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- EMDB-63447: The head-arm region of HBx-Smc5/6 ubiquitination complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63447
TitleThe head-arm region of HBx-Smc5/6 ubiquitination complex
Map data
Sample
  • Complex: The head-arm region of HBx-Smc5/6 ubiquitination complex
    • Protein or peptide: x 10 types
  • Ligand: x 1 types
KeywordsHBx / Smc5/6 / Cul4A-RBx / HBV / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


sex chromosome / cellular response to radiation / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of mitotic cytokinesis / positive regulation of chromosome segregation / Smc5-Smc6 complex / DNA secondary structure binding / symbiont-mediated activation of host NF-kappaB cascade / regulation of miRNA-mediated gene silencing / symbiont-mediated arrest of host cell cycle during G2/M transition ...sex chromosome / cellular response to radiation / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of mitotic cytokinesis / positive regulation of chromosome segregation / Smc5-Smc6 complex / DNA secondary structure binding / symbiont-mediated activation of host NF-kappaB cascade / regulation of miRNA-mediated gene silencing / symbiont-mediated arrest of host cell cycle during G2/M transition / interchromatin granule / SUMO ligase activity / regulation of cell cycle phase transition / regulation of stem cell population maintenance / cellular response to hydroxyurea / regulation of natural killer cell activation / host-mediated suppression of viral genome replication / negative regulation of adipose tissue development / negative regulation of beige fat cell differentiation / regulation of cellular response to stress / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / chromatin looping / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cellular response to chemical stress / positive regulation of mitotic metaphase/anaphase transition / positive regulation of protein autoubiquitination / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / positive regulation by virus of viral protein levels in host cell / RNA polymerase II transcription initiation surveillance / telomere maintenance via recombination / protein neddylation / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / NEDD8 ligase activity / regulation of telomere maintenance / negative regulation of response to oxidative stress / UV-damage excision repair / protein K27-linked ubiquitination / regulation of DNA-templated DNA replication initiation / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / biological process involved in interaction with symbiont / mitotic spindle pole / Cul3-RING ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / WD40-repeat domain binding / negative regulation of mitophagy / Prolactin receptor signaling / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / Cul4B-RING E3 ubiquitin ligase complex / ectopic germ cell programmed cell death / ubiquitin ligase complex scaffold activity / replication fork processing / viral release from host cell / regulation of embryonic development / protein sumoylation / chromosome, centromeric region / protein monoubiquitination / cullin family protein binding / host cell mitochondrion / positive regulation of viral genome replication / SUMOylation of DNA damage response and repair proteins / signal transduction in response to DNA damage / site of DNA damage / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / intrinsic apoptotic signaling pathway / post-translational protein modification / epigenetic regulation of gene expression / viral genome replication / positive regulation of protein ubiquitination / negative regulation of canonical NF-kappaB signal transduction / cellular response to amino acid stimulus / regulation of autophagy / Regulation of BACH1 activity / T cell activation / sperm end piece / sperm principal piece / G1/S transition of mitotic cell cycle / nucleotide-excision repair / proteasomal protein catabolic process / negative regulation of canonical Wnt signaling pathway
Similarity search - Function
Transactivation protein X / Trans-activation protein X / Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal ...Transactivation protein X / Trans-activation protein X / Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal / Binding domain of Nse4/EID3 to Nse3-MAGE / E3 SUMO-protein ligase Nse2 (Mms21) / Zinc-finger of the MIZ type in Nse subunit / Zinc finger, MIZ-type / MAGE conserved domain profile. / Zinc finger SP-RING-type profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / 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 / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-4A / DNA damage-binding protein 1 / Protein X / Structural maintenance of chromosomes protein 5 / EP300-interacting inhibitor of differentiation 3 / Non-structural maintenance of chromosomes element 1 homolog / E3 SUMO-protein ligase NSE2 / Non-structural maintenance of chromosomes element 3 homolog / Structural maintenance of chromosomes protein 6
Similarity search - Component
Biological speciesHomo sapiens (human) / Hepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.19 Å
AuthorsTong C / Lili D / Hongshuai L / Jinhong Z / Qian X / Lanfeng W
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303600 China
CitationJournal: Cell Res / Year: 2026
Title: Structural and functional insights into HBx-Smc6 targeting for HBV inhibition.
Authors: Tong Cheng / Jinhong Zhou / Wenjun Huang / Lili Du / Pengyu He / Renzheng Yang / Yan Gao / Menghan Hao / Kongying Hu / Jieliang Chen / Hongxia Wang / Zihe Rao / Zhenghong Yuan / Lanfeng Wang /
History
DepositionFeb 15, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63447.png

