[English] 日本語
Yorodumi
- EMDB-45761: HIV-2 CA hexamer bound with CPSF6 peptide; assembled via liposome... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45761
TitleHIV-2 CA hexamer bound with CPSF6 peptide; assembled via liposome templating
Map dataEM map of HIV-2 CA hexamers assembled via liposome templating and allowed to bind with CPSF6 peptide.
Sample
  • Complex: HIV-2 capsid protein assembled into a lattice via liposome templating and then bound with CPSF6 peptide.
    • Complex: HIV-2 capsid protein
      • Protein or peptide: Capsid protein p24
    • Complex: CPSF6 peptide
      • Protein or peptide: Isoform 2 of Cleavage and polyadenylation specificity factor subunit 6
  • Ligand: INOSITOL HEXAKISPHOSPHATE
KeywordsHIV-2 / Capsid / IP6 / CPSF6 / VIRAL PROTEIN
Function / homology
Function and homology information


exon-exon junction complex binding / HIV-2 retropepsin / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation ...exon-exon junction complex binding / HIV-2 retropepsin / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / mRNA 3'-end processing / paraspeckles / RNA Polymerase II Transcription Termination / protein heterotetramerization / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / Signaling by FGFR1 in disease / protein tetramerization / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / mRNA processing / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / nuclear speck / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / ribonucleoprotein complex / viral translational frameshifting / mRNA binding / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / gag protein p24 N-terminal domain / RNA recognition motif / RNA recognition motif / Reverse transcriptase connection / Reverse transcriptase connection domain / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Reverse transcriptase thumb ...Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / gag protein p24 N-terminal domain / RNA recognition motif / RNA recognition motif / Reverse transcriptase connection / Reverse transcriptase connection domain / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNA-binding domain superfamily / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Gag-Pol polyprotein / Cleavage and polyadenylation specificity factor subunit 6
Similarity search - Component
Biological speciesHuman immunodeficiency virus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsFreniere C / Cook M / Xiong Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32GM008283 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50AI150481 United States
CitationJournal: Cell Rep / Year: 2025
Title: Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single-particle cryo-EM.
Authors: Matthew Cook / Christian Freniere / Chunxiang Wu / Faith Lozano / Yong Xiong /
Abstract: One of the striking features of human immunodeficiency virus (HIV) is the capsid, a fullerene cone comprised of pleomorphic capsid protein (CA) that shields the viral genome and recruits cofactors. ...One of the striking features of human immunodeficiency virus (HIV) is the capsid, a fullerene cone comprised of pleomorphic capsid protein (CA) that shields the viral genome and recruits cofactors. Despite significant advances in understanding the mechanisms of HIV-1 CA assembly and host factor interactions, HIV-2 CA assembly remains poorly understood. By templating the assembly of HIV-2 CA on functionalized liposomes, we report high-resolution structures of the HIV-2 CA lattice, including both CA hexamers and pentamers, alone and with peptides of host phenylalanine-glycine (FG)-motif proteins Nup153 and CPSF6. While the overall fold and mode of FG-peptide binding is conserved with HIV-1, this study reveals distinctive features of the HIV-2 CA lattice, including differing structural character at regions of host factor interactions and divergence in the mechanism of formation of CA hexamers and pentamers. This study extends our understanding of HIV capsids and highlights an approach facilitating the study of lentiviral capsid biology.
History
DepositionJul 15, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45761.png

Downloads & links

-
Map

FileDownload / File: emd_45761.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of HIV-2 CA hexamers assembled via liposome templating and allowed to bind with CPSF6 peptide.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 180 pix.
= 192.24 Å		1.07 Å/pix.
x 180 pix.
= 192.24 Å		1.07 Å/pix.
x 180 pix.
= 192.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.21010216 - 0.56272465
Average (Standard dev.)0.012957965 (±0.040544137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 192.23999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: EM half map A of HIV-2 CA hexamers bound with CPSF6 peptide

Fileemd_45761_half_map_1.map
AnnotationEM half map A of HIV-2 CA hexamers bound with CPSF6 peptide
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: EM half map B of HIV-2 CA hexamers bound with CPSF6 peptide

Fileemd_45761_half_map_2.map
AnnotationEM half map B of HIV-2 CA hexamers bound with CPSF6 peptide
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HIV-2 capsid protein assembled into a lattice via liposome templa...

