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- EMDB-31766: CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-31766
TitleCryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex
Map data
Sample
  • Complex: DDB1-VprBP-Vpr-UNG2(94-313) complex
    • Protein or peptide: DDB1- and CUL4-associated factor 1
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein Vpr
    • Protein or peptide: Uracil-DNA glycosylase
KeywordsE3 ligase / HIV accessory protein / restriction factors / LIGASE / TRANSFERASE-DNA BINDING PROTEIN-VIRAL PROTEIN complex
Function / homology
Function and homology information


cell competition in a multicellular organism / symbiont-mediated perturbation of host cell cycle progression / symbiont-mediated arrest of host cell cycle during G2/M transition / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / single strand break repair / V(D)J recombination / positive regulation by virus of viral protein levels in host cell ...cell competition in a multicellular organism / symbiont-mediated perturbation of host cell cycle progression / symbiont-mediated arrest of host cell cycle during G2/M transition / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / single strand break repair / V(D)J recombination / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / isotype switching / Cul4-RING E3 ubiquitin ligase complex / uracil DNA N-glycosylase activity / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / ectopic germ cell programmed cell death / ubiquitin-like ligase-substrate adaptor activity / positive regulation of viral genome replication / proteasomal protein catabolic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / positive regulation of gluconeogenesis / post-translational protein modification / B cell differentiation / Chromatin modifications during the maternal to zygotic transition (MZT) / nuclear estrogen receptor binding / nucleotide-excision repair / symbiont-mediated activation of host apoptosis / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / base-excision repair / protein homooligomerization / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / virion component / Wnt signaling pathway / Formation of Incision Complex in GG-NER / viral penetration into host nucleus / fibrillar center / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / host cell / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / monoatomic ion transmembrane transport / proteasome-mediated ubiquitin-dependent protein catabolic process / host extracellular space / damaged DNA binding / eukaryotic translation initiation factor 2alpha kinase activity / chromosome, telomeric region / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein ubiquitination / symbiont entry into host cell / protein serine kinase activity / DNA repair / DNA-templated transcription / apoptotic process / centrosome / DNA damage response / regulation of DNA-templated transcription
Similarity search - Function
Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Uracil-DNA glycosylase family 1 / Lissencephaly type-1-like homology motif / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like ...Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Uracil-DNA glycosylase family 1 / Lissencephaly type-1-like homology motif / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Uracil-DNA glycosylase-like domain superfamily / 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 / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein Vpr / Uracil-DNA glycosylase / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang D / Xu J
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501100 China
National Natural Science Foundation of China (NSFC)31925023 China
National Natural Science Foundation of China (NSFC)21827810 China
National Natural Science Foundation of China (NSFC)31861143027 China
National Natural Science Foundation of China (NSFC)31470721 China
CitationJournal: To Be Published
Title: Structural insights into the HIV-1 Vpr mediated ubiquitination through the Cullin-RING E3 ubiquitin ligase
Authors: Wang D / Xu J / Liu Q / Xiang Y
History
DepositionAug 21, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31766.png

Downloads & links

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Map

FileDownload / File: emd_31766.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 343.744 Å		1.07 Å/pix.
x 320 pix.
= 343.744 Å		1.07 Å/pix.
x 320 pix.
= 343.744 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.039512962 - 2.0156863
Average (Standard dev.)0.002345064 (±0.034470778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 343.74402 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : DDB1-VprBP-Vpr-UNG2(94-313) complex

EntireName: DDB1-VprBP-Vpr-UNG2(94-313) complex
Components
  • Complex: DDB1-VprBP-Vpr-UNG2(94-313) complex
    • Protein or peptide: DDB1- and CUL4-associated factor 1
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein Vpr
    • Protein or peptide: Uracil-DNA glycosylase

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Supramolecule #1: DDB1-VprBP-Vpr-UNG2(94-313) complex

SupramoleculeName: DDB1-VprBP-Vpr-UNG2(94-313) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 0.66 kDa/nm

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Macromolecule #1: DDB1- and CUL4-associated factor 1

