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- PDB-7ovr: Mature HIV-1 matrix structure -

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Basic information

Entry
Database: PDB / ID: 7ovr
TitleMature HIV-1 matrix structure
ComponentsHIV-1 matrix
KeywordsVIRUS / HIV-1 / Gag / matrix
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / virion membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / 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 ...: / 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.
Similarity search - Domain/homology
MYRISTIC ACID / Chem-PIO / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7 Å
AuthorsQu, K. / Ke, Z.L. / Zila, V. / Anders-Oesswein, M. / Glass, B. / Muecksch, F. / Mueller, R. / Schultz, C. / Mueller, B. / Kraeusslich, H.G. / Briggs, J.A.G.
Funding supportEuropean Union, United Kingdom, Germany, United States, 8items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSIONEuropean Union
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
German Research Foundation (DFG)112927078 - TRR 83 Germany
German Research Foundation (DFG)240245660 - SFB1129 project 5 Germany
German Research Foundation (DFG)MU885-1 Germany
German Research Foundation (DFG)240245660 - SFB1129 project 6 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127631 United States
German Research Foundation (DFG)278001972 - TRR186 project Z1 Germany
CitationJournal: Science / Year: 2021
Title: Maturation of the matrix and viral membrane of HIV-1.
Authors: Kun Qu / Zunlong Ke / Vojtech Zila / Maria Anders-Össwein / Bärbel Glass / Frauke Mücksch / Rainer Müller / Carsten Schultz / Barbara Müller / Hans-Georg Kräusslich / John A G Briggs /
Abstract: Gag, the primary structural protein of HIV-1, is recruited to the plasma membrane for virus assembly by its matrix (MA) domain. Gag is subsequently cleaved into its component domains, causing ...Gag, the primary structural protein of HIV-1, is recruited to the plasma membrane for virus assembly by its matrix (MA) domain. Gag is subsequently cleaved into its component domains, causing structural maturation to repurpose the virion for cell entry. We determined the structure and arrangement of MA within immature and mature HIV-1 through cryo-electron tomography. We found that MA rearranges between two different hexameric lattices upon maturation. In mature HIV-1, a lipid extends out of the membrane to bind with a pocket in MA. Our data suggest that proteolytic maturation of HIV-1 not only assembles the viral capsid surrounding the genome but also repurposes the membrane-bound MA lattice for an entry or postentry function and results in the partial removal of up to 2500 lipids from the viral membrane.
History
DepositionJun 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 matrix
B: HIV-1 matrix
C: HIV-1 matrix
D: HIV-1 matrix
E: HIV-1 matrix
F: HIV-1 matrix
H: HIV-1 matrix
I: HIV-1 matrix
J: HIV-1 matrix
O: HIV-1 matrix
P: HIV-1 matrix
Q: HIV-1 matrix
R: HIV-1 matrix
S: HIV-1 matrix
U: HIV-1 matrix
W: HIV-1 matrix
Y: HIV-1 matrix
b: HIV-1 matrix
c: HIV-1 matrix
d: HIV-1 matrix
e: HIV-1 matrix
f: HIV-1 matrix
j: HIV-1 matrix
l: HIV-1 matrix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,43872
Polymers314,04024
Non-polymers23,39848
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
HIV-1 matrix


Mass: 13084.983 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) / References: UniProt: B6DRA0
#2: Chemical...
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Human immunodeficiency virus 1 / Type: VIRUS
Details: cHIV MA-SP1 Gag proteolytic cleavage mutant virus particles purified from HEK293T cells.
Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: cHIV MA-SP1 Gag proteolytic cleavage mutant virus particles purified from HEK293T cells.
VitrificationCryogen name: ETHANE

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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: 105000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1MATLABvolume selection
2SerialEMimage acquisition
4CTFFINDCTF correction
5NOVACTFCTF correction
8UCSF Chimeramodel fitting
14AV33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19586 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 65 / Num. of volumes extracted: 119343
Atomic model buildingProtocol: RIGID BODY FIT
Details: Only the backbone of the protein model was fitted as a rigid body.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12H3Q

2h3q

12H3Q1PDBexperimental model
22H3V

2h3v

12H3V2PDBexperimental model

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