[English] 日本語
![](img/lk-miru.gif)
- EMDB-27033: Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC d... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 1 | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() RUNX3 regulates RUNX1-mediated transcription / apolipoprotein B mRNA editing enzyme complex / RUNX1 regulates transcription of genes involved in BCR signaling / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Li Y / Langley C / Azumaya CM / Echeverria I / Chesarino NM / Emerman M / Cheng Y / Gross JD | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Authors: Yen-Li Li / Caroline A Langley / Caleigh M Azumaya / Ignacia Echeverria / Nicholas M Chesarino / Michael Emerman / Yifan Cheng / John D Gross / ![]() Abstract: The APOBEC3 (A3) proteins are host antiviral cellular proteins that hypermutate the viral genome of diverse viral families. In retroviruses, this process requires A3 packaging into viral particles. ...The APOBEC3 (A3) proteins are host antiviral cellular proteins that hypermutate the viral genome of diverse viral families. In retroviruses, this process requires A3 packaging into viral particles. The lentiviruses encode a protein, Vif, that antagonizes A3 family members by targeting them for degradation. Diversification of A3 allows host escape from Vif whereas adaptations in Vif enable cross-species transmission of primate lentiviruses. How this 'molecular arms race' plays out at the structural level is unknown. Here, we report the cryogenic electron microscopy structure of human APOBEC3G (A3G) bound to HIV-1 Vif, and the hijacked cellular proteins that promote ubiquitin-mediated proteolysis. A small surface explains the molecular arms race, including a cross-species transmission event that led to the birth of HIV-1. Unexpectedly, we find that RNA is a molecular glue for the Vif-A3G interaction, enabling Vif to repress A3G by ubiquitin-dependent and -independent mechanisms. Our results suggest a model in which Vif antagonizes A3G by intercepting it in its most dangerous form for the virus-when bound to RNA and on the pathway to packaging-to prevent viral restriction. By engaging essential surfaces required for restriction, Vif exploits a vulnerability in A3G, suggesting a general mechanism by which RNA binding helps to position key residues necessary for viral antagonism of a host antiviral gene. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 131.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 32.6 KB 32.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.5 KB | Display | ![]() |
Images | ![]() | 56.7 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 83.4 MB 140.9 MB 139.6 MB 19 MB 9.9 MB 131.8 MB 131.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cx1MC ![]() 8cx0C ![]() 8cx2C C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Composite map made by focused refinement of the...
File | emd_27033_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Composite map made by focused refinement of the second A3G-VCBC with weaker density | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Sharpened primary map by DeepEMhancer
File | emd_27033_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened primary map by DeepEMhancer | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: sharpened composite map by DeepEMhancer
File | emd_27033_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened composite map by DeepEMhancer | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Density modified primary map
File | emd_27033_additional_4.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Density modified primary map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Density modified composite map
File | emd_27033_additional_5.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Density modified composite map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_27033_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_27033_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : HIV-1 Vif-E3 ligase substrate receptor (VCBC) in complex with hum...
Entire | Name: HIV-1 Vif-E3 ligase substrate receptor (VCBC) in complex with human APOBEC3G and RNA |
---|---|
Components |
|
-Supramolecule #1: HIV-1 Vif-E3 ligase substrate receptor (VCBC) in complex with hum...
