[English] 日本語
Yorodumi
- EMDB-27885: APOBEC3G in complex with HIV-1 Vif/CBF-beta/EloB/EloC/Cul5/Rbx2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27885
TitleAPOBEC3G in complex with HIV-1 Vif/CBF-beta/EloB/EloC/Cul5/Rbx2
Map data
Sample
  • Complex: Complex of APOBEC3G with HIV-1 Vif, CBF-beta, Elongin-B, Elongin-C, Cullin-5, and RING-box protein 2
    • Protein or peptide: APOBEC3G
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-5
    • Protein or peptide: RING-box protein 2
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsIto F / Alvarez-Cabrera AL / Liu S / Yang H / Shiriaeva A / Zhou ZH / Chen XS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI150524 United States
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis for HIV-1 antagonism of host APOBEC3G via Cullin E3 ligase.
Authors: Fumiaki Ito / Ana L Alvarez-Cabrera / Shiheng Liu / Hanjing Yang / Anna Shiriaeva / Z Hong Zhou / Xiaojiang S Chen /
Abstract: Human APOBEC3G (A3G) is a virus restriction factor that inhibits HIV-1 replication and triggers lethal hypermutation on viral reverse transcripts. HIV-1 viral infectivity factor (Vif) breaches this ...Human APOBEC3G (A3G) is a virus restriction factor that inhibits HIV-1 replication and triggers lethal hypermutation on viral reverse transcripts. HIV-1 viral infectivity factor (Vif) breaches this host A3G immunity by hijacking a cellular E3 ubiquitin ligase complex to target A3G for ubiquitination and degradation. The molecular mechanism of A3G targeting by Vif-E3 ligase is unknown, limiting the antiviral efforts targeting this host-pathogen interaction crucial for HIV-1 infection. Here, we report the cryo-electron microscopy structures of A3G bound to HIV-1 Vif in complex with T cell transcription cofactor CBF-β and multiple components of the Cullin-5 RING E3 ubiquitin ligase. The structures reveal unexpected RNA-mediated interactions of Vif with A3G primarily through A3G's noncatalytic domain, while A3G's catalytic domain is poised for ubiquitin transfer. These structures elucidate the molecular mechanism by which HIV-1 Vif hijacks the host ubiquitin ligase to specifically target A3G to establish infection and offer structural information for the rational development of antiretroviral therapeutics.
History
DepositionAug 18, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27885.png

Downloads & links

-
Map

FileDownload / File: emd_27885.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: 0.04
Minimum - Maximum-0.07833676 - 0.2954117
Average (Standard dev.)-3.477456e-05 (±0.0054524182)
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_27885_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_27885_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of APOBEC3G with HIV-1 Vif, CBF-beta, Elongin-B, Elongin-...

EntireName: Complex of APOBEC3G with HIV-1 Vif, CBF-beta, Elongin-B, Elongin-C, Cullin-5, and RING-box protein 2
Components
  • Complex: Complex of APOBEC3G with HIV-1 Vif, CBF-beta, Elongin-B, Elongin-C, Cullin-5, and RING-box protein 2
    • Protein or peptide: APOBEC3G
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-5
    • Protein or peptide: RING-box protein 2

-
Supramolecule #1: Complex of APOBEC3G with HIV-1 Vif, CBF-beta, Elongin-B, Elongin-...

SupramoleculeName: Complex of APOBEC3G with HIV-1 Vif, CBF-beta, Elongin-B, Elongin-C, Cullin-5, and RING-box protein 2
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 210 KDa

-
Macromolecule #1: APOBEC3G

MacromoleculeName: APOBEC3G / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPGGSGGMKP QIRNMVEPMD PRTFVSNFNN RPILSGLDTV WLCCEVKTKD PSGPPLDAKI FQGKVYPKAK YHPEMRFLRW FHKWRQLHHD QEYKVTWYVS WSPCTRCANS VATFLAKDPK VTLTIFVARL YYFWDPDYQQ ALRILAEAGA TMKIMNYNEF QDCWNKFVDG ...String:
GPGGSGGMKP QIRNMVEPMD PRTFVSNFNN RPILSGLDTV WLCCEVKTKD PSGPPLDAKI FQGKVYPKAK YHPEMRFLRW FHKWRQLHHD QEYKVTWYVS WSPCTRCANS VATFLAKDPK VTLTIFVARL YYFWDPDYQQ ALRILAEAGA TMKIMNYNEF QDCWNKFVDG RGKPFKPWNN LPKHYTLLQA TLGELLRHLM DPGTFTSNFN NKPWVSGQHE TYLCYKVERL HNDTWVPLNQ HRGFLRNQAP NIHGFPKGRH AQLCFLDLIP FWKLDGQQYR VTCFTSWSPC FSCAQEMAKF ISNNEHVSLC IFAARIYDDQ GRYQEGLRTL HRDGAKIAMM NYSEFEYCWD TFVDRQGRPF QPWDGLDEHS QALSGRLRAI LQNQGN

-
Macromolecule #2: Virion infectivity factor

MacromoleculeName: Virion infectivity factor / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GP MENRWQV MIV WQVDRM RINT WKRLV KHHMY ISRK AKDWFY RHH YESTNPK IS SEVHIPLG D AKLVITTYW GLHTGERDWH LGQGVSIEW R KKRYSTQV DP DLADQLI HLH YFDCFS ESAI RNTIL GRIVS PRCE YQAGHN KVG SLQYLAL AA ...String:
GP MENRWQV MIV WQVDRM RINT WKRLV KHHMY ISRK AKDWFY RHH YESTNPK IS SEVHIPLG D AKLVITTYW GLHTGERDWH LGQGVSIEW R KKRYSTQV DP DLADQLI HLH YFDCFS ESAI RNTIL GRIVS PRCE YQAGHN KVG SLQYLAL AA LIKPKQIK P PLPSVRKLT EDRWNK

-
Macromolecule #3: Core-binding factor subunit beta

MacromoleculeName: Core-binding factor subunit beta / type: protein_or_peptide / ID: 3 / 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

-
Macromolecule #4: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 4 / 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

-
Macromolecule #5: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 5 / 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

-
Macromolecule #6: Cullin-5

MacromoleculeName: Cullin-5 / type: protein_or_peptide / ID: 6 / 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

-
Macromolecule #7: RING-box protein 2

MacromoleculeName: RING-box protein 2 / type: protein_or_peptide / ID: 7 / 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

-
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: 11803 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination 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 reconstructionResolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 38571
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
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