7MKC | pdb_00007mkc

N74D mutant of the HIV-1 capsid protein in complex with PF-3450074 (PF74)

PDB DOI: https://doi.org/10.2210/pdb7MKC/pdb

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-04-23 Released: 2022-05-04
Deposition Author(s): Kirby, K.A., Sarafianos, S.G.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.242 (Depositor), 0.246 (DCC)
R-Value Work:
0.183 (Depositor), 0.189 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

TRIM5alpha Restriction of HIV-1-N74D Viruses in Lymphocytes Is Caused by a Loss of Cyclophilin A Protection.

Selyutina, A., Simons, L.M., Kirby, K.A., Bulnes-Ramos, A., Hu, P., Sarafianos, S.G., Hultquist, J.F., Diaz-Griffero, F.

(2022) Viruses 14: 363

PubMed: 35215956 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/v14020363
Primary Citation Related Structures:
7MKC, 7MN0

PubMed Abstract:
The core of HIV-1 viruses bearing the capsid change N74D (HIV-1-N74D) do not bind the human protein CPSF6. In primary human CD4 ⁺ T cells, HIV-1-N74D viruses exhibit an infectivity defect when compared to wild-type. We first investigated whether loss of CPSF6 binding accounts for the loss of infectivity. Depletion of CPSF6 in human CD4 ⁺ T cells did not affect the early stages of wild-type HIV-1 replication, suggesting that defective infectivity in the case of HIV-1-N74D viruses is not due to the loss of CPSF6 binding. Based on our previous result that cyclophilin A (Cyp A) protected HIV-1 from human tripartite motif-containing protein 5α (TRIM5α _hu) restriction in CD4 ⁺ T cells, we found that depletion of TRIM5α _hu in CD4 ⁺ T cells rescued the infectivity of HIV-1-N74D, suggesting that HIV-1-N74D cores interacted with TRIM5α _hu. Accordingly, TRIM5α _hu binding to HIV-1-N74D cores was increased compared with that of wild-type cores, and consistently, HIV-1-N74D cores lost their ability to bind Cyp A. In agreement with the notion that N74D capsids are defective in their ability to bind Cyp A, we found that HIV-1-N74D viruses were 20-fold less sensitive to TRIMCyp restriction when compared to wild-type viruses in OMK cells. Structural analysis revealed that N74D hexameric capsid protein in complex with PF74 is different from wild-type hexameric capsid protein in complex with PF74, which explains the defect of N74D capsids to interact with Cyp A. In conclusion, we showed that the decreased infectivity of HIV-1-N74D in CD4 ⁺ T cells is due to a loss of Cyp A protection from TRIM5α _hu restriction activity.

Organizational Affiliation

Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Macromolecule Content

Total Structure Weight: 26.82 kDa
Atom Count: 1,779
Modeled Residue Count: 221
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
capsid protein	A	231	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12493 Go to UniProtKB: P12493
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12493
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1B0 (Subject of Investigation/LOI) Query on 1B0 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE C₂₇ H₂₇ N₃ O₂ ACDFWSNAQWFRRF-VWLOTQADSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]