[English] 日本語
Yorodumi
- EMDB-8981: Cryo-EM reconstruction of domain-swapped, glycan-reactive, neutra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8981
TitleCryo-EM reconstruction of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03
Map data
SampleTernary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.:
2G12 Light chain / 2G12 heavy chain / (Envelope glycoprotein ...) x 2 / VRC03 heavy chain / VRC03 Light chain
Function / homology
Function and homology information


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 / mitigation of host immune response by virus / 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 ...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 / mitigation of host immune response by virus / 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 / integral component of membrane / identical protein binding / plasma membrane
Envelope glycoprotein Gp160 / Retroviral envelope protein GP41-like / Gp120 core superfamily / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsAcharya P / Kwong PD
CitationJournal: Structure / Year: 2019
Title: Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition.
Authors: Gwo-Yu Chuang / Jing Zhou / Priyamvada Acharya / Reda Rawi / Chen-Hsiang Shen / Zizhang Sheng / Baoshan Zhang / Tongqing Zhou / Robert T Bailer / Venkata P Dandey / Nicole A Doria-Rose / ...Authors: Gwo-Yu Chuang / Jing Zhou / Priyamvada Acharya / Reda Rawi / Chen-Hsiang Shen / Zizhang Sheng / Baoshan Zhang / Tongqing Zhou / Robert T Bailer / Venkata P Dandey / Nicole A Doria-Rose / Mark K Louder / Krisha McKee / John R Mascola / Lawrence Shapiro / Peter D Kwong /
Abstract: Over the past decade, structures have been determined for broadly neutralizing antibodies that recognize all major exposed surfaces of the prefusion-closed HIV-1-envelope (Env) trimer. To understand ...Over the past decade, structures have been determined for broadly neutralizing antibodies that recognize all major exposed surfaces of the prefusion-closed HIV-1-envelope (Env) trimer. To understand this recognition and its implications, we analyzed 206 antibody-HIV-1 Env structures from the Protein Data Bank with resolution suitable to define interaction chemistries and measured antibody neutralization on a 208-strain panel. Those with >25% breadth segregated into almost two dozen classes based on ontogeny and recognition and into six epitope categories based on recognized Env residues. For paratope, the number of protruding loops and level of somatic hypermutation were significantly higher for broad HIV-1 neutralizing antibodies than for a comparison set of non-HIV-1 antibodies (p < 0.0001). For epitope, the number of independent sequence segments was higher (p < 0.0001), as well as the glycan component surface area (p = 0.0005). The unusual characteristics of epitope and paratope delineated here are likely to reflect respectively virus-immune evasion and antibody-recognition solutions that allow effective neutralization of HIV-1.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 21, 2018-
Header (metadata) releaseAug 29, 2018-
Map releaseFeb 13, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.734
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.734
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6e5p
  • Surface level: 0.734
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_8981.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 420.902 Å
1.1 Å/pix.
x 384 pix.
= 420.902 Å
1.1 Å/pix.
x 384 pix.
= 420.902 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0961 Å
Density
Contour LevelBy AUTHOR: 0.734 / Movie #1: 0.734
Minimum - Maximum-0.29414085 - 2.2027838
Average (Standard dev.)0.018640218 (±0.12520622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 420.9024 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09609895833331.09609895833331.0960989583333
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z420.902420.902420.902
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2942.2030.019

-
Supplemental data

-
Additional map: Unsharpened map from cryoSparc

Fileemd_8981_additional.map
AnnotationUnsharpened map from cryoSparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of an...

EntireName: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.
Number of components: 7

+
Component #1: protein, Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragme...

ProteinName: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.
Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

+
Component #2: protein, 2G12 Light chain

ProteinName: 2G12 Light chain / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 23.130762 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #3: protein, 2G12 heavy chain

ProteinName: 2G12 heavy chain / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 23.932869 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #4: protein, Envelope glycoprotein gp120

ProteinName: Envelope glycoprotein gp120 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 53.086102 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

+
Component #5: protein, Envelope glycoprotein gp160

ProteinName: Envelope glycoprotein gp160 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 19.102811 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

+
Component #6: protein, VRC03 heavy chain

ProteinName: VRC03 heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 24.699861 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #7: protein, VRC03 Light chain

ProteinName: VRC03 Light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.043652 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/mL / pH: 7.01
VitrificationInstrument: SPOTITON / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 %
Details: 0.005% dodecyl maltoside was added to sample before vitification.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 63.84 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 2206

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 5245
3D reconstructionSoftware: cryoSPARC / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (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

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