[English] 日本語
Yorodumi
- EMDB-2672: 35O22 Fab in complex with BG505 SOSIP.664 Trimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2672
Title35O22 Fab in complex with BG505 SOSIP.664 Trimer
Map dataNegative stain reconstruction of 35O22 Fab bound to BG505 SOSIP trimer
Sample
  • Sample: Fab fragment of bnAb 35O22 bound to recombinant gp140 Env trimer BG505 SOSIP.664
  • Protein or peptide: Soluble HIV-1 Envelope glycoprotein
  • Protein or peptide: Fab fragment of bnAb 35O22
KeywordsHIV-1 / Env / glycoprotein / bnAb / antibody / Fab
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 Å
AuthorsLee JH / Pancera M / Kwong PD / Connors M / Ward AB
CitationJournal: Nature / Year: 2014
Title: Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface.
Authors: Jinghe Huang / Byong H Kang / Marie Pancera / Jeong Hyun Lee / Tommy Tong / Yu Feng / Hiromi Imamichi / Ivelin S Georgiev / Gwo-Yu Chuang / Aliaksandr Druz / Nicole A Doria-Rose / Leo Laub / ...Authors: Jinghe Huang / Byong H Kang / Marie Pancera / Jeong Hyun Lee / Tommy Tong / Yu Feng / Hiromi Imamichi / Ivelin S Georgiev / Gwo-Yu Chuang / Aliaksandr Druz / Nicole A Doria-Rose / Leo Laub / Kwinten Sliepen / Marit J van Gils / Alba Torrents de la Peña / Ronald Derking / Per-Johan Klasse / Stephen A Migueles / Robert T Bailer / Munir Alam / Pavel Pugach / Barton F Haynes / Richard T Wyatt / Rogier W Sanders / James M Binley / Andrew B Ward / John R Mascola / Peter D Kwong / Mark Connors /
Abstract: The isolation of human monoclonal antibodies is providing important insights into the specificities that underlie broad neutralization of HIV-1 (reviewed in ref. 1). Here we report a broad and ...The isolation of human monoclonal antibodies is providing important insights into the specificities that underlie broad neutralization of HIV-1 (reviewed in ref. 1). Here we report a broad and extremely potent HIV-specific monoclonal antibody, termed 35O22, which binds a novel HIV-1 envelope glycoprotein (Env) epitope. 35O22 neutralized 62% of 181 pseudoviruses with a half-maximum inhibitory concentration (IC50) <50 μg ml(-1). The median IC50 of neutralized viruses was 0.033 μg ml(-1), among the most potent thus far described. 35O22 did not bind monomeric forms of Env tested, but did bind the trimeric BG505 SOSIP.664. Mutagenesis and a reconstruction by negative-stain electron microscopy of the Fab in complex with trimer revealed that it bound to a conserved epitope, which stretched across gp120 and gp41. The specificity of 35O22 represents a novel site of vulnerability on HIV Env, which serum analysis indicates to be commonly elicited by natural infection. Binding to this new site of vulnerability may thus be an important complement to current monoclonal-antibody-based approaches to immunotherapies, prophylaxis and vaccine design.
History
DepositionJun 10, 2014-
Header (metadata) releaseJul 23, 2014-
Map releaseOct 8, 2014-
UpdateNov 12, 2014-
Current statusNov 12, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0115
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0115
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2672.png

Downloads & links

-
Map

FileDownload / File: emd_2672.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain reconstruction of 35O22 Fab bound to BG505 SOSIP trimer
Voxel sizeX=Y=Z: 2.05 Å
Density
Contour LevelBy AUTHOR: 0.0115 / Movie #1: 0.0115
Minimum - Maximum-0.01338776 - 0.0447579
Average (Standard dev.)0.00027453 (±0.00399852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ0-51-100
NX/NY/NZ82103201
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0130.0450.000

-
Supplemental data

-
Sample components

-
Entire : Fab fragment of bnAb 35O22 bound to recombinant gp140 Env trimer ...

EntireName: Fab fragment of bnAb 35O22 bound to recombinant gp140 Env trimer BG505 SOSIP.664
Components
  • Sample: Fab fragment of bnAb 35O22 bound to recombinant gp140 Env trimer BG505 SOSIP.664
  • Protein or peptide: Soluble HIV-1 Envelope glycoprotein
  • Protein or peptide: Fab fragment of bnAb 35O22

-
Supramolecule #1000: Fab fragment of bnAb 35O22 bound to recombinant gp140 Env trimer ...

SupramoleculeName: Fab fragment of bnAb 35O22 bound to recombinant gp140 Env trimer BG505 SOSIP.664
type: sample / ID: 1000 / Oligomeric state: One Fab binds per gp140 monomer / Number unique components: 2
Molecular weightTheoretical: 570 KDa

-
Macromolecule #1: Soluble HIV-1 Envelope glycoprotein

MacromoleculeName: Soluble HIV-1 Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: BG505 SOSIP.664 / Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / synonym: HIV-1
Molecular weightTheoretical: 420 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

-
Macromolecule #2: Fab fragment of bnAb 35O22

MacromoleculeName: Fab fragment of bnAb 35O22 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4 / Details: 50 mM Tris, 150 mM NaCl
StainingType: NEGATIVE
Details: 3 uL of protein applied, blotted then applied 2% UF for 45 seconds.
GridDetails: 400 Cu mesh grid with carbon support, plasma cleaned.
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy #1

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.0 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
TemperatureAverage: 293 K
Microscopy ID1
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism corrected at 52,000x mag.
DateNov 27, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 139 / Average electron dose: 30 e/Å2
Tilt angle min0

-
Electron microscopy #2

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
TemperatureAverage: 293 K
Microscopy ID2
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism corrected at 52,000x mag.
DateJan 22, 2014
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 139 / Average electron dose: 30 e/Å2
Tilt angle min0

-
Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: OTHER / Software - Name: EMAN2, SPARX / Number images used: 4746

-
Atomic model buiding 1

Initial modelPDB ID:

4toy


Chain - #0 - Chain ID: H / Chain - #1 - Chain ID: L
SoftwareName: Chimera
DetailsThree copies of the Fab were fit into the EM map
RefinementSpace: REAL / Protocol: RIGID BODY FIT

-
Atomic model buiding 2

Initial modelPDB ID:

4nco


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: E / Chain - #3 - Chain ID: F / Chain - #4 - Chain ID: I / Chain - #5 - Chain ID: J
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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