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- PDB-7tv2: X-ray crystal structure of HIV-2 CA protein CTD -

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Basic information

Entry
Database: PDB / ID: 7tv2
TitleX-ray crystal structure of HIV-2 CA protein CTD
ComponentsCapsid protein p24
KeywordsSTRUCTURAL PROTEIN / viral protein
Function / homology
Function and homology information


viral process / viral nucleocapsid / host cell cytoplasm / structural molecule activity / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / 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 finger, CCHC-type superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsShi, K. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37-AI064064 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35-GM118047 United States
CitationJournal: J Mol Biol / Year: 2023
Title: HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation.
Authors: Nathaniel Talledge / Huixin Yang / Ke Shi / Raffaele Coray / Guichuan Yu / William G Arndt / Shuyu Meng / Gloria C Baxter / Luiza M Mendonça / Daniel Castaño-Díez / Hideki Aihara / Louis ...Authors: Nathaniel Talledge / Huixin Yang / Ke Shi / Raffaele Coray / Guichuan Yu / William G Arndt / Shuyu Meng / Gloria C Baxter / Luiza M Mendonça / Daniel Castaño-Díez / Hideki Aihara / Louis M Mansky / Wei Zhang /
Abstract: Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus ...Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10-12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_src_gen / pdbx_initial_refinement_model
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)9,7131
Polymers9,7131
Non-polymers00
Water45025
1
A: Capsid protein p24

A: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)19,4262
Polymers19,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1240 Å2
ΔGint-11 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.813, 30.919, 46.494
Angle α, β, γ (deg.)90.000, 90.560, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Capsid protein p24 / Matrix protein p17 / Nucleocapsid protein p7


Mass: 9713.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 2 (ISOLATE ROD)
Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7D6CKX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 31.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.2 M tri-sodium citrate, 0.1M Bis-Tris propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→26.12 Å / Num. obs: 4761 / % possible obs: 96.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 35.28 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.041 / Rrim(I) all: 0.072 / Net I/σ(I): 11.1 / Num. measured all: 12687
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.98-2.032.60.2579083480.9620.1840.3183.196.4
9.07-26.122.70.03146540.9990.0220.03721.590.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AXX

6axx


Resolution: 1.98→24.41 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 237 4.99 %
Rwork0.2035 4513 -
obs0.2056 4750 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.07 Å2 / Biso mean: 51.1976 Å2 / Biso min: 24.22 Å2
Refinement stepCycle: final / Resolution: 1.98→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms652 0 0 25 677
Biso mean---46.63 -
Num. residues----84
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-2.050.3189270.307345848596
2.05-2.130.306250.256644246797
2.13-2.230.274180.270246147996
2.23-2.350.2192170.250144646398
2.35-2.490.365200.242246448497
2.49-2.690.3161250.220145247797
2.69-2.960.2787290.227344547496
2.96-3.380.2365420.205644048297
3.38-4.250.1955230.181643846191
4.26-24.410.215110.164246747892
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.59455.5753-5.90227.6362-6.96487.71440.6249-0.99190.73270.7189-0.47360.2575-1.38390.3916-0.12240.3306-0.01510.05090.4148-0.00520.36797.7227-6.350341.1235
25.9727-2.24883.3263.9609-4.8896.1541-0.2645-0.3561-0.08930.4748-0.0858-0.2483-0.01240.36350.31710.32130.0310.04930.4265-0.05330.256411.9173-13.90839.7549
33.61173.5114-3.35459.0175-3.11993.5796-1.07810.1964-1.972-0.5901-0.0616-1.01290.7981-0.69051.10350.4299-0.04660.17650.5607-0.02070.67373.5929-22.201343.2963
45.9858-1.2012-0.81090.5832-0.09356.0940.07620.74240.3156-0.14110.42760.2990.0253-1.341-0.43540.2755-0.02530.04220.81070.21730.4025-0.1532-11.721832.7037
52.7446-1.18770.63787.3891-4.47043.5904-0.04810.87230.3625-0.73490.5333-0.20710.6315-0.2274-0.27650.3833-0.13440.05540.74710.05820.33677.7168-8.875822.4615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 282 through 294 )A282 - 294
2X-RAY DIFFRACTION2chain 'A' and (resid 295 through 309 )A295 - 309
3X-RAY DIFFRACTION3chain 'A' and (resid 310 through 321 )A310 - 321
4X-RAY DIFFRACTION4chain 'A' and (resid 322 through 344 )A322 - 344
5X-RAY DIFFRACTION5chain 'A' and (resid 345 through 365 )A345 - 365

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