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- EMDB-29490: HIV-1 Vif in complex with human APOBEC3H, CBF-beta, ELOB, ELOC, C... -

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Basic information

Entry
Database: EMDB / ID: EMD-29490
TitleHIV-1 Vif in complex with human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
Map data
Sample
  • Complex: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-5
    • Protein or peptide: RING-box protein 2
    • Protein or peptide: DNA dC->dU-editing enzyme APOBEC-3H
Keywordsvirus-host protein complex / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / mRNA Editing: C to U Conversion / Formation of the Editosome / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation ...RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / mRNA Editing: C to U Conversion / Formation of the Editosome / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / single-stranded DNA cytosine deaminase / negative regulation of CD4-positive, alpha-beta T cell differentiation / DNA cytosine deamination / cytidine to uridine editing / negative regulation by host of viral genome replication / deoxycytidine deaminase activity / lymphocyte differentiation / ERBB2 signaling pathway / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / retrotransposon silencing / NEDD8 transferase activity / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / target-directed miRNA degradation / elongin complex / RUNX3 Regulates Immune Response and Cell Migration / VCB complex / definitive hemopoiesis / protein neddylation / DNA demethylation / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / response to redox state / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX2 regulates osteoblast differentiation / site of DNA damage / cullin family protein binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RUNX3 regulates p14-ARF / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / cell maturation / viral life cycle / RNA Polymerase II Pre-transcription Events / post-translational protein modification / intrinsic apoptotic signaling pathway / transcription corepressor binding / virion component / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / G1/S transition of mitotic cell cycle / calcium channel activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Downregulation of ERBB2 signaling / osteoblast differentiation / Regulation of expression of SLITs and ROBOs / protein polyubiquitination / Transcriptional regulation of granulopoiesis / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / defense response to virus / Estrogen-dependent gene expression / host cell cytoplasm / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity
Similarity search - Function
APOBEC3H / APOBEC3 / Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / APOBEC/CMP deaminase, zinc-binding ...APOBEC3H / APOBEC3 / Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Elongin B / Cullin / Elongin-C / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cytidine deaminase-like / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Virion infectivity factor / Core-binding factor subunit beta / Elongin-C / Elongin-B / DNA dC->dU-editing enzyme APOBEC-3H / Cullin-5 / RING-box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 5.14 Å
AuthorsIto F / Alvarez-Cabrera AL / Zhou ZH / Chen XS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150524 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of HIV-1 Vif-mediated E3 ligase targeting of host APOBEC3H
Authors: Ito F / Alvarez-Cabrera AL / Kim K / Zhou ZH / Chen XS
History
DepositionJan 19, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29490.png

Downloads & links

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Map

FileDownload / File: emd_29490.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.92 Å
Density
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.16860732 - 0.28133452
Average (Standard dev.)-0.000096425705 (±0.005696302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 471.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29490_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29490_half_map_2.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 : Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-be...

EntireName: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
Components
  • Complex: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-5
    • Protein or peptide: RING-box protein 2
    • Protein or peptide: DNA dC->dU-editing enzyme APOBEC-3H

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Supramolecule #1: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-be...

SupramoleculeName: Hetero-heptameric complex of HIV-1 Vif and human APOBEC3H, CBF-beta, ELOB, ELOC, CUL5, and RBX2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Core-binding factor subunit beta

MacromoleculeName: Core-binding factor subunit beta / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRVVPDQRS KFENEEFFR K LSRECEIK YT GFRDRPH EER QARFQN ACRD GRSEI AFVAT GTNL SLQFFP ASW QGEQRQT PS REYVDLER E AGKVYLKAP MILNGVCVIW KGWIDLQRL D GMGCLEFD EE RAQQEDA LAQ QAFEEA RRRT REFED RD

UniProtKB: Core-binding factor subunit beta

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Macromolecule #2: Virion infectivity factor

MacromoleculeName: Virion infectivity factor / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: pNL4-3
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMENRWQVM IV WQVDRMR INT WKRLVK HHMY ISRKA KDWFY RHHY ESTHPK ISS EVHIPLG DA KLVITTYW G LHTGERDWH LGQGVSIEWR KKRYSTQVD P DLADQLIH LH YFDCFSE SAI RNTILG RIVS PRCEY QAGHN KVGS LQYLAL AAL ...String:
GPMENRWQVM IV WQVDRMR INT WKRLVK HHMY ISRKA KDWFY RHHY ESTHPK ISS EVHIPLG DA KLVITTYW G LHTGERDWH LGQGVSIEWR KKRYSTQVD P DLADQLIH LH YFDCFSE SAI RNTILG RIVS PRCEY QAGHN KVGS LQYLAL AAL IKPKQIK PP LPSVRKLT E DRWNK

