[English] 日本語
Yorodumi
- EMDB-20178: Modified BG505 SOSIP-based immunogen RC1 in complex with the elic... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: EMD-20178
TitleModified BG505 SOSIP-based immunogen RC1 in complex with the elicited V3-glycan patch antibody Ab275MUR
Map data
SampleComplex of RC1 variant of BG505 SOSIP.664 trimer with three Ab275MUR Fabs and three 8ANC195 Fabs
  • RC1 variant of BG505 SOSIP.664 trimer
  • Ab275MUR Fab
  • (RC1 variant of HIV-1 Env glycoprotein ...) x 2
  • (Ab275MUR antibody Fab ...) x 2
  • (ligand) x 3
Biological speciesHuman immunodeficiency virus 1 / Mus musculoides (Temminck's mouse) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsAbernathy ME / Gristick HB / Bjorkman PJ
CitationJournal: Nature / Year: 2019
Title: Immunization expands B cells specific to HIV-1 V3 glycan in mice and macaques.
Authors: Amelia Escolano / Harry B Gristick / Morgan E Abernathy / Julia Merkenschlager / Rajeev Gautam / Thiago Y Oliveira / Joy Pai / Anthony P West / Christopher O Barnes / Alexander A Cohen / Haoqing Wang / Jovana Golijanin / Daniel Yost / Jennifer R Keeffe / Zijun Wang / Peng Zhao / Kai-Hui Yao / Jens Bauer / Lilian Nogueira / Han Gao / Alisa V Voll / David C Montefiori / Michael S Seaman / Anna Gazumyan / Murillo Silva / Andrew T McGuire / Leonidas Stamatatos / Darrell J Irvine / Lance Wells / Malcolm A Martin / Pamela J Bjorkman / Michel C Nussenzweig /
Abstract: Broadly neutralizing monoclonal antibodies protect against infection with HIV-1 in animal models, suggesting that a vaccine that elicits these antibodies would be protective in humans. However, it ...Broadly neutralizing monoclonal antibodies protect against infection with HIV-1 in animal models, suggesting that a vaccine that elicits these antibodies would be protective in humans. However, it has not yet been possible to induce adequate serological responses by vaccination. Here, to activate B cells that express precursors of broadly neutralizing antibodies within polyclonal repertoires, we developed an immunogen, RC1, that facilitates the recognition of the variable loop 3 (V3)-glycan patch on the envelope protein of HIV-1. RC1 conceals non-conserved immunodominant regions by the addition of glycans and/or multimerization on virus-like particles. Immunization of mice, rabbits and rhesus macaques with RC1 elicited serological responses that targeted the V3-glycan patch. Antibody cloning and cryo-electron microscopy structures of antibody-envelope complexes confirmed that immunization with RC1 expands clones of B cells that carry the anti-V3-glycan patch antibodies, which resemble precursors of human broadly neutralizing antibodies. Thus, RC1 may be a suitable priming immunogen for sequential vaccination strategies in the context of polyclonal repertoires.
Validation ReportPDB-ID: 6orq

SummaryFull reportAbout validation report
DateDeposition: Apr 30, 2019 / Header (metadata) release: May 29, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6orq
  • Surface level: 1.02
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6orq
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_20178.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 256 pix.
= 367.616 Å
1.44 Å/pix.
x 256 pix.
= 367.616 Å
1.44 Å/pix.
x 256 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.436 Å
Density
Contour LevelBy AUTHOR: 1.02 / Movie #1: 1.02
Minimum - Maximum-2.3921328 - 3.5628066
Average (Standard dev.)-0.0004616329 (±0.14429614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4361.4361.436
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z367.616367.616367.616
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.3923.563-0.000

-
Supplemental data

-
Mask #1

Fileemd_20178_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire Complex of RC1 variant of BG505 SOSIP.664 trimer with three Ab275...

EntireName: Complex of RC1 variant of BG505 SOSIP.664 trimer with three Ab275MUR Fabs and three 8ANC195 Fabs
Details: Fab fragments generated by recombinant expression and complexed with the RC1 variant of BG505 SOSIP.664 trimer
Number of components: 10

+
Component #1: protein, Complex of RC1 variant of BG505 SOSIP.664 trimer with th...

ProteinName: Complex of RC1 variant of BG505 SOSIP.664 trimer with three Ab275MUR Fabs and three 8ANC195 Fabs
Details: Fab fragments generated by recombinant expression and complexed with the RC1 variant of BG505 SOSIP.664 trimer
Recombinant expression: No
MassTheoretical: 600 kDa
SourceSpecies: Human immunodeficiency virus 1

+
Component #2: protein, RC1 variant of BG505 SOSIP.664 trimer

ProteinName: RC1 variant of BG505 SOSIP.664 trimer / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: Expi293

+
Component #3: protein, Ab275MUR Fab

ProteinName: Ab275MUR Fab
Details: Fab fragment generated by proteolytic cleavage of IgG antibody using Ficin
Recombinant expression: No
SourceSpecies: Mus musculoides (Temminck's mouse)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: Expi293

+
Component #4: protein, RC1 variant of HIV-1 Env glycoprotein gp41

ProteinName: RC1 variant of HIV-1 Env glycoprotein gp41 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 17.346428 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

+
Component #5: protein, RC1 variant of HIV-1 Env glycoprotein gp120

ProteinName: RC1 variant of HIV-1 Env glycoprotein gp120 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 57.762633 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

+
Component #6: protein, Ab275MUR antibody Fab heavy chain

ProteinName: Ab275MUR antibody Fab heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 13.418949 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #7: protein, Ab275MUR antibody Fab light chain

ProteinName: Ab275MUR antibody Fab light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.943238 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 73 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

+
Component #9: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

+
Component #10: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.25 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %
Details: 0 blot force, 3 second blot time, 3 uL sample added to freshly glow-discharged grids.

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 73000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 328

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 49308
3D reconstructionSoftware: cryoSPARC / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 5T3Z, 5T3Z, 4FQQ, 4FQQ
Chain ID: G, B, B, A
Output model

+
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 PDBe / 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