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CryoEM Structure of Tubular Assembly of HIV-1 CA and Evidence for a Novel Interface

by helical reconstruction, at 16 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0055, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0055, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5136
TitleCryoEM Structure of Tubular Assembly of HIV-1 CA and Evidence for a Novel Interface
MapThis is a map of tubular assembly of HIV-1 CA
SampleHIV-1 CA A92E
AuthorsByeon IL, Meng X, Jung J, Zhao G, Ahn J, Concel J, Aiken C, Gronenborn AM, Zhang P
DateDeposition: 2009-10-20, Header release: 2009-11-09, Map release: 2010-05-05, Last update: 2011-09-27
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0055, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0055, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleCell, Vol. 139, Issue 4, Page 780-790, Year 2009
TitleStructural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
AuthorsIn-Ja L Byeon, Xin Meng, Jinwon Jung, Gongpu Zhao, Ruifeng Yang, Jinwoo Ahn, Jiong Shi, Jason Concel, Christopher Aiken, Peijun Zhang, Angela M Gronenborn
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
KeywordsCapsid Proteins (chemistry), Cryoelectron Microscopy, HIV-1 (chemistry), Nuclear Magnetic Resonance, Biomolecular, RNA, Viral (metabolism), Virus Assembly
LinksPubMed: 19914170, PII: S0092-8674(09)01298-7, DOI: 10.1016/j.cell.2009.10.010, PMC: PMC2782912
Map
Fileemd_5136.map.gz ( map file in CCP4 format, 27001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
2.15 A/pix
= 258. A
240 pix
2.15 A/pix
= 516. A
240 pix
2.15 A/pix
= 516. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.01 (by emdb), 0.0055 (movie #1):
Minimum - Maximum: -0.0263844 - 0.0278307
Average (Standard dev.): 0.00019507 (0.00626063)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240120
Origin000
Limit239239119
Spacing240240120
Unit CellA: 516 A, B: 516 A, C: 258 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.15 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.152.152.15
M x/y/z240240120
origin x/y/z0.0000.0000.000
length x/y/z516.000516.000258.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240120
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0260.0280.000
Annotation DetailsThis is a map of tubular assembly of HIV-1 CA
Supplement
Images
Images
Sample
NameHIV-1 CA A92E
Number of Components6
Detailscomponent name, HIV-1 CA protein
Component #1: protein - hexamer
Scientific nameHIV-1 CA protein
Common Namehexamer
Scientific Name of SpeciesHuman immunodeficiency virus
Common Name of SpeciesHuman immunodeficiency virus
NCBI taxonomy12721
Recombinant expressionYes
Experiment
Sample Preparation
Helical ParametersHand: RIGHT HANDED
Specimen Statefilament
Vitrification
Cryogen NameNITROGEN
InstrumentNONE
Imaging
MicroscopeFEI POLARA 300
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeSPOT SCAN
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
Holderliquid nitrogen-cooled cryo specimen holder
ModelGATAN LIQUID NITROGEN
Camera
Processing
Methodhelical reconstruction
3D reconstruction
Resolution By Author16 A
Resolution MethodFSC 0.5
Atomic Model Fitting
Model #0
SoftwareChimera
Refinement SpaceREAL
PDB Entry ID3DIK
Download
Data from EMDB
Header (meta data in XML format)emd-5136.xml (5.6 KB)
Map dataemd_5136.map.gz (11.1 MB)
Imagesemd_5136_1.tif (732.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5136
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.2 KB