[English] 日本語
Yorodumi
- EMDB-8168: BF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8168
TitleBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer
Map dataBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer
Sample
  • Complex: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
    • Complex: BF520.1 Fab
    • Complex: BG505.C2 T332N SOSIP.664 trimer
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 10.9 Å
AuthorsWilliams JA / Lee KK
CitationJournal: Cell / Year: 2016
Title: HIV-1 Neutralizing Antibodies with Limited Hypermutation from an Infant.
Authors: Cassandra A Simonich / Katherine L Williams / Hans P Verkerke / James A Williams / Ruth Nduati / Kelly K Lee / Julie Overbaugh /
Abstract: HIV-1 broadly neutralizing antibodies (bnAbs) develop in a subset of infected adults and exhibit high levels of somatic hypermutation (SHM) due to years of affinity maturation. There is no precedent ...HIV-1 broadly neutralizing antibodies (bnAbs) develop in a subset of infected adults and exhibit high levels of somatic hypermutation (SHM) due to years of affinity maturation. There is no precedent for eliciting highly mutated antibodies by vaccination, nor is it practical to wait years for a desired response. Infants develop broad responses early, which may suggest a more direct path to generating bnAbs. Here, we isolated ten neutralizing antibodies (nAbs) contributing to plasma breadth of an infant at ∼1 year post-infection, including one with cross-clade breadth. The nAbs bind to envelope trimer from the transmitted virus, suggesting that this interaction may have initiated development of the infant nAbs. The infant cross-clade bnAb targets the N332 supersite on envelope but, unlike adult bnAbs targeting this site, lacks indels and has low SHM. The identification of this infant bnAb illustrates that HIV-1-specific neutralization breadth can develop without prolonged affinity maturation and extensive SHM.
History
DepositionApr 29, 2016-
Header (metadata) releaseJul 13, 2016-
Map releaseJul 13, 2016-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8168.png

Downloads & links

-
Map

FileDownload / File: emd_8168.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.14 Å/pix.
x 84 pix.
= 347.76 Å		4.14 Å/pix.
x 84 pix.
= 347.76 Å		4.14 Å/pix.
x 84 pix.
= 347.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.56 / Movie #1: 1.5
Minimum - Maximum-10.246309 - 5.69479
Average (Standard dev.)0.01362123 (±0.3383385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-42-42-42
Dimensions848484
Spacing848484
CellA=B=C: 347.75998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.144.144.14
M x/y/z848484
origin x/y/z0.0000.0000.000
length x/y/z347.760347.760347.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-42-42-42
NC/NR/NS848484
D min/max/mean-10.2465.6950.014

-
Supplemental data

-
Half map: BF520.1 Fab fragment bound to BG505 T332N SOSIP.664...

Fileemd_8168_half_map_1.map
AnnotationBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: BF520.1 Fab fragment bound to BG505 T332N SOSIP.664...

Fileemd_8168_half_map_2.map
AnnotationBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer

EntireName: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
Components
  • Complex: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
    • Complex: BF520.1 Fab
    • Complex: BG505.C2 T332N SOSIP.664 trimer

-
Supramolecule #1: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer

SupramoleculeName: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
type: complex / ID: 1 / Parent: 0

-
Supramolecule #2: BF520.1 Fab

SupramoleculeName: BF520.1 Fab / type: complex / ID: 2 / Parent: 1
Details: Fab domains generated by papain digestion of BF520.1 IgG
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: BG505.C2 T332N SOSIP.664 trimer

SupramoleculeName: BG505.C2 T332N SOSIP.664 trimer / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505.C2 T332N
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293F / Recombinant plasmid: pPPI4

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.020 mg/mL
BufferpH: 7.5
StainingType: NEGATIVE / Material: methylamine tungstate
GridMaterial: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 24.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: EMAN (ver. 2.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5aco


Details: PDB entry 5ACO was filtered to 60 Angstrom resolution and used as an initial model.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.1) / Number images used: 18325
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.1)
FSC plot (resolution estimation)

+
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