected from other cellular proteins. Substrate discrimination and ubiquitin transferase activity were thought to be strictly separated. ...Cullin-RING ligases (CRLs) ubiquitylate specific substrates selected from other cellular proteins. Substrate discrimination and ubiquitin transferase activity were thought to be strictly separated. Substrates are recognized by substrate receptors, such as Fbox or BCbox proteins. Meanwhile, CRLs employ assorted ubiquitin-carrying enzymes (UCEs, which are a collection of E2 and ARIH-family E3s) specialized for either initial substrate ubiquitylation (priming) or forging poly-ubiquitin chains. We discovered specific human CRL-UCE pairings governing substrate priming. The results reveal pairing of CUL2-based CRLs and UBE2R-family UCEs in cells, essential for efficient PROTAC-induced neo-substrate degradation. Despite UBE2R2's intrinsic programming to catalyze poly-ubiquitylation, CUL2 employs this UCE for geometrically precise PROTAC-dependent ubiquitylation of a neo-substrate and for rapid priming of substrates recruited to diverse receptors. Cryo-EM structures illuminate how CUL2-based CRLs engage UBE2R2 to activate substrate ubiquitylation. Thus, pairing with a specific UCE overcomes E2 catalytic limitations to drive substrate ubiquitylation and targeted protein degradation.
History
DepositionAug 16, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18230.png

Downloads & links

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Map

FileDownload / File: emd_18230.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap sharpened in deepEMhancer
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 380 pix.
= 323.456 Å		0.85 Å/pix.
x 380 pix.
= 323.456 Å		0.85 Å/pix.
x 380 pix.
= 323.456 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0322
Minimum - Maximum-0.023646925 - 2.093302
Average (Standard dev.)0.0009702012 (±0.020980388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 323.456 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18230_msk_1.map
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Additional map: Postprocessed map

Fileemd_18230_additional_1.map
AnnotationPostprocessed map
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Additional map: Focused map sharpened in deepEMhancer

Fileemd_18230_additional_2.map
AnnotationFocused map sharpened in deepEMhancer
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Half map: #2

Fileemd_18230_half_map_1.map
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Half map: #1

Fileemd_18230_half_map_2.map
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Sample components

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Entire : Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc3...

EntireName: Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide
Components
  • Complex: Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide
    • Complex: RING E3 ligase (RBX1) and Cullin-2 (CUL2)
      • Protein or peptide: Cullin-2
      • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Complex: CDC34, NEDD8, ELOB, ELOC, FEM1C with UBE2R2-donor UB-Sil1 peptide
      • Protein or peptide: Protein fem-1 homolog C
      • Protein or peptide: Ubiquitin
      • Protein or peptide: Nucleotide exchange factor SIL1
      • Protein or peptide: Ubiquitin-conjugating enzyme E2 R2
      • Protein or peptide: Elongin-C
      • Protein or peptide: Elongin-B
  • Ligand: 5-azanyl-1-oxidanyl-pentan-2-one
  • Ligand: ZINC ION

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Supramolecule #1: Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc3...

SupramoleculeName: Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 180 KDa

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Supramolecule #2: RING E3 ligase (RBX1) and Cullin-2 (CUL2)

SupramoleculeName: RING E3 ligase (RBX1) and Cullin-2 (CUL2) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #8
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: CDC34, NEDD8, ELOB, ELOC, FEM1C with UBE2R2-donor UB-Sil1 peptide

SupramoleculeName: CDC34, NEDD8, ELOB, ELOC, FEM1C with UBE2R2-donor UB-Sil1 peptide
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.09893 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK ...String:
MSLKPRVVDF DETWNKLLTT IKAVVMLEYV ERATWNDRFS DIYALCVAYP EPLGERLYTE TKIFLENHVR HLHKRVLESE EQVLVMYHR YWEEYSKGAD YMDCLYRYLN TQFIKKNKLT EADLQYGYGG VDMNEPLMEI GELALDMWRK LMVEPLQAIL I RMLLREIK NDRGGEDPNQ KVIHGVINSF VHVEQYKKKF PLKFYQEIFE SPFLTETGEY YKQEASNLLQ ESNCSQYMEK VL GRLKDEE IRCRKYLHPS SYTKVIHECQ QRMVADHLQF LHAECHNIIR QEKKNDMANM YVLLRAVSTG LPHMIQELQN HIH DEGLRA TSNLTQENMP TLFVESVLEV HGKFVQLINT VLNGDQHFMS ALDKALTSVV NYREPKSVCK APELLAKYCD NLLK KSAKG MTENEVEDRL TSFITVFKYI DDKDVFQKFY ARMLAKRLIH GLSMSMDSEE AMINKLKQAC GYEFTSKLHR MYTDM SVSA DLNNKFNNFI KNQDTVIDLG ISFQIYVLQA GAWPLTQAPS STFAIPQELE KSVQMFELFY SQHFSGRKLT WLHYLC TGE VKMNYLGKPY VAMVTTYQMA VLLAFNNSET VSYKELQDST QMNEKELTKT IKSLLDVKMI NHDSEKEDID AESSFSL NM NFSSKRTKFK ITTSMQKDTP QEMEQTRSAV DEDRKMYLQA AIVRIMKARK VLRHNALIQE VISQSRARFN PSISMIKK C IEVLIDKQYI ERSQASADEY SYVA

UniProtKB: Cullin-2

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Macromolecule #2: Protein fem-1 homolog C

