[English] 日本語
Yorodumi
- PDB-6did: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6did
TitleHIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Components
  • (Envelope glycoprotein ...) x 2
  • (Monoclonal antibody 10A ...) x 2
KeywordsVIRAL PROTEIN / HIV / antibodies / antibody
Function / homologyRetroviral envelope protein GP41-like / Gp120 core superfamily / Immunoglobulin C1-set / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Immunoglobulin-like domain / Immunoglobulin subtype / Envelope glycoprotein Gp160 ...Retroviral envelope protein GP41-like / Gp120 core superfamily / Immunoglobulin C1-set / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Immunoglobulin-like domain / Immunoglobulin subtype / Envelope glycoprotein Gp160 / Envelope glycoprotein GP120 / Retroviral envelope protein / Immunoglobulin C1-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / host cell endosome membrane / evasion or tolerance by virus of host immune response / viral protein processing / antigen binding / fusion of virus membrane with host plasma membrane / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / integral component of membrane / identical protein binding / IgG heavy chain VDJ region / Ig kappa-b4 chain C region / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Function and homology information
Specimen sourceHuman immunodeficiency virus 1
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.71 Å resolution
AuthorsTurner, H.L. / Cottrell, C.A. / Oyen, D. / Wilson, I.A. / Ward, A.B.
CitationJournal: Immunity / Year: 2018
Title: Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization.
Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton / Andrew B Ward / Lars Hangartner
Abstract: Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a ...Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a barrier to fully understanding the humoral response to antigens and hinders rational vaccine design efforts. Here, we describe a method of characterizing polyclonal responses by using electron microscopy, and we applied this method to the immunization of rabbits with an HIV-1 envelope glycoprotein vaccine candidate, BG505 SOSIP.664. We detected known epitopes within the polyclonal sera and revealed how antibody responses evolved during the prime-boosting strategy to ultimately result in a neutralizing antibody response. We uncovered previously unidentified epitopes, including an epitope proximal to one recognized by human broadly neutralizing antibodies as well as potentially distracting non-neutralizing epitopes. Our method provides an efficient and semiquantitative map of epitopes that are targeted in a polyclonal antibody response and should be of widespread utility in vaccine and infection studies.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 23, 2018 / Release: Sep 5, 2018

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7896
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
F: Envelope glycoprotein gp160
I: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
J: Envelope glycoprotein gp160
C: Monoclonal antibody 10A light chain
D: Monoclonal antibody 10A heavy chain
E: Monoclonal antibody 10A light chain
K: Monoclonal antibody 10A heavy chain
H: Monoclonal antibody 10A light chain
L: Monoclonal antibody 10A heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)379,864159
Polyers349,56412
Non-polymers30,301147
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)70830
ΔGint (kcal/M)210
Surface area (Å2)144220
MethodPISA

-
Components

-
Envelope glycoprotein ... , 2 types, 6 molecules AFGBIJ

#1: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 54064.277 Da / Num. of mol.: 3 / Fragment: GP120 domain residues 30-505 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 17146.482 Da / Num. of mol.: 3 / Fragment: GP41 domain residues 509-661 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S7

-
Monoclonal antibody 10A ... , 2 types, 6 molecules CEHDKL

#3: Protein/peptide Monoclonal antibody 10A light chain


Mass: 23047.424 Da / Num. of mol.: 3 / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) / References: UniProt: P01840
#4: Protein/peptide Monoclonal antibody 10A heavy chain


Mass: 22263.018 Da / Num. of mol.: 3 / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human) / References: UniProt: A0A1Y1B8B1

-
Non-polymers , 3 types, 147 molecules

#5: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 93 / Formula: C8H15NO6 / N-Acetylglucosamine
#6: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 15 / Formula: C6H12O6
#7: Chemical...
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 39 / Formula: C6H12O6

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1
Type: COMPLEX
Details: Model includes fitted atomic structures for HIV Env BG505 SOSIP (PDB ID: 5v8m) and 10A Fab (PDB ID: 6cjk).
Entity ID: 1, 2, 3, 4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 5.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8.5 sec. / Electron dose: 52.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 34

-
Processing

EM software
IDNameCategory
1Appionparticle selection
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 170078
SymmetryPoint symmetry: C3
3D reconstructionResolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 161639 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

+
About Yorodumi

-
News

-
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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