+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15829 | |||||||||
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Title | CRL4CSA-E2-Ub (state 2) | |||||||||
Map data | The main map. | |||||||||
Sample |
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Keywords | DNA repair / transcription / ubiqutin / cryo-EM | |||||||||
Function / homology | Function and homology information regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / negative regulation of granulocyte differentiation / single strand break repair / (E3-independent) E2 ubiquitin-conjugating enzyme / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / positive regulation by virus of viral protein levels in host cell ...regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / negative regulation of granulocyte differentiation / single strand break repair / (E3-independent) E2 ubiquitin-conjugating enzyme / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / positive regulation by virus of viral protein levels in host cell / regulation of DNA damage checkpoint / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of nucleotide-excision repair / spindle assembly involved in female meiosis / regulation of proteolysis / epigenetic programming in the zygotic pronuclei / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / double-strand break repair via classical nonhomologous end joining / Cul4-RING E3 ubiquitin ligase complex / positive regulation of protein autoubiquitination / UV-damage excision repair / protein neddylation / NEDD8 ligase activity / biological process involved in interaction with symbiont / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / regulation of mitotic cell cycle phase transition / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / E2 ubiquitin-conjugating enzyme / negative regulation of reproductive process / negative regulation of developmental process / Prolactin receptor signaling / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / somatic stem cell population maintenance / viral release from host cell / hemopoiesis / cullin family protein binding / ubiquitin conjugating enzyme activity / ectopic germ cell programmed cell death / response to X-ray / transcription-coupled nucleotide-excision repair / anatomical structure morphogenesis / positive regulation of G1/S transition of mitotic cell cycle / protein autoubiquitination / proteasomal protein catabolic process / positive regulation of viral genome replication / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / response to UV / ubiquitin ligase complex / positive regulation of gluconeogenesis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of TORC1 signaling / VLDLR internalisation and degradation / intrinsic apoptotic signaling pathway / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / post-translational protein modification / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / positive regulation of DNA repair / Regulation of innate immune responses to cytosolic DNA / regulation of cellular response to insulin stimulus / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Kokic G / Cramer P | |||||||||
Funding support | Germany, European Union, 2 items
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Citation | Journal: To Be Published Title: C(N)RL4CSA-E2-Ub (state 2) Authors: Kokic G / Cramer P | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15829.map.gz | 141.6 MB | EMDB map data format | |
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Header (meta data) | emd-15829-v30.xml emd-15829.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15829_fsc.xml | 12.1 KB | Display | FSC data file |
Images | emd_15829.png | 129.7 KB | ||
Others | emd_15829_half_map_1.map.gz emd_15829_half_map_2.map.gz | 139.3 MB 139.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15829 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15829 | HTTPS FTP |
-Validation report
Summary document | emd_15829_validation.pdf.gz | 939.4 KB | Display | EMDB validaton report |
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Full document | emd_15829_full_validation.pdf.gz | 938.9 KB | Display | |
Data in XML | emd_15829_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | emd_15829_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15829 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15829 | HTTPS FTP |
-Related structure data
Related structure data | 8b3iMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15829.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | The main map. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map corresponding to the main map.
File | emd_15829_half_map_1.map | ||||||||||||
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Annotation | Half map corresponding to the main map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map corresponding to the main map.
File | emd_15829_half_map_2.map | ||||||||||||
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Annotation | Half map corresponding to the main map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C(N)RL4CSA-E2-Ub complex.
Entire | Name: C(N)RL4CSA-E2-Ub complex. |
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Components |
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-Supramolecule #1: C(N)RL4CSA-E2-Ub complex.