Downloads & links

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Map

FileDownload / File: emd_63447.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.86 Å/pix.
x 560 pix.
= 1043.84 Å		1.86 Å/pix.
x 560 pix.
= 1043.84 Å		1.86 Å/pix.
x 560 pix.
= 1043.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.864 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-3.4400976 - 7.7174234
Average (Standard dev.)-0.0007273225 (±0.13499346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 1043.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63447_msk_1.map
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Half map: #2

Fileemd_63447_half_map_1.map
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Half map: #1

Fileemd_63447_half_map_2.map
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Sample components

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Entire : The head-arm region of HBx-Smc5/6 ubiquitination complex

EntireName: The head-arm region of HBx-Smc5/6 ubiquitination complex
Components
  • Complex: The head-arm region of HBx-Smc5/6 ubiquitination complex
    • Protein or peptide: Structural maintenance of chromosomes protein 6
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein X
    • Protein or peptide: EP300-interacting inhibitor of differentiation 3
    • Protein or peptide: Non-structural maintenance of chromosomes element 3 homolog
    • Protein or peptide: Non-structural maintenance of chromosomes element 1 homolog
    • Protein or peptide: Cullin-4A
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Structural maintenance of chromosomes protein 5
    • Protein or peptide: E3 SUMO-protein ligase NSE2
  • Ligand: ZINC ION

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Supramolecule #1: The head-arm region of HBx-Smc5/6 ubiquitination complex

SupramoleculeName: The head-arm region of HBx-Smc5/6 ubiquitination complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Structural maintenance of chromosomes protein 6

MacromoleculeName: Structural maintenance of chromosomes protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 126.530883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAKRKEENFS SPKNAKRPRQ EELEDFDKDG DEDECKGTTL TAAEVGIIES IHLKNFMCHS MLGPFKFGSN VNFVVGNNGS GKSAVLTAL IVGLGGRAVA TNRGSSLKGF VKDGQNSADI SITLRNRGDD AFKASVYGNS ILIQQHISID GSRSYKLKSA T GSVVSTRK ...String:
MAKRKEENFS SPKNAKRPRQ EELEDFDKDG DEDECKGTTL TAAEVGIIES IHLKNFMCHS MLGPFKFGSN VNFVVGNNGS GKSAVLTAL IVGLGGRAVA TNRGSSLKGF VKDGQNSADI SITLRNRGDD AFKASVYGNS ILIQQHISID GSRSYKLKSA T GSVVSTRK EELIAILDHF NIQVDNPVSV LTQEMSKQFL QSKNEGDKYK FFMKATQLEQ MKEDYSYIME TKERTKEQIH QG EERLTEL KRQCVEKEER FQSIAGLSTM KTNLESLKHE MAWAVVNEIE KQLNAIRDNI KIGEDRAARL DRKMEEQQVR LNE AEQKYK DIQDKLEKIS EETNARAPEC MALKADVVAK KRAYNEAEVL YNRSLNEYKA LKKDDEQLCK RIEELKKSTD QSLE PERLE RQKKISWLKE RVKAFQNQEN SVNQEIEQFQ QAIEKDKEEH GKIKREELDV KHALSYNQRQ LKELKDSKTD RLKRF GPNV PALLEAIDDA YRQGHFTYKP VGPLGACIHL RDPELALAIE SCLKGLLQAY CCHNHADERV LQALMKRFYL PGTSRP PII VSEFRNEIYD VRHRAAYHPD FPTVLTALEI DNAVVANSLI DMRGIETVLL IKNNSVARAV MQSQKPPKNC REAFTAD GD QVFAGRYYSS ENTRPKFLSR DVDSEISDLE NEVENKTAQI LNLQQHLSAL EKDIKHNEEL LKRCQLHYKE LKMKIRKN I SEIRELENIE EHQSVDIATL EDEAQENKSK MKMVEEHMEQ QKENMEHLKS LKIEAENKYD AIKFKINQLS ELADPLKDE LNLADSEVDN QKRGKRHYEE KQKEHLDTLN KKKRELDMKE KELEEKMSQA RQICPERIEV EKSASILDKE INRLRQKIQA EHASHGDRE EIMRQYQEAR ETYLDLDSKV RTLKKFIKLL GEIMEHRFKT YQQFRRCLTL RCKLYFDNLL SQRAYCGKMN F DHKNETLS ISVQPGEGNK AAFNDMRALS GGERSFSTVC FILSLWSIAE SPFRCLDEFD VYMDMVNRRI AMDLILKMAD SQ RFRQFIL LTPQSMSSLP SSKLIRILRM SDPERGQTTL PFRPVTQEED DDQR

