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- PDB-4ard: Structure of the immature retroviral capsid at 8A resolution by c... -

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Entry
Database: PDB / ID: 4ard
TitleStructure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy
DescriptorCAPSID PROTEIN P27
KeywordsVIRAL PROTEIN / RETROVIRUS / GAG
Specimen sourceMASON-PFIZER MONKEY VIRUS / virus
MethodElectron microscopy (7 A resolution / Helical / Vitreous ice cryoem)
AuthorsBharat, T.A.M. / Davey, N.E. / Ulbrich, P. / Riches, J.D. / Marco, A.D. / Rumlova, M. / Sachse, C. / Ruml, T. / Briggs, J.A.G.
CitationNature, 2012, 487, 385-389

Nature, 2012, 487, 385-389 StrPapers
Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy.
Tanmay A M Bharat / Norman E Davey / Pavel Ulbrich / James D Riches / Alex de Marco / Michaela Rumlova / Carsten Sachse / Tomas Ruml / John A G Briggs

DateDeposition: Apr 23, 2012 / Release: May 30, 2012 / Last modification: Aug 1, 2012

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Assembly

Deposited unit
A: CAPSID PROTEIN P27
B: CAPSID PROTEIN P27


Theoretical massNumber of molelcules
Total (without water)25,7712
Polyers25,7712
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)CAPSID PROTEIN P27 / M-PMV DPRO CANC PROTEIN


Mass: 12885.351 Da / Num. of mol.: 2 / Fragment: M-PMV CA-NTD, RESIDUES 318-433 / Source: (gene. exp.) MASON-PFIZER MONKEY VIRUS / virus / References: UniProt: P07567

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: HELICAL / Specimen type: VITREOUS ICE CRYOEM

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Sample preparation

Assembly of specimenName: M-PMV CANC GAG TUBES / Aggregation state: FILAMENT
Buffer solutionName: 100MM NACL, 50MM TRIS-HCL, 1UM ZN
Sample preparationpH: 7.7
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: OTHER / Date: Jul 5, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.2 e/A2 / Illumination mode: LOW DOSE
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
CameraType: KODAK SO163 FILM
EM image scansNumber digital images: 46
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: SPIDER, AV3
3D reconstructionMethod: HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING
Resolution: 7 A / Nominal pixel size: 1.53 A/pix / Actual pixel size: 1.53 A/pix / CTF correction method: DIVISION BY 3D CTF SQ
Details: HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2090. (DEPOSITION ID: 10768).
Atomic model buildingMethod: RIGID BODY / Ref protocol: NMR / Ref space: REAL
Atomic model buildingPDB-ID: 2KGF
Least-squares processHighest resolution: 7 A
Refine hist #LASTHighest resolution: 7 A
Number of atoms included #LASTProtein: 232 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 232

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