EMDB-5325: Molecular structure of soluble trimeric HIV-1 glycopro...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5325
Authors	Harris 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
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie 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	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1930 Cite EMDB-5320 Cite EMDB-5321 Cite EMDB-5322 Cite EMDB-5323 Cite EMDB-5324 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-5323 EMDB-5020 EMDB-2013 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 28, Page 11440-5, Year 2011
Title	Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.
Authors	Audray 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.
Keywords	AIDS 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
Links	DOI: 10.1073/pnas.1101414108, PubMed: 21709254, PMC: PMC3136299

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 410.0 A , B = 410.0 A , C = 410.0 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 4.1 A , Y = 4.1 A , Z = 4.1 A

CCP4 map header info

Annotation Details

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

Sample
Name	SOSIP gp140 KNH1144 17b
Number of Components	4
Oligomeric State	trimeric
Component #1: protein - SOSIP gp140 KNH1144 17b
Scientific name	SOSIP gp140 KNH1144 17b
Scientific Name of Species	Human immunodeficiency virus 1 (NCBI Taxonomy: 11676)
Recombinant expression	Yes

Experiment
Sample Preparation
Specimen State	particle
Vitrification
Cryogen Name	ETHANE
Instrument	NONE
Imaging
Microscope	FEI POLARA 300
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Illumination Mode	FLOOD BEAM
Lens
Imaging Mode	BRIGHT FIELD
Specimen Holder
Holder	Eucentric ( GATAN LIQUID NITROGEN )
Camera
Image Acquisition

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

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