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- EMDB-15827: C(N)RL4CSA-UVSSA-E2-ubiquitin complex. -

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Basic information

Entry
Database: EMDB / ID: EMD-15827
TitleC(N)RL4CSA-UVSSA-E2-ubiquitin complex.
Map dataThe main map.
Sample
  • Complex: C(N)RL4CSA-UVSSA-E2-ubiquitin complex.
    • Protein or peptide: ubiquitin-conjugating enzyme E2 D2 isoform X3
    • Protein or peptide: NEDD8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Ubiquitin
    • Protein or peptide: DNA excision repair protein ERCC-8
    • Protein or peptide: UV-stimulated scaffold protein A
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Cullin-4A
  • Ligand: ZINC ION
Keywordstranscription / DNA repair / ubiquitin / cryo-EM
Function / homology
Function and homology information


regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / negative regulation of granulocyte differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / single strand break repair / cellular response to chemical stress / positive regulation by virus of viral protein levels in host cell / regulation of DNA damage checkpoint ...regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / negative regulation of granulocyte differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / single strand break repair / cellular response to chemical stress / 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 / double-strand break repair via classical nonhomologous end joining / regulation of nucleotide-excision repair / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul4-RING E3 ubiquitin ligase complex / positive regulation of protein autoubiquitination / UV-damage excision repair / protein neddylation / NEDD8 ligase activity / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / SCF ubiquitin ligase complex / WD40-repeat domain binding / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / negative regulation of reproductive process / negative regulation of developmental process / RNA polymerase II complex binding / TGF-beta receptor signaling activates SMADs / hemopoiesis / cullin family protein binding / viral release from host cell / regulation of postsynapse assembly / regulation of proteolysis / somatic stem cell population maintenance / anatomical structure morphogenesis / protein monoubiquitination / response to X-ray / positive regulation of G1/S transition of mitotic cell cycle / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / protein K48-linked ubiquitination / transcription-coupled nucleotide-excision repair / response to UV / protein autoubiquitination / Nuclear events stimulated by ALK signaling in cancer / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / regulation of cellular response to insulin stimulus / Prevention of phagosomal-lysosomal fusion / positive regulation of TORC1 signaling / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / positive regulation of gluconeogenesis / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / negative regulation of insulin receptor signaling pathway / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / post-translational protein modification / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / intrinsic apoptotic signaling pathway / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling
Similarity search - Function
UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Nedd8-like ubiquitin / ENTH/VHS / Zinc finger, RING-H2-type / RING-H2 zinc finger domain ...UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Nedd8-like ubiquitin / ENTH/VHS / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / 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. / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / 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 / 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 / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2 isoform X3 / Polyubiquitin-C / E3 ubiquitin-protein ligase RBX1 / DNA excision repair protein ERCC-8 / Cullin-4A / Ubiquitin-like protein NEDD8 / DNA damage-binding protein 1 / UV-stimulated scaffold protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsKokic G / Cramer P
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
European Research Council (ERC)Advanced Investigator Grant CHROMATRANS (grant agreement No. 882357)European Union
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair.
Authors: Goran Kokic / George Yakoub / Diana van den Heuvel / Annelotte P Wondergem / Paula J van der Meer / Yana van der Weegen / Aleksandar Chernev / Isaac Fianu / Thornton J Fokkens / Sonja Lorenz ...Authors: Goran Kokic / George Yakoub / Diana van den Heuvel / Annelotte P Wondergem / Paula J van der Meer / Yana van der Weegen / Aleksandar Chernev / Isaac Fianu / Thornton J Fokkens / Sonja Lorenz / Henning Urlaub / Patrick Cramer / Martijn S Luijsterburg /
Abstract: During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This ...During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This transition requires site-specific ubiquitylation of Pol II by the CRL4 ubiquitin ligase, a process that is facilitated by ELOF1 in an unknown way. Using cryogenic electron microscopy, biochemical assays and cell biology approaches, we found that ELOF1 serves as an adaptor to stably position UVSSA and CRL4 on arrested Pol II, leading to ligase neddylation and activation of Pol II ubiquitylation. In the presence of ELOF1, a transcription factor IIS (TFIIS)-like element in UVSSA gets ordered and extends through the Pol II pore, thus preventing reactivation of Pol II by TFIIS. Our results provide the structural basis for Pol II ubiquitylation and inactivation in TCR.
History
DepositionSep 16, 2022-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15827.png

Downloads & links

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Map

FileDownload / File: emd_15827.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe main map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 300 pix.
= 369. Å		1.23 Å/pix.
x 300 pix.
= 369. Å		1.23 Å/pix.
x 300 pix.
= 369. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.645
Minimum - Maximum-0.40935308 - 1.8065721
Average (Standard dev.)-0.0011034171 (±0.08611868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 369.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map corresponding to the main map.

