[English] 日本語
Yorodumi
- EMDB-6251: CH106 Fab in complex with BG505 SOSIP.664 Trimer -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 6251
TitleCH106 Fab in complex with BG505 SOSIP.664 Trimer
Map dataCH106 Fab in complex with BG505 SOSIP.664 Trimer
SampleFab of CH106 human monoclonal antibody bound to HIV-1 Env gp140 BG505 SOSIP.664:
Soluble HIV-1 Envelope glycoprotein / Fab of CH106 human monoclonal antibody
KeywordsHIV-1 / Fab / Env trimer
SourceHuman immunodeficiency virus 1 (HIV-1) / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / 19 Å resolution
AuthorsOzorowski G / Derking R / Sanders RW / Ward AB
CitationJournal: PLoS Pathog. / Year: 2015
Title: Comprehensive antigenic map of a cleaved soluble HIV-1 envelope trimer.
Authors: Ronald Derking / Gabriel Ozorowski / Kwinten Sliepen / Anila Yasmeen / Albert Cupo / Jonathan L Torres / Jean-Philippe Julien / Jeong Hyun Lee / Thijs van Montfort / Steven W de Taeye / Mark Connors / Dennis R Burton / Ian A Wilson / Per-Johan Klasse / Andrew B Ward / John P Moore / Rogier W Sanders
DateDeposition: Jan 19, 2015 / Header (metadata) release: Mar 11, 2015 / Map release: Mar 11, 2015 / Last update: Aug 26, 2015

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 14
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_6251.map.gz (map file in CCP4 format, 16001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.05 Å/pix.
= 328. Å
160 pix
2.05 Å/pix.
= 328. Å
160 pix
2.05 Å/pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density
Contour Level:14 (by author), 14 (movie #1):
Minimum - Maximum-29.90282059 - 78.88714600
Average (Standard dev.)0.36066312 (5.82088995)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin000
Limit159159159
Spacing160160160
CellA=B=C: 328.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-29.90378.8870.361

-
Supplemental data

-
Sample components

-
Entire Fab of CH106 human monoclonal antibody bound to HIV-1 Env gp140 B...

EntireName: Fab of CH106 human monoclonal antibody bound to HIV-1 Env gp140 BG505 SOSIP.664
Details: Size-exclusion-chromatography-purified gp140 trimers were used.
Number of components: 2
Oligomeric State: One Fab molecule binds to one BG505 SOSIP.664 gp140 monomer
MassTheoretical: 570 kDa

-
Component #1: protein, Soluble HIV-1 Envelope glycoprotein

ProteinName: Soluble HIV-1 Envelope glycoprotein / a.k.a: SOSIP / Oligomeric Details: Trimer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 420 kDa
SourceSpecies: Human immunodeficiency virus 1 (HIV-1) / Strain: BG505
Source (engineered)Expression System: Homo sapiens (human) / Vector: pPPI4 / Cell of expression system: HEK293F

-
Component #2: protein, Fab of CH106 human monoclonal antibody

ProteinName: Fab of CH106 human monoclonal antibody / Oligomeric Details: dimer (heavy chain + light chain) / Recombinant expression: Yes / Number of Copies: 3
MassTheoretical: 50 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293F

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.01 mg/ml / Buffer solution: 50 mM Tris-HCl, pH 7.4, 150 mM NaCl / pH: 7.4
Support film400 Cu mesh grid with carbon support, plasma-cleaned
Staining3 uL of protein was applied and blotted; then 2% w/v uranyl formate was applied for 45 seconds.
VitrificationInstrument: NONE / Cryogen name: NONE

-
Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Sep 29, 2014
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 52000 X (nominal), 52000 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 52,000x magnification.
Imaging mode: BRIGHT FIELD / Defocus: 1000 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Tilt Angle: -50 - 0 deg.
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 143

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 27144
Details: The particles were selected using an automatic selection program. Class averages with 3 Fabs bound to one gp140 trimer were placed into a substack and used for 3D reconstruction.
3D reconstructionAlgorithm: Cross-common lines, projection matching / Software: EMAN2, SPARX / Resolution: 19 Å / Resolution method: FSC 0.5, semi-independent

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. 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

+
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

Read more

-
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.

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