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- PDB-9rmx: CryoEM reconstruction of integrase filament at the lumen of nativ... -

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Basic information

Entry
Database: PDB / ID: 9rmx
TitleCryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 34.2 nm)
Components
  • Gag polyprotein
  • Integrase
KeywordsVIRAL PROTEIN / integrase / capsid / HIV-1 / RNA
Function / homology
Function and homology information


viral budding via host ESCRT complex / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...viral budding via host ESCRT complex / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal 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 / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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
INOSITOL HEXAKISPHOSPHATE / Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.63 Å
AuthorsCherepanov, P. / Singer, M.R. / Hope, J. / Zhang, P.
Funding support United States, United Kingdom, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
Wellcome TrustCC2058 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2058 United Kingdom
Cancer Research UKCC2058 United Kingdom
CitationJournal: To Be Published
Title: Structural bases for integrase-RNA binding and retention of viral RNA within HIV-1 capsid cores
Authors: Singer, M. / Li, Z. / Rey, J.S. / Hope, J. / Cook, N.J. / Punch, E. / Smith, J. / Zhou, Z. / Maslen, S. / Masino, L. / Nans, A. / Skehel, M. / Taylor, I.A. / Zhang, P. / Perilla, J.R. / ...Authors: Singer, M. / Li, Z. / Rey, J.S. / Hope, J. / Cook, N.J. / Punch, E. / Smith, J. / Zhou, Z. / Maslen, S. / Masino, L. / Nans, A. / Skehel, M. / Taylor, I.A. / Zhang, P. / Perilla, J.R. / Engelman, A.N. / Cherepanov, P.
History
DepositionJun 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
C: Integrase
D: Integrase
E: Integrase
F: Integrase
G: Integrase
H: Integrase
I: Integrase
J: Integrase
K: Integrase
L: Integrase
U: Gag polyprotein
V: Gag polyprotein
W: Gag polyprotein
X: Gag polyprotein
Y: Gag polyprotein
Z: Gag polyprotein
a: Gag polyprotein
b: Gag polyprotein
c: Gag polyprotein
d: Gag polyprotein
e: Gag polyprotein
f: Gag polyprotein
g: Gag polyprotein
h: Gag polyprotein
i: Gag polyprotein
j: Gag polyprotein
k: Gag polyprotein
l: Gag polyprotein
m: Gag polyprotein
n: Gag polyprotein
o: Gag polyprotein
p: Gag polyprotein
q: Gag polyprotein
r: Gag polyprotein
s: Gag polyprotein
t: Gag polyprotein
u: Gag polyprotein
v: Gag polyprotein
w: Gag polyprotein
x: Gag polyprotein
y: Gag polyprotein
z: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,213,15364
Polymers1,207,08744
Non-polymers6,06520
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
Integrase / IN


Mass: 32242.818 Da / Num. of mol.: 12 / Mutation: D64N, D116N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: gag-pol / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Protein ...
Gag polyprotein


Mass: 25630.426 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: gag / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q72497
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H18O24P6
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: single particle reconstruction

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Sample preparation

ComponentName: Human immunodeficiency virus 1 / Type: VIRUS
Details: Virus particles were produced by transfection of HEK293T cells with molecular clone
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens / Strain: NL4-3
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
225 mMTris hydrochlorideTRIS-HCl1
31 mMinositol hexaphosphateIP61
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
EM embeddingMaterial: vitreous ice
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE-PROPANE / Humidity: 100 %

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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 magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 49.6 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2Gautomatchparticle selection
3EPUimage acquisition
8UCSF Chimeramodel fitting
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.6.2classification
13cryoSPARC4.6.23D reconstruction
14PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58103 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11K6Y

1k6y

11K6Y1PDBexperimental model
29C9M

9c9m

19C9M2PDBexperimental model
38A1P

8a1p

18A1P3PDBexperimental model
42B4J

2b4j

12B4J4PDBexperimental model
56SKK

6skk

16SKK5PDBexperimental model
RefinementHighest resolution: 4.63 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00274391
ELECTRON MICROSCOPYf_angle_d0.481101069
ELECTRON MICROSCOPYf_dihedral_angle_d10.96928287
ELECTRON MICROSCOPYf_chiral_restr0.0411205
ELECTRON MICROSCOPYf_plane_restr0.00413095

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