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- EMDB-19856: Focused map 1- K48-linked ubiquitin chain formation with a cullin... -
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Basic information
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Title | Focused map 1- K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide | |||||||||
![]() | DeepEMhancer map | |||||||||
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![]() | CUL2 / FEM1C / ELOBC / SIL1 / Ubiquitin / Ubiquitin Ligase / Ubiquitin chain formation / Poliubiquitylation / LIGASE | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.55 Å | |||||||||
![]() | Liwocha J / Prabu JR / Kleiger G / Schulman BA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases. Authors: Joanna Liwocha / Jerry Li / Nicholas Purser / Chutima Rattanasopa / Samuel Maiwald / David T Krist / Daniel C Scott / Barbara Steigenberger / J Rajan Prabu / Brenda A Schulman / Gary Kleiger / ![]() ![]() Abstract: E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked ...E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked poly-ubiquitin chains to control an enormous swath of eukaryotic biology. Yet the molecular mechanisms underlying this exceptional linkage specificity and millisecond kinetics of poly-ubiquitylation remain unclear. Here we obtain cryogenic-electron microscopy (cryo-EM) structures that provide pertinent insight into how such poly-ubiquitin chains are forged. The CRL RING domain not only activates the E2-bound ubiquitin but also shapes the conformation of a distinctive UBE2R2 loop, positioning both the ubiquitin to be transferred and the substrate-linked acceptor ubiquitin within the active site. The structures also reveal how the ubiquitin-like protein NEDD8 uniquely activates CRLs during chain formation. NEDD8 releases the RING domain from the CRL, but unlike previous CRL-E2 structures, does not contact UBE2R2. These findings suggest how poly-ubiquitylation may be accomplished by many E2s and E3s. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 181.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.4 KB 25.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.5 KB | Display | ![]() |
Images | ![]() | 50.9 KB | ||
Masks | ![]() | 209.3 MB | ![]() | |
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() ![]() | 10.8 MB 166.5 MB 165.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 828.4 KB | Display | ![]() |
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Full document | ![]() | 828 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | DeepEMhancer map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8512 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Postprocessed map
File | emd_19856_additional_1.map | ||||||||||||
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Annotation | Postprocessed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19856_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19856_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : K48-linked ubiquitin chain formation with a cullin-RING E3 ligase...
Entire | Name: K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and CDC34:NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide |
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Components |
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-Supramolecule #1: K48-linked ubiquitin chain formation with a cullin-RING E3 ligase...
Supramolecule | Name: K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and CDC34:NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 190 KDa |
-Supramolecule #2: RING E3 ligase (RBX1) and Cullin-2 (CUL2)
Supramolecule | Name: RING E3 ligase (RBX1) and Cullin-2 (CUL2) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: Elongin-B (ELOB), Elongin-C (ELOC), Protein fem-1 homolog C (FEM1...
Supramolecule | Name: Elongin-B (ELOB), Elongin-C (ELOC), Protein fem-1 homolog C (FEM1C) and trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2, #5-#6 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Polyubiquitin-C,Nucleotide exchange factor SIL1
Macromolecule | Name: Polyubiquitin-C,Nucleotide exchange factor SIL1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 79.226711 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGCQL EDGRTLSDYN IQKESTLHLV LRLRGGMQIF VKTLTGKTI TLEVEPSDTI ENVKAKIQDK EGIPPDQQRL IFAGKQLEDG RTLSDYNIQK ESTLHLVLRL RGGMQIFVKT L TGKTITLE ...String: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGCQL 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 GGVEGYFQEL LGSVNPTQGR AR |
-Macromolecule #2: Protein fem-1 homolog C
Macromolecule | Name: Protein fem-1 homolog C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 68.767312 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: E3 ubiquitin-protein ligase RBX1
Macromolecule | Name: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.289977 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH |
-Macromolecule #4: Cullin-2
Macromolecule | Name: Cullin-2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 87.09893 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #5: Elongin-C
Macromolecule | Name: Elongin-C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.485135 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC |
-Macromolecule #6: Elongin-B
Macromolecule | Name: Elongin-B / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.147781 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |