[English] 日本語
Yorodumi
- EMDB-75888: Structural Insights into HIV-1 Vif-Mediated Ubiquitination and De... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75888
TitleStructural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H
Map data
Sample
  • Complex: Ternary complex of APOBEC3H and Vif of HIV-1
    • Protein or peptide: single-stranded DNA cytosine deaminase
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • RNA: RNA
    • RNA: RNA
  • Ligand: ZINC ION
KeywordsAPOBEC3H / HIV-2 Vif / VIRAL PROTEIN
Function / homology
Function and homology information


RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / 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 / RUNX2 regulates bone development / single-stranded DNA cytosine deaminase / negative regulation of CD4-positive, alpha-beta T cell differentiation ...RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / 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 / RUNX2 regulates bone development / single-stranded DNA cytosine deaminase / negative regulation of CD4-positive, alpha-beta T cell differentiation / clearance of foreign intracellular DNA / cytidine deaminase activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX2 regulates genes involved in cell migration / Transcriptional regulation by RUNX2 / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / RUNX2 regulates genes involved in differentiation of myeloid cells / transposable element silencing / RUNX3 Regulates Immune Response and Cell Migration / target-directed miRNA degradation / elongin complex / VCB complex / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / negative regulation of viral genome replication / Cul5-RING ubiquitin ligase complex / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / RUNX2 regulates osteoblast differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / 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 / ribosome-associated ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / transcription elongation by RNA polymerase II / Regulation of RUNX3 expression and activity / Inactivation of CSF3 (G-CSF) signaling / Vif-mediated degradation of APOBEC3G / transcription by RNA polymerase II / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Transcriptional regulation of granulopoiesis / protein polyubiquitination / Regulation of expression of SLITs and ROBOs / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / Regulation of RUNX2 expression and activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / defense response to virus / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / sequence-specific DNA binding / Estrogen-dependent gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / protein-macromolecule adaptor activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
APOBEC3H / APOBEC3H / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / : / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. ...APOBEC3H / APOBEC3H / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / : / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Elongin-C / Elongin B / 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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / single-stranded DNA cytosine deaminase / Core-binding factor subunit beta / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesPan troglodytes (chimpanzee) / Homo sapiens (human) / Human immunodeficiency virus 2 / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMatsuo H / Skorupka KA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 AI150478 United States
CitationJournal: Nat Commun / Year: 2026
Title: Divergent interfaces and convergent outcome in the structural basis of HIV-2 Vif antagonism of APOBEC3H
Authors: Skorupka KA / Matsuoka K / Imahashi M / Yokomaku Y / Iwatani Y / Matsuo H
History
DepositionMar 6, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75888.png

Downloads & links

-
Map

FileDownload / File: emd_75888.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.)
0.81 Å/pix.
x 512 pix.
= 414.72 Å		0.81 Å/pix.
x 512 pix.
= 414.72 Å		0.81 Å/pix.
x 512 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-0.1020402 - 32.770663999999996
Average (Standard dev.)-0.03995171 (±0.21825153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 414.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_75888_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_75888_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_75888_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of APOBEC3H and Vif of HIV-1

EntireName: Ternary complex of APOBEC3H and Vif of HIV-1
Components
  • Complex: Ternary complex of APOBEC3H and Vif of HIV-1
    • Protein or peptide: single-stranded DNA cytosine deaminase
    • Protein or peptide: Core-binding factor subunit beta
    • Protein or peptide: Virion infectivity factor
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • RNA: RNA
    • RNA: RNA
  • Ligand: ZINC ION

-
Supramolecule #1: Ternary complex of APOBEC3H and Vif of HIV-1

SupramoleculeName: Ternary complex of APOBEC3H and Vif of HIV-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

