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- PDB-9ek2: HIV-1 immature L20K/E73K/A82T matrix protein p17 lattice -

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Basic information

Entry
Database: PDB / ID: 9ek2
TitleHIV-1 immature L20K/E73K/A82T matrix protein p17 lattice
ComponentsMatrix protein p17
KeywordsVIRAL PROTEIN / MATRIX / HIV-1 / p17 / HIV-1 p17 / VIRUS / GAG / STRUCTURAL PROTEIN
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / symbiont-mediated activation of host apoptosis / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / symbiont-mediated activation of host apoptosis / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection 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 ...Reverse transcriptase connection / Reverse transcriptase connection 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. / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
MYRISTIC ACID / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.3 Å
AuthorsRey, J.S. / Perilla, J.R. / Chen, L. / Zhang, P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI178846 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI184080 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150560 United States
CitationJournal: To Be Published
Title: Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity
Authors: Rey, J.S. / Perilla, J.R. / Chen, L. / Zhang, P.
History
DepositionNov 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein p17
D: Matrix protein p17
e: Matrix protein p17
h: Matrix protein p17
k: Matrix protein p17
G: Matrix protein p17
J: Matrix protein p17
M: Matrix protein p17
P: Matrix protein p17
S: Matrix protein p17
V: Matrix protein p17
Y: Matrix protein p17
b: Matrix protein p17
B: Matrix protein p17
E: Matrix protein p17
f: Matrix protein p17
i: Matrix protein p17
l: Matrix protein p17
H: Matrix protein p17
K: Matrix protein p17
N: Matrix protein p17
Q: Matrix protein p17
T: Matrix protein p17
W: Matrix protein p17
Z: Matrix protein p17
c: Matrix protein p17
C: Matrix protein p17
F: Matrix protein p17
g: Matrix protein p17
j: Matrix protein p17
m: Matrix protein p17
I: Matrix protein p17
L: Matrix protein p17
O: Matrix protein p17
R: Matrix protein p17
U: Matrix protein p17
X: Matrix protein p17
a: Matrix protein p17
d: Matrix protein p17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)521,01978
Polymers512,11339
Non-polymers8,90639
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Matrix protein p17 / MA


Mass: 13131.099 Da / Num. of mol.: 39 / Mutation: L20K,E73K,A82T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: pNL4-3 / Gene: gag-pol / Production host: Homo sapiens (human) / References: UniProt: P12497
#2: Chemical...
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C14H28O2
Has ligand of interestN
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: HIV-1 / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: HIV-1 (virus) / Strain: pNL4-3
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 123 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
7UCSF ChimeraX1.8model fittingRigid-body fitting
13NAMD3model refinementMoleculary Dynamics Flexible Fitting
14Rosetta3.14model refinementAutomated model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8600 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 78 / Num. of volumes extracted: 8600
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17TBP

7tbp

17TBP1PDBexperimental model
22LYB

2lyb

12LYB2PDBexperimental model

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