Supramolecule | Name: HIV-1 Vif-E3 ligase substrate receptor (VCBC) in complex with human APOBEC3G and RNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: DNA dC->dU-editing enzyme APOBEC-3G
Macromolecule | Name: DNA dC->dU-editing enzyme APOBEC-3G / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ![]() |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50.034598 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MKPHFRNTVE RMYRDTFSYN FYNRPILSRR NTVWLCYEVK TKGPSRPPLD AKIFRGQVYS ELKYHPEMRF FHWFSKWRKL HRDQEYEVT WYISWSPCTK CTRDMATFLA EDPKVTLTIF VARLYYFWDP DYQEALRSLC QKRDGPRATM KIMNYDEFQH C WSKFVYSQ ...String: MKPHFRNTVE RMYRDTFSYN FYNRPILSRR NTVWLCYEVK TKGPSRPPLD AKIFRGQVYS ELKYHPEMRF FHWFSKWRKL HRDQEYEVT WYISWSPCTK CTRDMATFLA EDPKVTLTIF VARLYYFWDP DYQEALRSLC QKRDGPRATM KIMNYDEFQH C WSKFVYSQ RELFEPWNNL PKYYILLHIM LGEILRHSMD PPTFTFNFNN EPWVRGRHET YLCYEVERMH NDTWVLLNQR RG FLCNQAP HKHGFLEGRH AELCFLDVIP FWKLDLDQDY RVTCFTSWSP CFSCAQEMAK FISKNKHVSL CIFTARIYDD QGR CQEGLR TLAEAGAKIS IMTYSEFKHC WDTFVDHQGC PFQPWDGLDE HSQDLSGRLR AILQNQENGS SLEGGGGWSH PQFE KGGGS GGGSGGGSWS HPQFEK UniProtKB: DNA dC->dU-editing enzyme APOBEC-3G |
-Macromolecule #2: Virion infectivity factor
Macromolecule | Name: Virion infectivity factor / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 22.556002 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MENRWQVMIV WQVDRMRIRT WKSLVKHHMY VSGKARGWFY RHHYESPHPR ISSEVHIPLG DARLVITTYW GLHTGERDWH LGQGVSIEW RKKRYSTQVD PELADQLIHL YYFDCFSDSA IRKALLGHIV SPRCEYQAGH NKVGSLQYLA LAALITPKKI K PPLPSVTK ...String: MENRWQVMIV WQVDRMRIRT WKSLVKHHMY VSGKARGWFY RHHYESPHPR ISSEVHIPLG DARLVITTYW GLHTGERDWH LGQGVSIEW RKKRYSTQVD PELADQLIHL YYFDCFSDSA IRKALLGHIV SPRCEYQAGH NKVGSLQYLA LAALITPKKI K PPLPSVTK LTEDRWNKPQ KTKGHRGSHT MNGH UniProtKB: Virion infectivity factor |
-Macromolecule #3: Core-binding factor subunit beta
Macromolecule | Name: Core-binding factor subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.542188 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MPRVVPDQRS KFENEEFFRK LSRECEIKYT GFRDRPHEER QARFQNACRD GRSEIAFVAT GTNLSLQFFP ASWQGEQRQT PSREYVDLE REAGKVYLKA PMILNGVCVI WKGWIDLQRL DGMGCLEFDE ERAQQEDALA QQAFEEARRR TREFEDRDRS H REEMEVRV SQLLAVTGKK TTRP UniProtKB: Core-binding factor subunit beta |
-Macromolecule #4: Elongin-B
Macromolecule | Name: Elongin-B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.147781 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ UniProtKB: Elongin-B |
-Macromolecule #5: Elongin-C
Macromolecule | Name: Elongin-C / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.485135 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC UniProtKB: Elongin-C |
-Macromolecule #6: RNA (5'-R(P*UP*AP*AP*AP*UP*AP*UP*U)-3')
Macromolecule | Name: RNA (5'-R(P*UP*AP*AP*AP*UP*AP*UP*U)-3') / type: rna / ID: 6 / Number of copies: 1 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 2.496529 KDa |
Sequence | String: UAAAUAUU |
-Macromolecule #7: RNA (5'-R(P*AP*AP*AP*AP*UP*AP*UP*U)-3')
Macromolecule | Name: RNA (5'-R(P*AP*AP*AP*AP*UP*AP*UP*U)-3') / type: rna / ID: 7 / Number of copies: 1 |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 2.519569 KDa |
Sequence | String: AAAAUAUU |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 6 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.46 mg/mL |
---|---|
Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |