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- PDB-8cky: HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to Nup153 peptide -

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Basic information

Entry
Database: PDB / ID: 8cky
TitleHIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to Nup153 peptide
Components
  • Gag polyproteinGroup-specific antigen
  • Nuclear pore complex protein Nup153Nuclear pore
KeywordsVIRUS LIKE PARTICLE / Capsid / Hexamer / HIV-1 / Mature / Nup153
Function / homology
Function and homology information


negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA ...negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / host cell / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / protein-membrane adaptor activity / viral process / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / viral penetration into host nucleus / nuclear envelope / snRNP Assembly / viral nucleocapsid / nuclear membrane / host cell cytoplasm / symbiont entry into host cell / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Gag polyprotein / Nuclear pore complex protein Nup153
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsStacey, J.C.V. / Briggs, J.A.G.
Funding support Germany, United States, United Kingdom, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI147890 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5U54AI150472-09 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170855-01 United States
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Two structural switches in HIV-1 capsid regulate capsid curvature and host factor binding.
Authors: James C V Stacey / Aaron Tan / John M Lu / Leo C James / Robert A Dick / John A G Briggs /
Abstract: The mature HIV-1 capsid protects the viral genome and interacts with host proteins to travel from the cell periphery into the nucleus. To achieve this, the capsid protein, CA, constructs conical ...The mature HIV-1 capsid protects the viral genome and interacts with host proteins to travel from the cell periphery into the nucleus. To achieve this, the capsid protein, CA, constructs conical capsids from a lattice of hexamers and pentamers, and engages in and then relinquishes multiple interactions with cellular proteins in an orchestrated fashion. Cellular host factors including Nup153, CPSF6, and Sec24C engage the same pocket within CA hexamers. How CA assembles pentamers and hexamers of different curvatures, how CA oligomerization states or curvature might modulate host-protein interactions, and how binding of multiple cofactors to a single site is coordinated, all remain to be elucidated. Here, using single-particle cryoEM, we have determined the structure of the mature HIV-1 CA pentamer and hexamer from conical CA-IP polyhedra to ~3 Å resolution. We also determined structures of hexamers in the context of multiple lattice curvatures and number of pentamer contacts. Comparison of these structures, bound or not to host protein peptides, revealed two structural switches within HIV-1 CA that modulate peptide binding according to CA lattice curvature and whether CA is hexameric or pentameric. These observations suggest that the conical HIV-1 capsid has different host-protein binding properties at different positions on its surface, which may facilitate cell entry and represent an evolutionary advantage of conical morphology.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gag polyprotein
B: Nuclear pore complex protein Nup153


Theoretical massNumber of molelcules
Total (without water)27,4492
Polymers27,4492
Non-polymers00
Water0
1
A: Gag polyprotein
B: Nuclear pore complex protein Nup153
x 6


Theoretical massNumber of molelcules
Total (without water)164,69612
Polymers164,69612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
Buried area660 Å2
ΔGint-3 kcal/mol
Surface area12530 Å2

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Components

#1: Protein Gag polyprotein / Group-specific antigen


Mass: 25761.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B6DRA0
#2: Protein/peptide Nuclear pore complex protein Nup153 / Nuclear pore / 153 kDa nucleoporin / Nucleoporin Nup153


Mass: 1687.721 Da / Num. of mol.: 1 / Fragment: UNP residues 1407-1423 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49790

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HIV-1 Mature Capsid / Type: COMPLEX
Details: Hexamer bound to FG repeat containing Nup153 peptide.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.027 MDa / Experimental value: NO
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.1
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMsodium chlorideNaClSodium chloride1
22 mMTCEPC9H15O6P1
350 mMMESC6H13NO4S1
42.5 mMinositol hexakisphosphatePhytic acidC6H18O24P61
50.1 %DMSODimethyl sulfoxideC2H6OS1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: VLP assembly, bound to Nup153 peptide.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4770
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 20 eV
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: dev_3689: / Classification: refinement
EM software
IDNameVersionCategory
1crYOLO1.82particle selection
2EPUimage acquisition
4cryoSPARC3.3.2CTF correction
7UCSF Chimeramodel fitting
9cryoSPARC3.3.2initial Euler assignment
10cryoSPARC3.3.2final Euler assignment
11cryoSPARC3.3.2classification
12cryoSPARC3.3.23D reconstruction
13ISOLDEmodel refinement
14Cootmodel refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1457736
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 595899 / Algorithm: BACK PROJECTION / Num. of class averages: 4 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeSource nameType
14XFX

4xfx

14XFXPDBexperimental model
25TSX

5tsx

15TSXPDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0091769
ELECTRON MICROSCOPYf_angle_d0.8742405
ELECTRON MICROSCOPYf_dihedral_angle_d12.59652
ELECTRON MICROSCOPYf_chiral_restr0.049273
ELECTRON MICROSCOPYf_plane_restr0.007311

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