Supramolecule | Name: C(N)RL4CSA-E2-Ub complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ubiquitin-conjugating enzyme E2 D2
Macromolecule | Name: Ubiquitin-conjugating enzyme E2 D2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.755227 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MALKRIHKEL NDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSICSL LCDPNPDDPL VPEIARIYKT DREKYNRIAR EWTQKYAM UniProtKB: Ubiquitin-conjugating enzyme E2 D2 |
-Macromolecule #2: NEDD8
Macromolecule | Name: NEDD8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.573978 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGG UniProtKB: NEDD8 |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 12.289977 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH UniProtKB: E3 ubiquitin-protein ligase RBX1 |
-Macromolecule #4: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.576831 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG UniProtKB: Polyubiquitin-C |
-Macromolecule #5: DNA excision repair protein ERCC-8
Macromolecule | Name: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.10716 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV ...String: MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV QLCDLKSGSC SHILQGHRQE ILAVSWSPRY DYILATASAD SRVKLWDVRR ASGCLITLDQ HNGKKSQAVE SA NTAHNGK VNGLCFTSDG LHLLTVGTDN RMRLWNSSNG ENTLVNYGKV CNNSKKGLKF TVSCGCSSEF VFVPYGSTIA VYT VYSGEQ ITMLKGHYKT VDCCVFQSNF QELYSGSRDC NILAWVPSLY EPVPDDDETT TKSQLNPAFE DAWSSSDEEG UniProtKB: DNA excision repair protein ERCC-8 |
-Macromolecule #6: DNA damage-binding protein 1
Macromolecule | Name: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 127.097469 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK ...String: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRNGIGI HEHA SIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFCGNVAH QQLIQITSAS VRLVS QEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVACLDIT PLGDSNGLSP LCAIGL WTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIETGLL SDRKKVTLGT QPTVLRT FR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLTIG TIDEIQKLHI RTVPLYES P RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHETS FGEEVEVHNL LIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME GNFEEIARDF NPNWMSAVEI L DDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ETSTPTQGSV LFGTVNGMIG LV TSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGM KREATA DDLIKVVEEL TRIH UniProtKB: DNA damage-binding protein 1 |
-Macromolecule #7: Cullin-4A
Macromolecule | Name: Cullin-4A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 87.814297 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MADEAPRKGS FSALVGRTNG LTKPAALAAA PAKPGGAGGS KKLVIKNFRD RPRLPDNYTQ DTWRKLHEAV RAVQSSTSIR YNLEELYQA VENLCSHKVS PMLYKQLRQA CEDHVQAQIL PFREDSLDSV LFLKKINTCW QDHCRQMIMI RSIFLFLDRT Y VLQNSTLP ...String: MADEAPRKGS FSALVGRTNG LTKPAALAAA PAKPGGAGGS KKLVIKNFRD RPRLPDNYTQ DTWRKLHEAV RAVQSSTSIR YNLEELYQA VENLCSHKVS PMLYKQLRQA CEDHVQAQIL PFREDSLDSV LFLKKINTCW QDHCRQMIMI RSIFLFLDRT Y VLQNSTLP SIWDMGLELF RTHIISDKMV QSKTIDGILL LIERERSGEA VDRSLLRSLL GMLSDLQVYK DSFELKFLEE TN CLYAAEG QRLMQEREVP EYLNHVSKRL EEEGDRVITY LDHSTQKPLI ACVEKQLLGE HLTAILQKGL DHLLDENRVP DLA QMYQLF SRVRGGQQAL LQHWSEYIKT FGTAIVINPE KDKDMVQDLL DFKDKVDHVI EVCFQKNERF VNLMKESFET FINK RPNKP AELIAKHVDS KLRAGNKEAT DEELERTLDK IMILFRFIHG KDVFEAFYKK DLAKRLLVGK SASVDAEKSM LSKLK HECG AAFTSKLEGM FKDMELSKDI MVHFKQHMQN QSDSGPIDLT VNILTMGYWP TYTPMEVHLT PEMIKLQEVF KAFYLG KHS GRKLQWQTTL GHAVLKAEFK EGKKEFQVSL FQTLVLLMFN EGDGFSFEEI KMATGIEDSE LRRTLQSLAC GKARVLI KS PKGKEVEDGD KFIFNGEFKH KLFRIKINQI QMKETVEEQV STTERVFQDR QYQIDAAIVR IMKMRKTLGH NLLVSELY N QLKFPVKPGD LKKRIESLID RDYMERDKDN PNQYHYVA UniProtKB: Cullin-4A |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-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: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.15 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |