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Database: PDB / ID: 5upw
TitleCryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations
DescriptorGag polyprotein
KeywordsVIRAL PROTEIN / Cryo-EM / HIV capsid / Chemical shift / Molecular Dynamics / hydrolase / viral protein
Specimen sourceHuman immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) / virus
MethodElectron microscopy (5 Å resolution / Helical array / Helical)
AuthorsPerilla, J.R.
CitationJ Phys Chem B, 2017, 121, 3853-3863

J Phys Chem B, 2017, 121, 3853-3863 Yorodumi Papers
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 4, 2017 / Release: Mar 1, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 1, 2017Structure modelrepositoryInitial release
1.1May 3, 2017Structure modelDatabase references
1.2Aug 2, 2017Structure modelData collectionem_software_em_software.name
1.3Dec 6, 2017Structure modelStructure summarystruct_keywords_struct_keywords.pdbx_keywords / _struct_keywords.text

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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

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)14440
ΔGint (kcal/M)-77
Surface area (Å2)66770


#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

Cellular component

Molecular function

Biological process

Experimental details


EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

Sample preparation

ComponentName: HIV-1 Capsid Protein Assembly / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 24 deg. / Units: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
11Msodium chlorideNaCl1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins
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

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
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 / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / Cs: 2.2 mm / C2 aperture diameter: 100 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingAverage exposure time: 6 sec. / Electron dose: 41 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 523
Image scansMovie frames/image: 30


EM software
IDNameVersionCategoryImage processing IDFitting ID
Helical symmertyAngular rotation/subunit: -31.13 deg. / Axial rise/subunit: 6.94 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 39712
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 38452 / Algorithm: FOURIER SPACE / Number of class averages: 3 / Symmetry type: HELICAL
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model buildingPDB-ID: 4XFX
Pdb chain residue range: 1-220

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