MacromoleculeName: DDB1- and CUL4-associated factor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 169.194781 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTTVVVHVDS KAELTTLLEQ WEKEHGSGQD MVPILTRMSQ LIEKETEEYR KGDPDPFDDR HPGRADPECM LGHLLRILFK NDDFMNALV NAYVMTSREP PLNTAACRLL LDIMPGLETA VVFQEKEGIV ENLFKWAREA DQPLRTYSTG LLGGAMENQD I AANYRDEN ...String:
MTTVVVHVDS KAELTTLLEQ WEKEHGSGQD MVPILTRMSQ LIEKETEEYR KGDPDPFDDR HPGRADPECM LGHLLRILFK NDDFMNALV NAYVMTSREP PLNTAACRLL LDIMPGLETA VVFQEKEGIV ENLFKWAREA DQPLRTYSTG LLGGAMENQD I AANYRDEN SQLVAIVLRR LRELQLQEVA LRQENKRPSP RKLSSEPLLP LDEEAVDMDY GDMAVDVVDG DQEEASGDME IS FHLDSGH KTSSRVNSTT KPEDGGLKKN KSAKQGDREN FRKAKQKLGF SSSDPDRMFV ELSNSSWSEM SPWVIGTNYT LYP MTPAIE QRLILQYLTP LGEYQELLPI FMQLGSRELM MFYIDLKQTN DVLLTFEALK HLASLLLHNK FATEFVAHGG VQKL LEIPR PSMAATGVSM CLYYLSYNQD AMERVCMHPH NVLSDVVNYT LWLMECSHAS GCCHATMFFS ICFSFRAVLE LFDRY DGLR RLVNLISTLE ILNLEDQGAL LSDDEIFASR QTGKHTCMAL RKYFEAHLAI KLEQVKQSLQ RTEGGILVHP QPPYKA CSY THEQIVEMME FLIEYGPAQL YWEPAEVFLK LSCVQLLLQL ISIACNWKTY YARNDTVRFA LDVLAILTVV PKIQLQL AE SVDVLDEAGS TVSTVGISII LGVAEGEFFI HDAEIQKSAL QIIINCVCGP DNRISSIGKF ISGTPRRKLP QNPKSSEH T LAKMWNVVQS NNGIKVLLSL LSIKMPITDA DQIRALACKA LVGLSRSSTV RQIISKLPLF SSCQIQQLMK EPVLQDKRS DHVKFCKYAA ELIERVSGKP LLIGTDVSLA RLQKADVVAQ SRISFPEKEL LLLIRNHLIS KGLGETATVL TKEADLPMTA ASHSSAFTP VTAAASPVSL PRTPRIANGI ATRLGSHAAV GASAPSAPTA HPQPRPPQGP LALPGPSYAG NSPLIGRISF I RERPSPCN GRKIRVLRQK SDHGAYSQSP AIKKQLDRHL PSPPTLDSII TEYLREQHAR CKNPVATCPP FSLFTPHQCP EP KQRRQAP INFTSRLNRR ASFPKYGGVD GGCFDRHLIF SRFRPISVFR EANEDESGFT CCAFSARERF LMLGTCTGQL KLY NVFSGQ EEASYNCHNS AITHLEPSRD GSLLLTSATW SQPLSALWGM KSVFDMKHSF TEDHYVEFSK HSQDRVIGTK GDIA HIYDI QTGNKLLTLF NPDLANNYKR NCATFNPTDD LVLNDGVLWD VRSAQAIHKF DKFNMNISGV FHPNGLEVII NTEIW DLRT FHLLHTVPAL DQCRVVFNHT GTVMYGAMLQ ADDEDDLMEE RMKSPFGSSF RTFNATDYKP IATIDVKRNI FDLCTD TKD CYLAVIENQG SMDALNMDTV CRLYEVGRQR LAEDEDEEED QEEEEQEEED DDEDDDDTDD LDELDTDQLL EAELEED DN NENAGEDGDN DFSPSDEELA NLLEEGEDGE DEDSDADEEV ELILGDTDSS DNSDLEDDII LSLNE

UniProtKB: DDB1- and CUL4-associated factor 1

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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: 2 / 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 #3: Protein Vpr

MacromoleculeName: Protein Vpr / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 11.396878 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEQAPEDQGP QREPYNEWTL ELLEELKSEA VRHFPRIWLH NLGQHIYETY GDTWAGVEAI IRILQQLLFI HFRIGCRHSR IGVTRQRRA RNGASRS

UniProtKB: Protein Vpr

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Macromolecule #4: Uracil-DNA glycosylase

MacromoleculeName: Uracil-DNA glycosylase / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: uracil-DNA glycosylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.136654 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FGESWKKHLS GEFGKPYFIK LMGFVAEERK HYTVYPPPHQ VFTWTQMCDI KDVKVVILGQ DPYHGPNQAH GLCFSVQRPV PPPPSLENI YKELSTDIED FVHPGHGDLS GWAKQGVLLL NAVLTVRAHQ ANSHKERGWE QFTDAVVSWL NQNSNGLVFL L WGSYAQKK ...String:
FGESWKKHLS GEFGKPYFIK LMGFVAEERK HYTVYPPPHQ VFTWTQMCDI KDVKVVILGQ DPYHGPNQAH GLCFSVQRPV PPPPSLENI YKELSTDIED FVHPGHGDLS GWAKQGVLLL NAVLTVRAHQ ANSHKERGWE QFTDAVVSWL NQNSNGLVFL L WGSYAQKK GSAIDRKRHH VLQTAHPSPL SVYRGFFGCR HFSKTNELLQ KSGKKPIDWK EL

UniProtKB: Uracil-DNA glycosylase

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 145568
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7v7c:
CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex

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