Fileemd_15827_half_map_1.map
AnnotationHalf map corresponding to the main map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map corresponding to the main map.

Fileemd_15827_half_map_2.map
AnnotationHalf map corresponding to the main map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C(N)RL4CSA-UVSSA-E2-ubiquitin complex.

EntireName: C(N)RL4CSA-UVSSA-E2-ubiquitin complex.
Components
  • Complex: C(N)RL4CSA-UVSSA-E2-ubiquitin complex.
    • Protein or peptide: ubiquitin-conjugating enzyme E2 D2 isoform X3
    • Protein or peptide: NEDD8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Ubiquitin
    • Protein or peptide: DNA excision repair protein ERCC-8
    • Protein or peptide: UV-stimulated scaffold protein A
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Cullin-4A
  • Ligand: ZINC ION

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Supramolecule #1: C(N)RL4CSA-UVSSA-E2-ubiquitin complex.

SupramoleculeName: C(N)RL4CSA-UVSSA-E2-ubiquitin complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ubiquitin-conjugating enzyme E2 D2 isoform X3

MacromoleculeName: ubiquitin-conjugating enzyme E2 D2 isoform X3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.755227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALKRIHKEL NDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSICSL LCDPNPDDPL VPEIARIYKT DREKYNRIAR EWTQKYAM

UniProtKB: Ubiquitin-conjugating enzyme E2 D2 isoform X3

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Macromolecule #2: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.573978 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGG

UniProtKB: Ubiquitin-like protein NEDD8

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Macromolecule #3: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 3 / 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 #4: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

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Macromolecule #5: DNA excision repair protein ERCC-8

MacromoleculeName: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.10716 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #6: UV-stimulated scaffold protein A

MacromoleculeName: UV-stimulated scaffold protein A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.72168 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELFV RSHQFRMLVV SNFQEFLEL TLGTDPAQPL PPPREAAQRL RQATTRAVEG WNEKFGEAYK KLALGYHFLR HNKKVDFQDT NARSLAERKR E EEKQKHLD ...String:
MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELFV RSHQFRMLVV SNFQEFLEL TLGTDPAQPL PPPREAAQRL RQATTRAVEG WNEKFGEAYK KLALGYHFLR HNKKVDFQDT NARSLAERKR E EEKQKHLD KIYQERASQA EREMQEMSGE IESCLTEVES CFRLLVPFDF DPNPETESLG MASGMSDALR SSCAGQVGPC RS GTPDPRD GEQPCCSRDL PASAGHPRAG GGAQPSQTAT GDPSDEDEDS DLEEFVRSHG LGSHKYTLDV ELCSEGLKVQ ENE DNLALI HAARDTLKLI RNKFLPAVCS WIQRFTRVGT HGGCLKRAID LKAELELVLR KYKELDIEPE GGERRRTEAL GDAE EDEDD EDFVEVPEKE GYEPHIPDHL RPEYGLEAAP EKDTVVRCLR TRTRMDEEVS DPTSAAAQLR QLRDHLPPPS SASPS RALP EPQEAQKLAA ERARAPVVPY GVDLHYWGQE LPTAGKIVKS DSQHRFWKPS EVEEEVVNAD ISEMLRSRHI TFAGKF EPV QHWCRAPRPD GRLCERQDRL KCPFHGKIVP RDDEGRPLDP EDRAREQRRQ LQKQERPEWQ DPELMRDVEA ATGQDLG SS RYSGKGRGKK RRYPSLTNLK AQADTARARI GRKVFAKAAV RRVVAAMNRM DQKKHEKFSN QFNYALN

UniProtKB: UV-stimulated scaffold protein A

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Macromolecule #7: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.097469 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #8: Cullin-4A

MacromoleculeName: Cullin-4A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.814297 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / 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

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5500000000000003 µm / Nominal defocus min: 0.4 µm

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio reconstruction in CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67365
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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