EntireName: HIV-2 capsid protein assembled into a lattice via liposome templating and then bound with CPSF6 peptide.
Components
  • Complex: HIV-2 capsid protein assembled into a lattice via liposome templating and then bound with CPSF6 peptide.
    • Complex: HIV-2 capsid protein
      • Protein or peptide: Capsid protein p24
    • Complex: CPSF6 peptide
      • Protein or peptide: Isoform 2 of Cleavage and polyadenylation specificity factor subunit 6
  • Ligand: INOSITOL HEXAKISPHOSPHATE

-
Supramolecule #1: HIV-2 capsid protein assembled into a lattice via liposome templa...

SupramoleculeName: HIV-2 capsid protein assembled into a lattice via liposome templating and then bound with CPSF6 peptide.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: C-terminally hexahistidine tagged HIV-2 CA associated with a liposome decorated with NiNTA headgroups which results in the assembly of a lattice of CA. CPSF6 peptide was then introduced and ...Details: C-terminally hexahistidine tagged HIV-2 CA associated with a liposome decorated with NiNTA headgroups which results in the assembly of a lattice of CA. CPSF6 peptide was then introduced and allowed to equilibrate binding.
Molecular weightTheoretical: 26.9 KDa

-
Supramolecule #2: HIV-2 capsid protein

SupramoleculeName: HIV-2 capsid protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 2 / Strain: GL-AN

-
Supramolecule #3: CPSF6 peptide

SupramoleculeName: CPSF6 peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

-
Macromolecule #1: Capsid protein p24

MacromoleculeName: Capsid protein p24 / type: protein_or_peptide / ID: 1
Details: HIV-2 capsid protein with C-terminal Gly-Ser-Ser linker to hexahistidine tag following proteolytic processing of the N-terminal Met.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 2 / Strain: GL-AN
Molecular weightTheoretical: 26.80949 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PVQQTGGGNY IHVPLSPRTL NAWVKLVEDK KFGAEVVPGF QALSEGCTPY DINQMLNCVG DHQAAMQIIR EIINDEAADW DAQHPIPGP LPAGQLRDPR GSDIAGTTST VEEQIQWMYR PQNPVPVGNI YRRWIQIGLQ KCVRMYNPTN ILDVKQGPKE P FQSYVDRF ...String:
PVQQTGGGNY IHVPLSPRTL NAWVKLVEDK KFGAEVVPGF QALSEGCTPY DINQMLNCVG DHQAAMQIIR EIINDEAADW DAQHPIPGP LPAGQLRDPR GSDIAGTTST VEEQIQWMYR PQNPVPVGNI YRRWIQIGLQ KCVRMYNPTN ILDVKQGPKE P FQSYVDRF YKSLRAEQTD PAVKNWMTQT LLIQNANPDC KLVLKGLGMN PTLEEMLTAC QGVGGPGQKA RLMGSSHHHH HH

UniProtKB: Gag-Pol polyprotein

-
Macromolecule #2: Isoform 2 of Cleavage and polyadenylation specificity factor subunit 6

MacromoleculeName: Isoform 2 of Cleavage and polyadenylation specificity factor subunit 6
type: protein_or_peptide / ID: 2 / Details: Truncation peptide of CPSF6 (313-327) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.550796 KDa
SequenceString:
PVLFPGQPFG QPPLG

UniProtKB: Cleavage and polyadenylation specificity factor subunit 6

-
Macromolecule #3: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10.7 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mMHEPES
250.0 mMSodium chlorideNaCl
0.1 mMTCEP
4.0 mMIP6

Details: The mixed buffer of storage buffer for the protein and lipid components with IP6 supplemented.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.015 kPa / Details: 15 mA discharge current.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: Grids were dual-side blotted with blot force 0 for 5.5 sec before plunge freezing in liquid ethane..
DetailsSample was prepared with 400 uM HIV-2 CA-6xHis protein, 5.9 mM lipid mix (described in publication), and 4 mM IP6 as final concentrations following subsequent addition of CPSF6 peptide. After assembly, CPSF6 was added to a final concentration of 400 uM. Sample was well-distributed on the grid, mostly monodisperse. Perhaps slightly more particles on carbon versus in the hole.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 23033474
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2537344
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

9clj


Chain - Chain ID: A / Chain - Residue range: 1-223 / Chain - Source name: Other / Chain - Initial model type: experimental model
Details: NTDs matched well, but the CTD had to be realigned.
DetailsThe HIV-2 CA pentamer chain derived from micelle-templated icosahedra described in this publication was used as an initial model for fitting. Flexible fitting was used to move the CTD into its proper location. Backbone tracing was used to model the CPSF6 peptide.
RefinementSpace: REAL / Protocol: OTHER / Target criteria: Cross-correlation coefficient
Output model

PDB-9cnv:
HIV-2 CA hexamer bound with CPSF6 peptide; assembled via liposome templating

+
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