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Yorodumi- EMDB-3076: Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonica... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3076 | |||||||||
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Title | Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonical Binding Site | |||||||||
Map data | Reconstruction by aligning both CA and Cypa | |||||||||
Sample |
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Function / homology | Function and homology information host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / negative regulation of protein K48-linked ubiquitination / negative regulation of viral life cycle / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / viral release from host cell / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / Membrane binding and targetting of GAG proteins / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / platelet aggregation / host multivesicular body / integrin binding / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / viral nucleocapsid / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / host cell nucleus / Neutrophil degranulation / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / protein-containing complex / RNA binding / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | Liu C / Perilla JR / Ning J / Lu M / Hou G / Ramalhu R / Bedwell GJ / Ahn J / Shi J / Gronenborn AM ...Liu C / Perilla JR / Ning J / Lu M / Hou G / Ramalhu R / Bedwell GJ / Ahn J / Shi J / Gronenborn AM / Prevelige Jr PE / Rousso I / Aiken C / Polenova T / Schulten K / Zhang P | |||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site. Authors: Chuang Liu / Juan R Perilla / Jiying Ning / Manman Lu / Guangjin Hou / Ruben Ramalho / Benjamin A Himes / Gongpu Zhao / Gregory J Bedwell / In-Ja Byeon / Jinwoo Ahn / Angela M Gronenborn / ...Authors: Chuang Liu / Juan R Perilla / Jiying Ning / Manman Lu / Guangjin Hou / Ruben Ramalho / Benjamin A Himes / Gongpu Zhao / Gregory J Bedwell / In-Ja Byeon / Jinwoo Ahn / Angela M Gronenborn / Peter E Prevelige / Itay Rousso / Christopher Aiken / Tatyana Polenova / Klaus Schulten / Peijun Zhang / Abstract: The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the ...The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection. | |||||||||
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_3076.map.gz | 91.6 MB | EMDB map data format | |
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Header (meta data) | emd-3076-v30.xml emd-3076.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | EMDB_3076.png | 353.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3076 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3076 | HTTPS FTP |
-Validation report
Summary document | emd_3076_validation.pdf.gz | 248.6 KB | Display | EMDB validaton report |
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Full document | emd_3076_full_validation.pdf.gz | 247.7 KB | Display | |
Data in XML | emd_3076_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3076 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3076 | HTTPS FTP |
-Related structure data
Related structure data | 5fjbMC 3075C 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_3076.map.gz / Format: CCP4 / Size: 184.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction by aligning both CA and Cypa | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 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 : Helical assembly of HIV-1 capsid protein and host cell factor Cyc...
Entire | Name: Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A |
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Components |
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-Supramolecule #1000: Helical assembly of HIV-1 capsid protein and host cell factor Cyc...
Supramolecule | Name: Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A type: sample / ID: 1000 / Oligomeric state: hexamer / Number unique components: 1 |
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Molecular weight | Experimental: 42 KDa / Theoretical: 42 KDa |
-Macromolecule #1: Human immunodeficiency virus 1
Macromolecule | Name: Human immunodeficiency virus 1 / type: protein_or_peptide / ID: 1 / Name.synonym: HIV-1 capsid protein with CypA / Oligomeric state: Hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Experimental: 42 KDa / Theoretical: 42 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 / Details: 1m NaCl,50mM Tris-Hcl |
Grid | Details: Glow discharged perforated Quantifoil R2/1 grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER Method: With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl,50mM Tris,PH 8.0)to back side. Blot 3-5 seconds from back side. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Jun 20, 2013 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.349 µm / Number real images: 19 / Average electron dose: 15 e/Å2 / Bits/pixel: 32 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | The particles were aligned using IHRSR |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 7.393 Å Applied symmetry - Helical parameters - Δ&Phi: 138.133 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Software - Name: SPIDER, IHRSR |
CTF correction | Details: Each particle |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-5fjb: |