MacromoleculeName: Protein fem-1 homolog C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.767312 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MDLKTAVFNA ARDGKLRLLT KLLASKSKEE VSSLISEKTN GATPLLMAAR YGHLDMVEFL LEQCSASIEV GGSVNFDGET IEGAPPLWA ASAAGHLKVV QSLLNHGASV NNTTLTNSTP LRAACFDGHL EIVKYLVEHK ADLEVSNRHG HTCLMISCYK G HKEIAQYL ...String:
MDLKTAVFNA ARDGKLRLLT KLLASKSKEE VSSLISEKTN GATPLLMAAR YGHLDMVEFL LEQCSASIEV GGSVNFDGET IEGAPPLWA ASAAGHLKVV QSLLNHGASV NNTTLTNSTP LRAACFDGHL EIVKYLVEHK ADLEVSNRHG HTCLMISCYK G HKEIAQYL LEKGADVNRK SVKGNTALHD CAESGSLDIM KMLLMYCAKM EKDGYGMTPL LSASVTGHTN IVDFLTHHAQ TS KTERINA LELLGATFVD KKRDLLGALK YWKKAMNMRY SDRTNIISKP VPQTLIMAYD YAKEVNSAEE LEGLIADPDE MRM QALLIR ERILGPSHPD TSYYIRYRGA VYADSGNFKR CINLWKYALD MQQSNLDPLS PMTASSLLSF AELFSFMLQD RAKG LLGTT VTFDDLMGIL CKSVLEIERA IKQTQCPADP LQLNKALSII LHLICLLEKV PCTLEQDHFK KQTIYRFLKL HPRGK NNFS PLHLAVDKNT TCVGRYPVCK FPSLQVTAIL IECGADVNVR DSDDNSPLHI AALNNHPDIM NLLIKSGAHF DATNLH KQT ASDLLDEKEI AKNLIQPINH TTLQCLAARV IVNHRIYYKG HIPEKLETFV SLHR

UniProtKB: Protein fem-1 homolog C

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Macromolecule #3: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 3
Details: ...Details: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGV
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.146438 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGMQIF VKTLTGKTI TLEVEPSDTI ENVKAKIQDK EGIPPDQQRL IFAGKQLEDG RTLSDYNIQK ESTLHLVLRL RGGMQIFVKT L TGKTITLE ...String:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGMQIF VKTLTGKTI TLEVEPSDTI ENVKAKIQDK EGIPPDQQRL IFAGKQLEDG RTLSDYNIQK ESTLHLVLRL RGGMQIFVKT L TGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRGG MQIFVKTLTG KT ITLEVEP SDTIENVKAK IQDKEGIPPD QQRLIFAGKQ LEDGRTLSDY NIQKESTLHL VLRLRGGMQI FVKTLTGKTI TLE VEPSDT IENVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLSDYNIQ KESTLHLVLR LRGGMQIFVK TLTGKTITLE VEPS DTIEN VKAKIQDKEG IPPDQQRLIF AGKQLEDGRT LSDYNIQKES TLHLVLRLRG GMQIFVKTLT GKTITLEVEP SDTIE NVKA KIQDKEGIPP DQQRLIFAGK QLEDGRTLSD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVEPSDT IENVKA KIQ DKEGIPPDQQ RLIFAGKQLE DGRTLSDYNI QKESTLHLVL RLRGGMQIFV KTLTGKTITL EVEPSDTIEN VKAKIQD KE GIPPDQQRLI FAGKQLEDGR TLSDYNIQKE STLHLVLRLR GGV

UniProtKB: Polyubiquitin-C

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Macromolecule #4: Nucleotide exchange factor SIL1

MacromoleculeName: Nucleotide exchange factor SIL1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.227457 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
CEGYFQELLG SVNPTQGRAR

UniProtKB: Nucleotide exchange factor SIL1

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Macromolecule #5: Ubiquitin-conjugating enzyme E2 R2

MacromoleculeName: Ubiquitin-conjugating enzyme E2 R2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.190932 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAQQQMTSSQ KALMLELKSL QEEPVEGFRI TLVDESDLYN WEVAIFGPPN TLYEGGYFKA HIKFPIDYPY SPPTFRFLTK MWHPNIYEN GDVCISILHP PVDDPQSGEL PSERWNPTQN VRTILLSVIS LLNEPNTFSP ANVDASVMFR KWRDSKGKDK E YAEIIRKQ ...String:
MAQQQMTSSQ KALMLELKSL QEEPVEGFRI TLVDESDLYN WEVAIFGPPN TLYEGGYFKA HIKFPIDYPY SPPTFRFLTK MWHPNIYEN GDVCISILHP PVDDPQSGEL PSERWNPTQN VRTILLSVIS LLNEPNTFSP ANVDASVMFR KWRDSKGKDK E YAEIIRKQ VSATKAEAEK DGVKVPTTLA EYCIKTKVPS NDNSSDLLYD DLYDDDIDDE DEEEEDADCY DDDDSGNEES

UniProtKB: Ubiquitin-conjugating enzyme E2 R2

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Macromolecule #6: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.485135 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC

UniProtKB: Elongin-C

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Macromolecule #7: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.147781 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

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Macromolecule #8: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 8 / 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 #9: 5-azanyl-1-oxidanyl-pentan-2-one

MacromoleculeName: 5-azanyl-1-oxidanyl-pentan-2-one / type: ligand / ID: 9 / Number of copies: 1 / Formula: U9O
Molecular weightTheoretical: 117.146 Da

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 3 / 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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5n4w

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135564
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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