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CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

by helical reconstruction, at 5 A resolution

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#1: Deposited structure unit, Imaged by Jmol

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Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
AuthorsPerilla, J.R.
DateDeposition: 2017-02-04, Release: 2017-03-01
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-8595, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
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EMDB-8595

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Article
Citation - primary
ArticleJ Phys Chem B, Vol. 121, Issue 15, Page 3853-3863, Year 2017
TitleCryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
AuthorsJuan R Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L Byeon, Angela M Gronenborn, Tatyana Polenova, Peijun Zhang
Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.
Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.
Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States.
Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN, U.K.
Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus , Didcot OX11 0DE, U.K.
LinksPubMed: 28181439, DOI: 10.1021/acs.jpcb.6b13105, PMC: PMC5459578
Components
ID 1 : Pr55Gag
DescriptionGag polyprotein
Typepolypeptide(L)
FragmentUNP residues 133-353
MutationA92E
Formula weight24654.268 Da
Number of molecules6
ID1
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Alt source flag: sample
Beg seq num: 1
End seq num: 221
Gene: gag, ID:11698, Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Host: ID:562, Escherichia coli


Seq type: Biological sequence
LinksUniProt: P12493, Sequence view
Sample
Entity assembly
Entity id list1
NameHIV-1 Capsid Protein Assembly
SourceRECOMBINANT
TypeCOMPLEX
Buffer
Specimen id1
PH8
Experiment
Aggregation stateHELICAL ARRAY
Reconstruction methodHELICAL
Sample support
Specimen id1
Grid materialCOPPER
Grid mesh size300
Grid typeQuantifoil R2/1
Vitrification
Specimen id1
Chamber temperature295
Cryogen nameETHANE
DetailsThe 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
Humidity100
InstrumentHOMEMADE PLUNGER
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI POLARA 300
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationNominal: 31000 X
CsNominal: 2.2 mm
Nominal defocusMax: 2200 nm, Min: 700 nm
Specimen holder
Specimen holderModel: SIDE ENTRY, EUCENTRIC
Image scans
Image recording id1
Frames per image30
Processing
Helical entity
Image processing id1
Angular rotation per subunit-31.13 degrees
Axial rise per subunit6.94 A
Axial symmetryC1
3D reconstruction
Image processing id1
AlgorithmFOURIER SPACE
Num class averages3
Number of particles38452
Resolution5 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typeHELICAL
3D fitting
Refinement ProtocolFLEXIBLE FIT
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
Pdb chain residue range1-220
PDB entry ID4XFX
Download
PDB format
Allpdb5upw.ent.gz
pdb5upw.ent (uncompressed file)
Header onlypdb5upw.ent.gz
mmCIF format
mmCIF5upw.cif.gz
XML format
All5upw.xml.gz
No-atom5upw-noatom.xml.gz
Ext-atom5upw-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 6.2 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 6.3 MB