UniProtKB: Virion infectivity factor

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Macromolecule #3: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFLMIRRH KTTIFTDAK E SSTVFELK RI VEGILKR PPD EQRLYK DDQL LDDGK TLGEC GFTS QTARPQ APA TVGLAFR AD DTFEALCI E PFSSPPELP DV

UniProtKB: Elongin-B

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Macromolecule #4: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYVKLISSDG HEFIVKREH A LTSGTIKA ML SGPGQFA ENE TNEVNF REIP SHVLS KVCMY FTYK VRYTNS STE IPEFPIA PE IALELLMA A NFLDC

UniProtKB: Elongin-C

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Macromolecule #5: Cullin-5

MacromoleculeName: Cullin-5 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SLQFEDKWD FMRPIVLKLL RQESVTKQQ W FDLFSDVH AV CLWDDKG PAK IHQALK EDIL EFIKQ AQARV LSHQ DDTALL KAY IVEWRKF FT QCDILPKP F CQLEITLMG KQGSNKKSNV EDSIVRKLM L DTWNESIF SN IKNRLQD SAM KLVHAE RLGE ...String:
SLQFEDKWD FMRPIVLKLL RQESVTKQQ W FDLFSDVH AV CLWDDKG PAK IHQALK EDIL EFIKQ AQARV LSHQ DDTALL KAY IVEWRKF FT QCDILPKP F CQLEITLMG KQGSNKKSNV EDSIVRKLM L DTWNESIF SN IKNRLQD SAM KLVHAE RLGE AFDSQ LVIGV RESY VNLCSN PED KLQIYRD NF EKAYLDST E RFYRTQAPS YLQQNGVQNY MKYADAKLK E EEKRALRY LE TRRECNS VEA LMECCV NALV TSFKE TILAE CQGM IKRNET EKL HLMFSLM DK VPNGIEPM L KDLEEHIIS AGLADMVAAA ETITTDSEK Y VEQLLTLF NR FSKLVKE AFQ DDPRFL TARD KAYKA VVNDA TIFK LELPLK QKG VGLKTQP ES KCPELLAN Y CDMLLRKTP LSKKLTSEEI EAKLKEVLL V LKYVQNKD VF MRYHKAH LTR RLILDI SADS EIEEN MVEWL REVG MPADYV NKL ARMFQDI KV SEDLNQAF K EMHKNNKLA LPADSVNIKI LNAGAWSRS S EKVFVSLP TE LEDLIPE VEE FYKKNH SGRK LHWHH LMSNG IITF KNEVGQ YDL EVTTFQL AV LFAWNQRP R EKISFENLK LATELPDAEL RRTLWSLVA F PKLKRQVL LY EPQVNSP KDF TEGTLF SVNQ EFSLI KNAKV QKRG KINLIG RLQ LTTERMR EE ENEGIVQL R ILRTQEAII QIMKMRKKIS NAQLQTELV E ILKNMFLP QK KMIKEQI EWL IEHKYI RRDE SDINT FIYMA

UniProtKB: Cullin-5

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Macromolecule #6: RING-box protein 2

MacromoleculeName: RING-box protein 2 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADVEDGEET CALASHSGS S GSKSGGDK MF SLKKWNA VAM WSWDVE CDTC AICRV QVMDA CLRC QAENKQ EDC VVVWGEC NH SFHNCCMS L WVKQNNRCP LCQQDWVVQR IGK

UniProtKB: RING-box protein 2

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Macromolecule #7: DNA dC->dU-editing enzyme APOBEC-3H

MacromoleculeName: DNA dC->dU-editing enzyme APOBEC-3H / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO / EC number: single-stranded DNA cytosine deaminase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGGSGGMAL LTAETFR LQ FNNKRRLR R PYYPRKALL CYQLTPQNGS TPTRGYFEN K KKCHAEIC FI NEIKSMG LDE TQCYQV TCYL TWSPC SSCAW ELVD FIQAHD HLN LRIFASR LY YHWCKPQQ D GLRLLCGSQ VPVEVMGFPE FADCWENFV D ...String:
GPGGSGGMAL LTAETFR LQ FNNKRRLR R PYYPRKALL CYQLTPQNGS TPTRGYFEN K KKCHAEIC FI NEIKSMG LDE TQCYQV TCYL TWSPC SSCAW ELVD FIQAHD HLN LRIFASR LY YHWCKPQQ D GLRLLCGSQ VPVEVMGFPE FADCWENFV D HEKPLSFN PY KMLEELD KNS RAIKRR LDRI KS

UniProtKB: DNA dC->dU-editing enzyme APOBEC-3H

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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

Concentration0.15 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 150000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 12546 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2

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Image processing

Particle selectionNumber selected: 5032127
Startup modelType of model: INSILICO MODEL
In silico model: Generated by stochastic gradient descent using ab intio reconstruction in cryoSPARC.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 5.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 98939
FSC plot (resolution estimation)

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