[English] 日本語
Yorodumi
- EMDB-8729: Cryo-EM reconstruction of the HIV-1 BG505 SOSIP.664 Env trimer in... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8729
TitleCryo-EM reconstruction of the HIV-1 BG505 SOSIP.664 Env trimer in complex with soluble CD4 (D1-D2)
SampleHIV-1 Env BG505 SOSIP.664 in complex with soluble CD4 (2-domain)
SourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Homo sapiens / human
Map dataBG505 SOSIP trimer bound to sCD4
Methodsingle particle reconstruction, at 10.5 Å resolution
AuthorsLyumkis D / de Val N / Ward AB
CitationNature, 2017, 547, 360-363

Nature, 2017, 547, 360-363 StrPapers
Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike.
Gabriel Ozorowski / Jesper Pallesen / Natalia de Val / Dmitry Lyumkis / Christopher A Cottrell / Jonathan L Torres / Jeffrey Copps / Robyn L Stanfield / Albert Cupo / Pavel Pugach / John P Moore / Ian A Wilson / Andrew B Ward

DateDeposition: May 13, 2017 / Header (metadata) release: Jan 11, 2017 / Map release: Jul 26, 2017 / Last update: Aug 2, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_8729.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.62 Å/pix.
= 335.36 Å
128 pix
2.62 Å/pix.
= 335.36 Å
128 pix
2.62 Å/pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.62 Å
Density
Contour Level:0.11 (by author), 0.11 (movie #1):
Minimum - Maximum-0.07420437 - 0.21470392
Average (Standard dev.)-0.0013202264 (0.01583887)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 335.36 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0740.215-0.001

-
Supplemental data

-
Sample components

+
Entire HIV-1 Env BG505 SOSIP.664 in complex with soluble CD4 (2-domain)

EntireName: HIV-1 Env BG505 SOSIP.664 in complex with soluble CD4 (2-domain)
Number of components: 6
MassTheoretical: 75 kDa

+
Component #1: protein, HIV-1 Env BG505 SOSIP.664 in complex with soluble CD4 (2...

ProteinName: HIV-1 Env BG505 SOSIP.664 in complex with soluble CD4 (2-domain)
Recombinant expression: No
MassTheoretical: 75 kDa
SourceSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: HEK293F

+
Component #2: protein, HIV-1 Env BG505 SOSIP.664

ProteinName: HIV-1 Env BG505 SOSIP.664 / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: HEK293F

+
Component #3: protein, CD4 (2-domain)

ProteinName: CD4 (2-domain) / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: HEK293F

+
Component #4: protein, HIV-1 Env BG505 SOSIP.664 gp120

ProteinName: HIV-1 Env BG505 SOSIP.664 gp120 / Recombinant expression: No
Source (engineered)Expression System: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1

+
Component #5: protein, HIV-1 Env BG505 SOSIP.664 gp41

ProteinName: HIV-1 Env BG505 SOSIP.664 gp41 / Recombinant expression: No
Source (engineered)Expression System: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1

+
Component #6: protein, Soluble CD4 (2-domain)

ProteinName: Soluble CD4 (2-domain) / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens / human

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 50 %
Details: 5 microliters of the complex was incubated with 3 microliters of a fresh 1.8 mM DDM solution. A 3 microliter aliquot of the complex was applied to a C-Flat grid (CF-2/2-4C, Electron Microscopy Sciences, Protochips, Inc.) which had been plasma cleaned for 5 seconds using a mixture of Ar/O2 (Gatan Solarus 950 Plasma system), blotted off, and then immediately plunged into liquid ethane using a manual freeze plunger.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 32 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal), 38167 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 90 - 90 K)
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionSampling size: 5 microns
Details: Individual frames were gain-corrected, aligned, and summed using MotionCor.

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 1754
3D reconstructionAlgorithm: FOURIER SPACE / Software: Frealign / CTF correction: performed internally in Relion and Frealign / Resolution: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Resolution-limited refinement used throughout / Euler angles: Frealign 3D classification and refinement

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more