|Entry||Database: EMDB / ID: 3076|
|Title||Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonical Binding Site|
|Sample||Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A|
|Source||Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1|
|Map data||Reconstruction by aligning both CA and Cypa|
|Method||helical reconstruction, at 8 Å resolution|
|Authors||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||Nat Commun, 2016, 7, 10714-10714|
Nat Commun, 2016, 7, 10714-10714 Yorodumi Papers
|Validation Report||PDB-ID: 5fjb|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 5, 2015 / Header (metadata) release: Jul 29, 2015 / Map release: Mar 16, 2016 / Last update: Apr 6, 2016|
Downloads & links
|File||emd_3076.map.gz (map file in CCP4 format, 193068 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.06 Å|
CCP4 map header:
-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|
Number of components: 1 / Oligomeric State: hexamer
|Mass||Theoretical: 42 kDa / Experimental: 42 kDa|
-Component #1: protein, Human immunodeficiency virus 1
|Protein||Name: Human immunodeficiency virus 1 / a.k.a: HIV-1 capsid protein with CypA / Oligomeric Details: Hexamer / Recombinant expression: Yes|
|Mass||Theoretical: 42 kDa / Experimental: 42 kDa|
|Source||Species: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1|
|Source (engineered)||Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli|
|Specimen state||helical array|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Hand: LEFT HANDED / Delta z: 7.393 Å / Delta phi: 138.133 deg.|
|Sample solution||Specimen conc.: 2 mg/ml / Buffer solution: 1m NaCl,50mM Tris-Hcl / pH: 8|
|Support film||Glow discharged perforated Quantifoil R2/1 grid|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 100 %|
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 imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Jun 20, 2013|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm|
|Specimen Holder||Holder: side entry / Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 19 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.349 microns / Bit depth: 32|
|Processing||Method: helical reconstruction / Details: The particles were aligned using IHRSR|
|3D reconstruction||Software: SPIDER, IHRSR / CTF correction: Each particle / Resolution: 8 Å / Resolution method: FSC 0.5, gold-standard|
-Atomic model buiding
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
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External links: The 2017 Nobel Prize in Chemistry - Press Release
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