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Yorodumi- EMDB-8582: Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8582 | |||||||||
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Title | Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM | |||||||||
Map data | CryoEM structure of HIV-1 capsid protein and spacer peptide-1 (CA-SP1) | |||||||||
Sample |
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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 | helical reconstruction / cryo EM / Resolution: 9.0 Å | |||||||||
Authors | Zhang P / Randall S | |||||||||
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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8582.map.gz | 428.7 MB | EMDB map data format | |
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Header (meta data) | emd-8582-v30.xml emd-8582.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8582_fsc.xml | 17.8 KB | Display | FSC data file |
Images | emd_8582.png | 257 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8582 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8582 | HTTPS FTP |
-Validation report
Summary document | emd_8582_validation.pdf.gz | 287.6 KB | Display | EMDB validaton report |
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Full document | emd_8582_full_validation.pdf.gz | 286.7 KB | Display | |
Data in XML | emd_8582_validation.xml.gz | 15.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8582 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8582 | HTTPS FTP |
-Related structure data
Related structure data | 5up4MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8582.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM structure of HIV-1 capsid protein and spacer peptide-1 (CA-SP1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HIV-1 CA-SP1
Entire | Name: HIV-1 CA-SP1 |
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Components |
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-Supramolecule #1: HIV-1 CA-SP1
Supramolecule | Name: HIV-1 CA-SP1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: HIV-1 Capsid Protein and spacer peptide 1
Macromolecule | Name: HIV-1 Capsid Protein and spacer peptide 1 / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 24.654268 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF ...String: PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPG ATLEEMMTAC QGV |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 2.2 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: KODAK SO-163 FILM / Number real images: 200 / Average electron dose: 23.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Output model | PDB-5up4: |