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- EMDB-5325: Molecular structure of soluble trimeric HIV-1 glycoprotein gp140 ... -

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Basic information

Entry
Database: EMDB / ID: 5325
TitleMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
KeywordsHIV/AIDS vaccine / immunogen / HIV glycoprotein structure / gp140 trimer / cryo-electron tomography / sub-tomogram averaging / cryo-electron microscopy
SampleSOSIP gp140 KNH1144 17b
SourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Map dataMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
Methodsubtomogram averaging, at 20 Å resolution
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
CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 11440-11445

Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 11440-11445 StrPapers
Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.
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

DateDeposition: Jul 11, 2011 / Header (metadata) release: May 31, 2012 / Map release: May 31, 2012 / Last update: May 31, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
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Map

Fileemd_5325.map.gz (map file in CCP4 format, 3908 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
4.1 Å/pix.
= 410. Å
100 pix
4.1 Å/pix.
= 410. Å
100 pix
4.1 Å/pix.
= 410. Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.1 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-6.37717438 - 8.50566101
Average (Standard dev.)-0.00243358 (0.6463089)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
CellA=B=C: 410 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-6.3778.506-0.002

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Supplemental data

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Sample components

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Entire SOSIP gp140 KNH1144 17b

EntireName: SOSIP gp140 KNH1144 17b / Number of components: 4 / Oligomeric State: trimeric

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Component #1: protein, SOSIP gp140 KNH1144 17b

ProteinName: SOSIP gp140 KNH1144 17b / Recombinant expression: Yes
SourceSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN

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Image processing

ProcessingMethod: subtomogram averaging
3D reconstructionResolution: 20 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera / Refinement space: REAL
Input PDB model: 3DNO

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