-
Macromolecule #1: single-stranded DNA cytosine deaminase

MacromoleculeName: single-stranded DNA cytosine deaminase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: single-stranded DNA cytosine deaminase
Source (natural)Organism: Pan troglodytes (chimpanzee)
Molecular weightTheoretical: 21.912309 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSMALLTAET FRLQFNNRRR LRRPYYPRKA LLCYQLTPQN GSTPTRGYFE NKKKCHAEIC FINEIKSMGL DETQCYQVTC YLTWSPCSS CAWKLVDFIQ AHDHLNLRIF ASRLYYHWCK PQQEGLRLLC GSQVPVEVMG LPEFNDCWEN FVDHEKPLSF D PCKMLEEL DKNSRAIKRR LERIKQS

UniProtKB: single-stranded DNA cytosine deaminase

-
Macromolecule #2: Core-binding factor subunit beta

MacromoleculeName: Core-binding factor subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.272629 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPRVVPDQRS KFENEEFFRK LSRECEIKYT GFRDRPHEER QARFQNACRD GRSEIAFVAT GTNLSLQFFP ASWQGEQRQT PSREYVDLE REAGKVYLKA PMILNGVCVI WKGWIDLQRL DGMGCLEFDE ERAQQEDALA QQAFEEARRR TREFEDRDRS H REEMEVRV SQ

UniProtKB: Core-binding factor subunit beta

-
Macromolecule #3: Virion infectivity factor

MacromoleculeName: Virion infectivity factor / type: protein_or_peptide / ID: 3
Details: loop region 160-204 is unresolved in the cryo-EM structure
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 2
Molecular weightTheoretical: 25.137543 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEEEKNWIVV PTWRIPGRLE RWHSLVKYLK HRTGELQQVS YVPHHKVGWA WWTCSRVIFP LNKGAWLEVQ GYWNLTPERG FLSSYAVRL TWYEESFYTD VTPDVADQLL HGTYFSCFTA NEVRRAIRGE KILSYCNYPS AHERQVPSLQ FLALRVVQER K NGSKGEGA ...String:
MEEEKNWIVV PTWRIPGRLE RWHSLVKYLK HRTGELQQVS YVPHHKVGWA WWTCSRVIFP LNKGAWLEVQ GYWNLTPERG FLSSYAVRL TWYEESFYTD VTPDVADQLL HGTYFSCFTA NEVRRAIRGE KILSYCNYPS AHERQVPSLQ FLALRVVQER K NGSKGEGA TRKQRRRDSR RGIQLARKNN NRAQQGSSQP FAPGTHFPGL AEVLGILA

UniProtKB: UNIPROTKB: A0A173DUN4

-
Macromolecule #4: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.48803 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDV

UniProtKB: Elongin-B

-
Macromolecule #5: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.84342 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MYVKLISSDG HEFIVKREHA LTSGTIKAML SGPGQFAENE TNEVNFREIP SHVLSKVCMY FTYKVRYTNS STEIPEFPIA PEIALELLM AANFLDC

UniProtKB: Elongin-C

-
Macromolecule #6: RNA

MacromoleculeName: RNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 3.194917 KDa
SequenceString:
UUGGUUGGCA

-
Macromolecule #7: RNA

MacromoleculeName: RNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 3.142981 KDa
SequenceString:
ACGCCAACCA

-
Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
350.0 mMNaClsodium chloride
1.0 mMTCEP
0.25 %glycerol
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 44142 / Average electron dose: 45.0 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: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 7413018
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5z98

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 294824
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

4n9z

chain_id: m, source_name: PDB, initial_model_type: experimental model

4n9z

chain_id: n, source_name: PDB, initial_model_type: experimental model

4n9z

chain_id: o, source_name: PDB, initial_model_type: experimental model

4n9z

chain_id: p, source_name: PDB, initial_model_type: experimental model

5z98

chain_id: A, source_name: PDB, initial_model_type: experimental model

5z98

chain_id: B, source_name: PDB, initial_model_type: experimental model

5z98

chain_id: C, source_name: PDB, initial_model_type: experimental model

5z98

chain_id: D, source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT / Overall B value: 135
Output model

PDB-11on:
Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H

+
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