[English] 日本語
Yorodumi
- EMDB-7106: HIV-1 Envelope Glycoprotein clone PC64M18c043 SOSIP.664 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 7106
TitleHIV-1 Envelope Glycoprotein clone PC64M18c043 SOSIP.664
SampleHIV-1 Envelope Glycoprotein clone PC64M18c043 SOSIP.664
SourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Map dataprimary map
Methodsingle particle reconstruction, at 24 Å resolution
AuthorsBerndsen ZT / Rantalainen K / Ward AB
CitationImmunity, 2017, 47, 990-1003.e9

Immunity, 2017, 47, 990-1003.e9 Yorodumi Papers
HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage.
Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de Val / Mengyu Wu / Audrey Cappelletti / Jeffrey Umotoy / Yolanda Lie / Terri Wrin / Paul Algate / Po-Ying Chan-Hui / Etienne Karita / / / Andrew B Ward / Ian A Wilson / Dennis R Burton / Davey Smith / Sergei L Kosakovsky Pond / Pascal Poignard

DateDeposition: Nov 7, 2017 / Header (metadata) release: Dec 6, 2017 / Map release: Dec 6, 2017 / Last update: Dec 6, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • 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_7106.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
4.1 Å/pix.
= 262.4 Å
64 pix
4.1 Å/pix.
= 262.4 Å
64 pix
4.1 Å/pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.1 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.061363697 - 0.20005023
Average (Standard dev.)0.0012045413 (0.017774114)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
CellA=B=C: 262.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.0610.2000.001

-
Supplemental data

-
Mask #1

Fileemd_7106_msk_1.map ( map file in CCP4 format, 1049 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsMask
Space group number1

-
Mask #1~

Fileemd_7106_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

-
Sample components

-
Entire HIV-1 Envelope Glycoprotein clone PC64M18c043 SOSIP.664

EntireName: HIV-1 Envelope Glycoprotein clone PC64M18c043 SOSIP.664
Number of components: 2
MassTheoretical: 225 kDa

-
Component #1: protein, HIV-1 Envelope Glycoprotein clone PC64M18c043 SOSIP.664

ProteinName: HIV-1 Envelope Glycoprotein clone PC64M18c043 SOSIP.664
Recombinant expression: No
MassTheoretical: 225 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

-
Component #2: protein, HIV-1 Envelope Glycoprotein clone PC64M18c043 SOSIP.664

ProteinName: HIV-1 Envelope Glycoprotein clone PC64M18c043 SOSIP.664
Recombinant expression: No
Source (engineered)Expression System: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
Support filmunspecified
VitrificationCryogen name: NONE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 7654
3D reconstructionSoftware: RELION / Resolution: 24 Å / Resolution method: FSC 0.5 CUT-OFF
FSC plot (resolution assessment)

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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)

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