3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-5325

Molecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b

by subtomogram averaging, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA

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

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5325
TitleMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
MapMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
SampleSOSIP gp140 KNH1144 17b
KeywordsHIV/AIDS vaccine, immunogen, HIV glycoprotein structure, gp140 trimer, cryo-electron tomography, sub-tomogram averaging, cryo-electron microscopy
AuthorsHarris A, Borgnia MJ, Shi D, Bartesaghi A, He H, Pejchal R, Kang YK, Depetris R, Marozsan AJ, Sanders RW, Klasse PJ, Milne JL, Wilson IA, Olson WC, Moore JP, Subramaniam S
DateDeposition: 2011-07-11, Header release: 2012-05-31, Map release: 2012-05-31, Last update: 2012-05-31
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2, Made by UCSF CHIMERA

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

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 28, Page 11440-5, Year 2011
TitleTrimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.
AuthorsAudray Harris, Mario J Borgnia, Dan Shi, Alberto Bartesaghi, Haifeng He, Robert Pejchal, Yun Kenneth Kang, Rafael Depetris, Andre J Marozsan, Rogier W Sanders, Per Johan Klasse, Jacqueline L S Milne, Ian A Wilson, William C Olson, John P Moore, Sriram Subramaniam
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
KeywordsAIDS Vaccines (chemistry), Antigens, CD4 (chemistry), Biophysical Phenomena, Cryoelectron Microscopy, HIV Antibodies (chemistry), HIV Antigens (chemistry), HIV Envelope Protein gp120 (chemistry), HIV-1 (chemistry), Humans, Immunoglobulin Fab Fragments (chemistry), Ligands, Models, Molecular, Protein Structure, Quaternary, env Gene Products, Human Immunodeficiency Virus (chemistry), gp120 protein, Human immunodeficiency virus 1, gp140 envelope protein, Human immunodeficiency virus 1
LinksDOI: 10.1073/pnas.1101414108, PubMed: 21709254, PMC: PMC3136299
Map
Fileemd_5325.map.gz ( map file in CCP4 format, 3908 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
4.1 A/pix
= 410. A
100 pix
4.1 A/pix
= 410. A
100 pix
4.1 A/pix
= 410. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum: -6.37717438 - 8.50566101
Average (Standard dev.): -0.00243358 (0.6463089)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
Unit CellA= B= C: 410 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.1 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z4.14.14.1
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z410.000410.000410.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-6.3778.506-0.002
Annotation DetailsMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
Supplement
Images
Images
Sample
NameSOSIP gp140 KNH1144 17b
Number of Components4
Oligomeric Statetrimeric
Component #1: protein - SOSIP gp140 KNH1144 17b
Scientific nameSOSIP gp140 KNH1144 17b
Scientific Name of SpeciesHuman immunodeficiency virus 1
NCBI taxonomy11676
Recombinant expressionYes
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeFEI POLARA 300
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Camera
Processing
Methodsubtomogram averaging
3D reconstruction
Resolution By Author20 A
Resolution MethodFSC 0.5
Atomic Model Fitting
Model #0
SoftwareChimera
Refinement SpaceREAL
PDB Entry ID3DNO
Download
Data from EMDB
Header (meta data in XML format)emd-5325.xml (5.8 KB)
Map dataemd_5325.map.gz (2.9 MB)
Imagesemd_5325_1.jpg (29.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5325
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.7 KB