[English] 日本語
Yorodumi
- EMDB-1216: Cryo-electron tomographic structure of an immunodeficiency virus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1216
TitleCryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ.
Map dataThis is the volume of the averaged SIV envelope complex
Sample
  • Sample: Simian Immunodeficiency Virus mne Envelope Complex
  • Virus: viral envelope (unknown)
  • Protein or peptide: gp120Envelope glycoprotein GP120
  • Protein or peptide: gp41
Biological speciesSimian immunodeficiency virus / viral envelope (unknown)
Methodsubtomogram averaging / cryo EM / negative staining / Resolution: 28.0 Å
AuthorsZanetti G / Briggs JAG / Gruenewald K / Sattentau Q / Fuller SD
CitationJournal: PLoS Pathog / Year: 2006
Title: Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ.
Authors: Giulia Zanetti / John A G Briggs / Kay Grünewald / Quentin J Sattentau / Stephen D Fuller /
Abstract: The envelope glycoprotein (Env) complexes of the human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate viral entry and are a target for neutralizing antibodies. The receptor ...The envelope glycoprotein (Env) complexes of the human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate viral entry and are a target for neutralizing antibodies. The receptor binding surfaces of Env are in large part sterically occluded or conformationally masked prior to receptor binding. Knowledge of the unliganded, trimeric Env structure is key for an understanding of viral entry and immune escape, and for the design of vaccines to elicit neutralizing antibodies. We have used cryo-electron tomography and averaging to obtain the structure of the SIV Env complex prior to fusion. Our result reveals novel details of Env organisation, including tight interaction between monomers in the gp41 trimer, associated with a three-lobed, membrane-distal gp120 trimer. A cavity exists at the gp41-gp120 trimer interface. Our model for the spike structure agrees with previously predicted interactions between gp41 monomers, and furthers our understanding of gp120 interactions within an intact spike.
History
DepositionApr 18, 2006-
Header (metadata) releaseApr 18, 2006-
Map releaseSep 5, 2006-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7410.144914449
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7410.144914449
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1216.gif

Downloads & links

-
Map

FileDownload / File: emd_1216.map.gz / Format: CCP4 / Size: 955.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the volume of the averaged SIV envelope complex
Voxel sizeX=Y=Z: 5.47 Å
Density
Contour Level1: 8160.0 / Movie #1: 7410.1449144
Minimum - Maximum-15307.0 - 20000.0
Average (Standard dev.)117.353999999999999 (±3616.260000000000218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-31-31-31
Dimensions636363
Spacing636363
CellA=B=C: 344.61 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.475.475.47
M x/y/z636363
origin x/y/z0.0000.0000.000
length x/y/z344.610344.610344.610
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS-31-31-31
NC/NR/NS636363
D min/max/mean-15307.00020000.000117.354

-
Supplemental data

-
Segmentation: The mask for the averaged SIV envelope complex

AnnotationThe mask for the averaged SIV envelope complex
Fileemd_1216_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Segmentation: Protein with the mask applied is the simple...

AnnotationProtein with the mask applied is the simple multiplication of the spike protein map (emd_1216.map) with the mask (emd_1216_mask_1.map)
Fileemd_1216_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Simian Immunodeficiency Virus mne Envelope Complex

EntireName: Simian Immunodeficiency Virus mne Envelope Complex
Components
  • Sample: Simian Immunodeficiency Virus mne Envelope Complex
  • Virus: viral envelope (unknown)
  • Protein or peptide: gp120Envelope glycoprotein GP120
  • Protein or peptide: gp41

-
Supramolecule #1000: Simian Immunodeficiency Virus mne Envelope Complex

SupramoleculeName: Simian Immunodeficiency Virus mne Envelope Complex / type: sample / ID: 1000
Details: The envelope complex wasn't purified but it was analysed on the virus
Oligomeric state: trimer of Gp120 and trimer of Gp41 and membrane
Number unique components: 3
Molecular weightExperimental: 500 KDa / Theoretical: 500 KDa
Method: sum of individual components is an underestimate due to the presence of the membrane

-
Supramolecule #1: viral envelope

SupramoleculeName: viral envelope / type: virus / ID: 1 / Name.synonym: viral membrane / Details: viral membrane / Sci species name: viral envelope / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: viral membrane
Host (natural)Organism: Macaca nemestrina (pig-tailed macaque) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: membrane / Diameter: 1200 Å

-
Macromolecule #1: gp120

MacromoleculeName: gp120 / type: protein_or_peptide / ID: 1 / Name.synonym: SIV envelope receptor binding protein / Details: trimeric / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Simian immunodeficiency virus / Strain: SIVMneCL8 / synonym: SIVmne / Cell: HuT 78 / Location in cell: viral membrane
Molecular weightExperimental: 120 KDa / Theoretical: 120 KDa

-
Macromolecule #2: gp41

MacromoleculeName: gp41 / type: protein_or_peptide / ID: 2 / Name.synonym: SIV envelope transmembrane protein / Details: trimeric / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Simian immunodeficiency virus / Strain: SIVMneCL8 / synonym: SIVmne / Cell: HuT 78 / Location in cell: viral membrane
Molecular weightExperimental: 41 KDa / Theoretical: 41 KDa

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.2 / Details: PBS
StainingType: NEGATIVE
Details: Samples were mixed with BSA adsorbed 10 nm colloidal gold and vitrified for cryoelectron microscopy.
GridDetails: holey carbon film
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home built / Method: blot for two seconds before plunging

-
Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/ST
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 0.6 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 27500
Specialist opticsEnergy filter - Name: GATAN GIF 2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 69.0 ° / Tilt series - Axis1 - Max angle: 63 °
TemperatureAverage: 77 K
DetailsWe collected a tilt series
DateOct 1, 2005
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Digitization - Sampling interval: 30 µm / Number real images: 3 / Average electron dose: 57 e/Å2

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: TOM
Details: envelope complexes were averaged to give a final map of 28A resolution as determined by FSC at 0.5 cut-off.
DetailsAverage number of projections used in the 3D reconstructions: 2986.

-
Atomic model buiding 1

Initial modelPDB ID:

2bf1


Chain - Chain ID: A
SoftwareName: URO
DetailsPDBEntryID_givenInChain. Protocol: rigid body. The gp120 monomer was manually fitted and three-fold symmetry was imposed during fitting with URO
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: quadratic misfit

+
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