[English] 日本語
Yorodumi- PDB-5up4: Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM -
+Open data
-Basic information
Entry | Database: PDB / ID: 5up4 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM | ||||||
Components | HIV-1 Capsid Protein and spacer peptide 1 | ||||||
Keywords | VIRUS / HIV-1 / spacer peptide 1 / capsid protein / cryoEM / Helical assembly / reconstruction | ||||||
Function / homology | Function and homology information viral process / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9 Å | ||||||
Authors | Perilla, J.R. / Schirra, R. / Zhang, P. / Schulten, K. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Quenching protein dynamics interferes with HIV capsid maturation. Authors: Mingzhang Wang / Caitlin M Quinn / Juan R Perilla / Huilan Zhang / Randall Shirra / Guangjin Hou / In-Ja Byeon / Christopher L Suiter / Sherimay Ablan / Emiko Urano / Theodore J Nitz / ...Authors: Mingzhang Wang / Caitlin M Quinn / Juan R Perilla / Huilan Zhang / Randall Shirra / Guangjin Hou / In-Ja Byeon / Christopher L Suiter / Sherimay Ablan / Emiko Urano / Theodore J Nitz / Christopher Aiken / Eric O Freed / Peijun Zhang / Klaus Schulten / Angela M Gronenborn / Tatyana Polenova / Abstract: Maturation of HIV-1 particles encompasses a complex morphological transformation of Gag via an orchestrated series of proteolytic cleavage events. A longstanding question concerns the structure of ...Maturation of HIV-1 particles encompasses a complex morphological transformation of Gag via an orchestrated series of proteolytic cleavage events. A longstanding question concerns the structure of the C-terminal region of CA and the peptide SP1 (CA-SP1), which represents an intermediate during maturation of the HIV-1 virus. By integrating NMR, cryo-EM, and molecular dynamics simulations, we show that in CA-SP1 tubes assembled in vitro, which represent the features of an intermediate assembly state during maturation, the SP1 peptide exists in a dynamic helix-coil equilibrium, and that the addition of the maturation inhibitors Bevirimat and DFH-055 causes stabilization of a helical form of SP1. Moreover, the maturation-arresting SP1 mutation T8I also induces helical structure in SP1 and further global dynamical and conformational changes in CA. Overall, our results show that dynamics of CA and SP1 are critical for orderly HIV-1 maturation and that small molecules can inhibit maturation by perturbing molecular motions. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5up4.cif.gz | 646.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5up4.ent.gz | 536.9 KB | Display | PDB format |
PDBx/mmJSON format | 5up4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5up4_validation.pdf.gz | 945.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5up4_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5up4_validation.xml.gz | 116.4 KB | Display | |
Data in CIF | 5up4_validation.cif.gz | 174.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/5up4 ftp://data.pdbj.org/pub/pdb/validation_reports/up/5up4 | HTTPS FTP |
-Related structure data
Related structure data | 8582MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 24654.268 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: B6DRA0 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: HIV-1 CA-SP1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Human immunodeficiency virus 1 | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
| |||||||||||||||
Specimen | Conc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil | |||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 23 e/Å2 / Film or detector model: KODAK SO-163 FILM / Num. of real images: 200 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 128.88 ° / Axial rise/subunit: 13.46 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14000 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
|