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

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8168
TitleBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer
Map dataBF520.1 Fab fragment bound to BG505 T332N SOSIP.664 trimer
SampleBF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer:
BF520.1 Fab / BG505.C2 T332N SOSIP.664 trimer
SourceHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / 10.9 Å resolution
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.
DateDeposition: Apr 29, 2016 / Header (metadata) release: Jul 13, 2016 / Map release: Jul 13, 2016 / Last update: Feb 14, 2018

-
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

Downloads & links

-
Map

Fileemd_8168.map.gz (map file in CCP4 format, 2371 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
84 pix
4.14 Å/pix.
= 347.76 Å
84 pix
4.14 Å/pix.
= 347.76 Å
84 pix
4.14 Å/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
Contour Level:1.56 (by author), 1.5 (movie #1):
Minimum - Maximum-10.246309 - 5.69479
Average (Standard dev.)0.01362123 (0.3383385)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions848484
Origin-42.0-42.0-42.0
Limit41.041.041.0
Spacing848484
CellA=B=C: 347.75998 Å
α=β=γ: 90.0 deg.

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

-
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
Number of components: 3

-
Component #1: protein, BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer

ProteinName: BF520.1 Fab complexed with BG505.C2 T332N SOSIP.664 trimer
Recombinant expression: No

-
Component #2: protein, BF520.1 Fab

ProteinName: BF520.1 Fab
Details: Fab domains generated by papain digestion of BF520.1 IgG
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

-
Component #3: protein, BG505.C2 T332N SOSIP.664 trimer

ProteinName: BG505.C2 T332N SOSIP.664 trimer / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1 / Strain: BG505.C2 T332N
Source (engineered)Expression System: Homo sapiens (human) / Vector: pPPI4 / Cell of expression system: HEK 293F

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle
Sample solutionSpecimen conc.: 0.02 mg/ml / pH: 7.5
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: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 52000.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3000.0 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 18325
3D reconstructionSoftware: EMAN / Resolution: 10.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

+
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