[English] 日本語
Yorodumi
- EMDB-1800: Single particle cryo-electron microscopy analysis of CD4 bound HI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1800
TitleSingle particle cryo-electron microscopy analysis of CD4 bound HIV-1 Env
Map dataThis is an image of a surface rendered CD4 bound HIV-1 Env
Sample
  • Sample: CD4 bound HIV-1 Env
  • Protein or peptide: gp160deltaCTSOS
  • Protein or peptide: soluble CD4 (2 domain)
KeywordsHIV-1 spike / Membrane Fusion / Structural Transition / Cryo-EM / Single Particle
Function / homology: / T-cell surface antigen CD4 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope
Function and homology information
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 21.0 Å
AuthorsWu SR / Loving R / Lindqvist B / Hebert H / Koeck P / Sjoberg M / Garoff H
CitationJournal: AIDS Res Hum Retroviruses / Year: 1990
Title: Escherichia coli expression, purification, and biological activity of a truncated soluble CD4.
Authors: R L Garlick / R J Kirschner / F M Eckenrode / W G Tarpley / C S Tomich /
Abstract: A truncated molecule containing the N-terminal 183 amino acid residues of CD4 (sCD4-183) has been produced in Escherichia coli at high levels, using the trp promoter and an AT-rich ribosome binding ...A truncated molecule containing the N-terminal 183 amino acid residues of CD4 (sCD4-183) has been produced in Escherichia coli at high levels, using the trp promoter and an AT-rich ribosome binding site to direct expression in a pBR322-derived vector. A culture has been selected which allows large-scale fermentation and production of this material as an insoluble inclusion body protein. Procedures which solubilize, refold, and purify sCD4-183 have been developed. The purified sCD4-183 binds gp120 in solution and blocks human immunodeficiency virus (HIV) infection of human peripheral blood lymphocytes in vitro.
History
DepositionSep 29, 2010-
Header (metadata) releaseOct 13, 2010-
Map releaseOct 29, 2010-
UpdateMay 24, 2012-
Current statusMay 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD_1800.jpg

Downloads & links

-
Map

FileDownload / File: emd_1800.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered CD4 bound HIV-1 Env
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.5 Å/pix.
x 72 pix.
= 252. Å		3.5 Å/pix.
x 72 pix.
= 252. Å		3.5 Å/pix.
x 72 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.3 / Movie #1: 2.6
Minimum - Maximum-3.59058 - 5.97472
Average (Standard dev.)0.0786333 (±1.02616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 252 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-3.5915.9750.079

-
Supplemental data

-
Sample components

-
Entire : CD4 bound HIV-1 Env

EntireName: CD4 bound HIV-1 Env
Components
  • Sample: CD4 bound HIV-1 Env
  • Protein or peptide: gp160deltaCTSOS
  • Protein or peptide: soluble CD4 (2 domain)

-
Supramolecule #1000: CD4 bound HIV-1 Env

SupramoleculeName: CD4 bound HIV-1 Env / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Trimer / Number unique components: 2
Molecular weightExperimental: 700 KDa / Theoretical: 500 KDa / Method: Blue Native PAGE

-
Macromolecule #1: gp160deltaCTSOS

MacromoleculeName: gp160deltaCTSOS / type: protein_or_peptide / ID: 1 / Name.synonym: HIV-1 Env / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: JR-FL / synonym: HIV-1
Molecular weightTheoretical: 420 KDa
Recombinant expressionOrganism: 293T / Recombinant plasmid: pCAGGS JRFL 160deltaCTSOS
SequenceGO: viral envelope
InterPro: Human immunodeficiency virus 1, envelope glycoprotein Gp120

-
Macromolecule #2: soluble CD4 (2 domain)

MacromoleculeName: soluble CD4 (2 domain) / type: protein_or_peptide / ID: 2 / Name.synonym: sCD4-2d
Details: sCD4-183 was obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH
Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 26 KDa
SequenceGO: GO: 0006948 / InterPro: T-cell surface antigen CD4

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 50 mM HEPES, 100 mM NaCl, 1.8 mM CaCl2
StainingType: NEGATIVE / Details: No stain was applied
GridDetails: 200 mesh Cu Holey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 3 seconds once before plunging

-
Electron microscopy

MicroscopeJEOL 2100F
TemperatureMin: 93 K / Max: 96 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected using online FFT
Legacy - Electron beam tilt params: No Tilt
DateOct 23, 2009
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 3.5 µm / Number real images: 336 / Average electron dose: 9 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 43300
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

DetailsThe 3D structures reconstructed by processing particle images using standard single particle procedure in EMAN version 1.9.
CTF correctionDetails: Each Digitized Image
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 9870
Final two d classificationNumber classes: 131

-
Atomic model buiding 1

Initial modelPDB ID:

3jwd


Chain - Chain ID: A
SoftwareName: O
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more