top_cornerHomeEMD-5582  Contact EMDataBank 
Image unavailable
Title:Cryo-EM structure of HIV-1 capsid assembly
Authors:Zhao G, Perilla JR, Yufenyuy E, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P
Sample:HIV-1 CA A92E
Method:Helical reconstruction (8.6 angstroms resolution)
Red flagLatest update:2013-07-31
Other Views:
Sample
Sample name: HIV-1 CA A92E
Oligomeric state: helical assembly of hexamers
Theoretical molecular weight of the sample: 0.025
Components:
ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details
1proteinHIV-1 capsid protein0.025hexamertrueHuman immunodeficiency virus 1
Experiment
Specimen state: Filament
Specimen preparation:
pHSpecimen conc.DetailsStainingSpecimen support details
8.02 mg/mL1 M NaCl, 50 mM Tris-HCl200 mesh quantifoil R2/1 copper grid
Helical parameters:
HandPhi incrementAzimuthal (Z) increment
LEFT HANDED31.13°7.247 Å
Vitrification:
Cryogen nameHumidityTemp.Instr.MethodTime resolvedDetails
ETHANE80%90 KHOMEMADE PLUNGERWith 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side. ms
Imaging:
MicroscopeVoltageIllumination modeImaging modeCsDefocus min.Defocus max.Nominal mag.Calibrated mag.Electron sourceDetectorDetector distanceAstigmatism
FEI POLARA 300200 kVFLOOD BEAMBRIGHT FIELD2 mm1000 nm3500 nm5900058257FIELD EMISSION GUNKODAK SO-163 FILM mm

Specimen holderHolder modelTilt min.Tilt max.Energy filterEnergy windowTemp.Temp. min.Temp. max.Beam tiltElectron doseOther detailsDate
SIDE ENTRY, EUCENTRIC°° eV82 K80 K85 K mrad15 e/Å211-DEC-2010
Processing
Software:Frealign
CTF correction:each filament
Resolution by author:8.6 Å
Resolution method:FSC 0.5
Processing details:The segments were aligned and reconstructed using Frealign. Twofold symmetry was imposed using IHRSR++.
Scanned images:
Num. imagesSampling sizeOD rangeQuant. bit numberOther detailsScanner
276.35 μm/pixel16NIKON SUPER COOLSCAN 9000
Fitting:
PDBProtocolTarget crit.SoftwareB valueFitting spacePDB chainDetails
2KOD flexibleMDFFREAL
3H47 flexibleMDFFREAL