UniProtKB: Structural maintenance of chromosomes protein 6

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Macromolecule #2: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.097469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #3: Protein X

MacromoleculeName: Protein X / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 16.587289 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAARLCCQLD PARDVLCLRP VGAESCGRPF SGSLGTLSSP SPSAVPTDHG AHLSLRGLPV CAFSSAGPCA LRFTSARRME TTVNAHQIL PKVLHKRTLG LSAMSTTDLE AYFKDCLFKD WEELGEEIRL KVFVLGGCRH KLVCAPAPCN FFTSA

UniProtKB: Protein X

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Macromolecule #4: EP300-interacting inhibitor of differentiation 3

MacromoleculeName: EP300-interacting inhibitor of differentiation 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.213258 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKMDVSVRAA GCSDDLSSGE ADVDPKLLEL TADEEKCRSI RRQYRQLMYC VRQNREDIVS SANNSLTEAL EEANVLFDGV SRTREAALD ARFLVMASDL GKEKAKQLNS DMNFFNQLAF CDFLFLFVGL NWMEGDPDKL SDCDDSIALS FWKAIEKEAT S WMVKAETF ...String:
MKMDVSVRAA GCSDDLSSGE ADVDPKLLEL TADEEKCRSI RRQYRQLMYC VRQNREDIVS SANNSLTEAL EEANVLFDGV SRTREAALD ARFLVMASDL GKEKAKQLNS DMNFFNQLAF CDFLFLFVGL NWMEGDPDKL SDCDDSIALS FWKAIEKEAT S WMVKAETF HFVFGSFKLE RSAPKPRLEH QKKVRKMEEN GNMPTKLQKL DLSSYPEATE KNVERILGLL QTYFRKYPDT PV SYFEFVI DPNSFSRTVE NIFYVSFIVR DGFARIRLDE DRLPILEPMN VNQMGEGNDS SCHGRKQGVI SLTLQEWKNI VAA FEISEA MITYSSY

UniProtKB: EP300-interacting inhibitor of differentiation 3

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Macromolecule #5: Non-structural maintenance of chromosomes element 3 homolog

MacromoleculeName: Non-structural maintenance of chromosomes element 3 homolog
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.361 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLQKPRNRGR SGGQAERDRD WSHSGNPGAS RAGEDARVLR DGFAEEAPST SRGPGGSQGS QGPSPQGARR AQAAPAVGPR SQKQLELKV SELVQFLLIK DQKKIPIKRA DILKHVIGDY KDIFPDLFKR AAERLQYVFG YKLVELEPKS NTYILINTLE P VEEDAEMR ...String:
MLQKPRNRGR SGGQAERDRD WSHSGNPGAS RAGEDARVLR DGFAEEAPST SRGPGGSQGS QGPSPQGARR AQAAPAVGPR SQKQLELKV SELVQFLLIK DQKKIPIKRA DILKHVIGDY KDIFPDLFKR AAERLQYVFG YKLVELEPKS NTYILINTLE P VEEDAEMR GDQGTPTTGL LMIVLGLIFM KGNTIKETEA WDFLRRLGVY PTKKHLIFGD PKKLITEDFV RQRYLEYRRI PH TDPVDYE FQWGPRTNLE TSKMKVLKFV AKVHNQDPKD WPAQYCEALA DEENRARPQP SGPAPSS

UniProtKB: Non-structural maintenance of chromosomes element 3 homolog

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Macromolecule #6: Non-structural maintenance of chromosomes element 1 homolog

MacromoleculeName: Non-structural maintenance of chromosomes element 1 homolog
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.903527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQGSTRRMGV MTDVHRRFLQ LLMTHGVLEE WDVKRLQTHC YKVHDRNATV DKLEDFINNI NSVLESLYIE IKRGVTEDDG RPIYALVNL ATTSISKMAT DFAENELDLF RKALELIIDS ETGFASSTNI LNLVDQLKGK KMRKKEAEQV LQKFVQNKWL I EKEGEFTL ...String:
MQGSTRRMGV MTDVHRRFLQ LLMTHGVLEE WDVKRLQTHC YKVHDRNATV DKLEDFINNI NSVLESLYIE IKRGVTEDDG RPIYALVNL ATTSISKMAT DFAENELDLF RKALELIIDS ETGFASSTNI LNLVDQLKGK KMRKKEAEQV LQKFVQNKWL I EKEGEFTL HGRAILEMEQ YIRETYPDAV KICNICHSLL IQGQSCETCG IRMHLPCVAK YFQSNAEPRC PHCNDYWPHE IP KVFDPEK ERESGVLKSN KKSLRSRQH

