[English] 日本語
Yorodumi
- EMDB-29490: HIV-1 Vif in complex with human APOBEC3H, CBF-beta, ELOB, ELOC, C... -

+
Open data


ID or keywords:

Loading...

-
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 / lymphocyte differentiation / negative regulation by host of viral genome replication / cytidine to uridine editing / ERBB2 signaling pathway / clearance of foreign intracellular DNA / cytidine deaminase activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of neuron migration / reelin-mediated signaling pathway / Transcriptional regulation by RUNX2 / cullin-RING-type E3 NEDD8 transferase / transposable element silencing / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / NEDD8 transferase activity / myeloid cell differentiation / target-directed miRNA degradation / RUNX3 Regulates Immune Response and Cell Migration / elongin complex / VCB complex / definitive hemopoiesis / protein K11-linked ubiquitination / protein neddylation / 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 / response to redox state / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / 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 / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cullin family protein binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RUNX3 regulates p14-ARF / 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 / endoplasmic reticulum unfolded protein response / cell maturation / RNA Polymerase II Pre-transcription Events / viral life cycle / post-translational protein modification / intrinsic apoptotic signaling pathway / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / virion component / P-body / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RING-type E3 ubiquitin transferase / Inactivation of CSF3 (G-CSF) signaling / calcium channel activity / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Downregulation of ERBB2 signaling / Regulation of expression of SLITs and ROBOs / Transcriptional regulation of granulopoiesis / protein polyubiquitination / osteoblast differentiation / ubiquitin-protein transferase activity / G1/S transition of mitotic cell cycle / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / signaling receptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein-containing complex assembly
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 ...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 / : / Elongin B / Elongin-C / Cytidine deaminase-like / 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. / 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 domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 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: Fumiaki Ito / Ana L Alvarez-Cabrera / Kyumin Kim / Z Hong Zhou / Xiaojiang S Chen /
Abstract: Human APOBEC3 (A3) cytidine deaminases are antiviral factors that are particularly potent against retroviruses. As a countermeasure, HIV-1 uses a viral infectivity factor (Vif) to target specific ...Human APOBEC3 (A3) cytidine deaminases are antiviral factors that are particularly potent against retroviruses. As a countermeasure, HIV-1 uses a viral infectivity factor (Vif) to target specific human A3s for proteasomal degradation. Vif recruits cellular transcription cofactor CBF-β and Cullin-5 (CUL5) RING E3 ubiquitin ligase to bind different A3s distinctively, but how this is accomplished remains unclear in the absence of the atomic structure of the complex. Here, we present the cryo-EM structures of HIV-1 Vif in complex with human A3H, CBF-β and components of CUL5 ubiquitin ligase (CUL5, ELOB, and ELOC). Vif nucleates the entire complex by directly binding four human proteins, A3H, CBF-β, CUL5, and ELOC. The structures reveal a large interface area between A3H and Vif, primarily mediated by an α-helical side of A3H and a five-stranded β-sheet of Vif. This A3H-Vif interface unveils the basis for sensitivity-modulating polymorphism of both proteins, including a previously reported gain-of-function mutation in Vif isolated from HIV/AIDS patients. Our structural and functional results provide insights into the remarkable interplay between HIV and humans and would inform development efforts for anti-HIV therapeutics.
History
DepositionJan 19, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29490.png

Downloads & links

-
Map

FileDownload / File: emd_29490.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 512 pix.
= 471.04 Å		0.92 Å/pix.
x 512 pix.
= 471.04 Å		0.92 Å/pix.
x 512 pix.
= 471.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
Half map: #1

Fileemd_29490_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_29490_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
Electron microscopy

MicroscopeTFS GLACIOS
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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 150000

+
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.
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more