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- PDB-5upw: CryoEM Structure Refinement by Integrating NMR Chemical Shifts wi... -

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Entry
Database: PDB / ID: 5upw
TitleCryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations
DescriptorGag polyprotein
KeywordsHYDROLASE / Cryo-EM / HIV capsid / Chemical shift / Molecular Dynamics / hydrolase
Specimen sourceHuman immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) / virus
MethodElectron microscopy (5 A resolution / Helical)
AuthorsPerilla, J.R.
CitationJ Phys Chem B, 2017

J Phys Chem B, 2017 StrPapers
CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
Juan R Perilla / Gongpu Zhao / Manman Lu / Jiying Ning / Guangjin Hou / In-Ja L Byeon / Angela M Gronenborn / Tatyana Polenova / Peijun Zhang

DateDeposition: Feb 4, 2017 / Release: Mar 1, 2017

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Assembly

Deposited unit
A: Gag polyprotein
B: Gag polyprotein
C: Gag polyprotein
D: Gag polyprotein
E: Gag polyprotein
F: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)147,9266
Polyers147,9266
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)14440
ΔGint (kcal/M)-77
Surface area (A2)66770
MethodPISA

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Components

#1: Polypeptide(L)
Gag polyprotein / Pr55Gag


Mass: 24654.268 Da / Num. of mol.: 6 / Fragment: UNP residues 133-353 / Mutation: A92E
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) / virus
References: UniProt: P12493

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: HELICAL

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Sample preparation

ComponentName: HIV-1 Capsid Protein Assembly / Type: COMPLEX
Specimen supportGrid material: COPPER / Grid mesh size: 300 /inch. / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100
Details: The assembled sample (1.5 microliter) was applied to the carbon side of a glow discharged perforated Quantifoil grid, followed by application of 3 microliter of low salt buffer (100 milimolar NaCl, 50 milimolar Tris pH 8.0) on the back side of the grid, and blotting, from the back side, with a filter paper, before plunge-freezing in liquid ethane

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Electron microscopy imaging

MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 31000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / Cs: 2.2 mm
Specimen holderSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Processing

EM helical entityAngular rotation per subunit: -31.13 deg. / Axial rise per subunit: 6.94 A / Axial symmetry: C1
3D reconstructionResolution: 5 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 38452 / Number of class averages: 3
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model buildingPDB-ID: 4XFX

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