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- PDB-8cl0: HIV-1 mature capsid hexamer next to pentamer (type I) from CA-IP6... -

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Basic information

Entry
Database: PDB / ID: 8cl0
TitleHIV-1 mature capsid hexamer next to pentamer (type I) from CA-IP6 CLPs bound to Nup153 peptide.
Components
  • Gag polyprotein
  • Nuclear pore complex protein Nup153
KeywordsVIRUS LIKE PARTICLE / Capsid / Hexamer / Pentamer / 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 / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / 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 / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / nuclear localization sequence binding / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / protein-membrane adaptor activity / nuclear periphery / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / molecular condensate scaffold activity / ISG15 antiviral mechanism / viral penetration into host nucleus / HCMV Early Events / protein import into nucleus / nuclear envelope / host cell / viral nucleocapsid / snRNP Assembly / nuclear membrane / amyloid fibril formation / host cell cytoplasm / viral translational frameshifting / symbiont entry into host cell / nucleolus / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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. / Orthogonal Bundle / Mainly Alpha
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: 3.12 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
Revision 1.1Jul 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.initial_refinement_model_id / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein
G: Nuclear pore complex protein Nup153
B: Gag polyprotein
H: Nuclear pore complex protein Nup153
C: Gag polyprotein
I: Nuclear pore complex protein Nup153
D: Gag polyprotein
J: Nuclear pore complex protein Nup153
E: Gag polyprotein
K: Nuclear pore complex protein Nup153
F: Gag polyprotein
L: Nuclear pore complex protein Nup153


Theoretical massNumber of molelcules
Total (without water)164,69612
Polymers164,69612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Assembled in presence of IP6
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21080 Å2
ΔGint-128 kcal/mol
Surface area58660 Å2

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Components

#1: Protein
Gag polyprotein


Mass: 25761.623 Da / Num. of mol.: 6
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 / 153 kDa nucleoporin / Nucleoporin Nup153


Mass: 1687.721 Da / Num. of mol.: 6 / 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: Pentamer adjacent Hexamer (type I) 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) / Strain: BL21
Buffer solutionpH: 6.1
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMsodium chlorideNaCl1
22 mMTCEPC9H15O6P1
350 mMMESC6H13NO4S1
42.5 mMinositol hexakisphosphateC6H18O24P61
50.1 %DMSOC2H6OS1
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 FIELD / 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
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
9ISOLDEmodel refinement
10Cootmodel refinement
11PHENIXmodel refinement
12cryoSPARC3.3.2initial Euler assignment
13cryoSPARC3.3.2final Euler assignment
14cryoSPARC3.3.2classification
15cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1457736
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277125 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14XFX

4xfx

14XFX1PDBexperimental model
25TSX

5tsx

15TSX2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610617
ELECTRON MICROSCOPYf_angle_d0.89814433
ELECTRON MICROSCOPYf_dihedral_angle_d12.7773915
ELECTRON MICROSCOPYf_chiral_restr0.0591640
ELECTRON MICROSCOPYf_plane_restr0.0081870

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