UniProtKB: Non-structural maintenance of chromosomes element 1 homolog

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Macromolecule #7: Cullin-4A

MacromoleculeName: Cullin-4A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.871352 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 PNQYHYVAG

UniProtKB: Cullin-4A

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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: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #9: Structural maintenance of chromosomes protein 5

MacromoleculeName: Structural maintenance of chromosomes protein 5 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.014594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATPSKKTST PSPQPSKRAL PRDPSSEVPS KRKNSAPQLP LLQSSGPFVE GSIVRISMEN FLTYDICEVS PGPHLNMIVG ANGTGKSSI VCAICLGLAG KPAFMGRADK VGFFVKRGCS RGMVEIELFR ASGNLVITRE IDVAKNQSFW FINKKSTTQK I VEEKVAAL ...String:
MATPSKKTST PSPQPSKRAL PRDPSSEVPS KRKNSAPQLP LLQSSGPFVE GSIVRISMEN FLTYDICEVS PGPHLNMIVG ANGTGKSSI VCAICLGLAG KPAFMGRADK VGFFVKRGCS RGMVEIELFR ASGNLVITRE IDVAKNQSFW FINKKSTTQK I VEEKVAAL NIQVGNLCQF LPQDKVGEFA KLSKIELLEA TEKSIGPPEM HKYHCELKNL REKEKQLETS CKEKTEYLQK MV QRNERYK QDVERFYERK RHLDLIEMLE AKRPWVEYEN VRQEYEEVKL VRDRVKEEVR KLKEGQIPVT CRIEEMENER HNL EARIKE KATDIKEASQ KCKQKQDVIE RKDKHIEELQ QALIVKQNEE LDRQRRIGNT RKMIEDLQNE LKTTENCENL QPQI DAITN DLRRIQDEKA LCEGEIIDKR RERETLEKEK KSVDDHIVRF DNLMNQKEDK LRQRFRDTYD AVLWLRNNRD KFKQR VCEP IMLTINMKDN KNAKYIENHI PSNDLRAFVF ESQEDMEVFL KEVRDNKKLR VNAVIAPKSS YADKAPSRSL NELKQY GFF SYLRELFDAP DPVMSYLCCQ YHIHEVPVGT EKTRERIERV IQETRLKQIY TAEEKYVVKT SFYSNKVISS NTSLKVA QF LTVTVDLEQR RHLEEQLKEI HRKLQAVDSG LIALRETSKH LEHKDNELRQ KKKELLERKT KKRQLEQKIS SKLGSLKL M EQDTCNLEEE ERKASTKIKE INVQKAKLVT ELTNLIKICT SLHIQKVDLI LQNTTVISEK NKLESDYMAA SSQLRLTEQ HFIELDENRQ RLLQKCKELM KRARQVCNLG AEQTLPQEYQ TQVPTIPNGH NSSLPMVFQD LPNTLDEIDA LLTEERSRAS CFTGLNPTI VQEYTKREEE IEQLTEELKG KKVELDQYRE NISQVKERWL NPLKELVEKI NEKFSNFFSS MQCAGEVDLH T ENEEDYDK YGIRIRVKFR SSTQLHELTP HHQSGGERSV STMLYLMALQ ELNRCPFRVV DEINQGMDPI NERRVFEMVV NT ACKENTS QYFFITPKLL QNLPYSEKMT VLFVYNGPHM LEPNTWNLKA FQRRRRRITF TQPS

UniProtKB: Structural maintenance of chromosomes protein 5

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Macromolecule #10: E3 SUMO-protein ligase NSE2

MacromoleculeName: E3 SUMO-protein ligase NSE2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.977586 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPGRSSSNSG STGFISFSGV ESALSSLKNF QACINSGMDT ASSVALDLVE SQTEVSSEYS MDKAMVEFAT LDRQLNHYVK AVQSTINHV KEERPEKIPD LKLLVEKKFL ALQSKNSDAD FQNNEKFVQF KQQLKELKKQ CGLQADREAD GTEGVDEDII V TQSQTNFT ...String:
MPGRSSSNSG STGFISFSGV ESALSSLKNF QACINSGMDT ASSVALDLVE SQTEVSSEYS MDKAMVEFAT LDRQLNHYVK AVQSTINHV KEERPEKIPD LKLLVEKKFL ALQSKNSDAD FQNNEKFVQF KQQLKELKKQ CGLQADREAD GTEGVDEDII V TQSQTNFT CPITKEEMKK PVKNKVCGHT YEEDAIVRMI ESRQKRKKKA YCPQIGCSHT DIRKSDLIQD EALRRAIENH NK KRHRHSE

UniProtKB: E3 SUMO-protein ligase NSE2

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 6 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 48.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20327
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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