[English] 日本語
Yorodumi
- EMDB-20274: Negative stain reconstruction of HIV-1 Env 16055 NFL TD 2CC+ trim... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20274
TitleNegative stain reconstruction of HIV-1 Env 16055 NFL TD 2CC+ trimer in complex with rabbit antibody 1C2 fragment antigen binding
Map datanegative-stain 3D reconstruction
Sample
  • Complex: HIV-1 Env 16055 NFL TD 2CC+ trimer in complex with rabbit antibody 1C2 fragment antigen binding
    • Protein or peptide: HIV-1 Env 16055 NFL TD 2CC+ trimer
    • Protein or peptide: Rabbit antibody 1C2 fragment antigen binding heavy chain
    • Protein or peptide: Rabbit antibody 1C2 fragment antigen binding kappa chain
Biological speciesHuman immunodeficiency virus 1 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsTorres JL / Ozorowski G / Andrew AB
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUM AI100663 United States
Bill & Melinda Gates FoundationOPP1084519 United States
Bill & Melinda Gates FoundationOPP1115782 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI136621 United States
CitationJournal: Immunity / Year: 2019
Title: Vaccination with Glycan-Modified HIV NFL Envelope Trimer-Liposomes Elicits Broadly Neutralizing Antibodies to Multiple Sites of Vulnerability.
Authors: Viktoriya Dubrovskaya / Karen Tran / Gabriel Ozorowski / Javier Guenaga / Richard Wilson / Shridhar Bale / Christopher A Cottrell / Hannah L Turner / Gemma Seabright / Sijy O'Dell / Jonathan ...Authors: Viktoriya Dubrovskaya / Karen Tran / Gabriel Ozorowski / Javier Guenaga / Richard Wilson / Shridhar Bale / Christopher A Cottrell / Hannah L Turner / Gemma Seabright / Sijy O'Dell / Jonathan L Torres / Lifei Yang / Yu Feng / Daniel P Leaman / Néstor Vázquez Bernat / Tyler Liban / Mark Louder / Krisha McKee / Robert T Bailer / Arlette Movsesyan / Nicole A Doria-Rose / Marie Pancera / Gunilla B Karlsson Hedestam / Michael B Zwick / Max Crispin / John R Mascola / Andrew B Ward / Richard T Wyatt /
Abstract: The elicitation of broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer remains a major vaccine challenge. Most cross-conserved protein determinants are ...The elicitation of broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer remains a major vaccine challenge. Most cross-conserved protein determinants are occluded by self-N-glycan shielding, limiting B cell recognition of the underlying polypeptide surface. The exceptions to the contiguous glycan shield include the conserved receptor CD4 binding site (CD4bs) and glycoprotein (gp)41 elements proximal to the furin cleavage site. Accordingly, we performed heterologous trimer-liposome prime:boosting in rabbits to drive B cells specific for cross-conserved sites. To preferentially expose the CD4bs to B cells, we eliminated proximal N-glycans while maintaining the native-like state of the cleavage-independent NFL trimers, followed by gradual N-glycan restoration coupled with heterologous boosting. This approach successfully elicited CD4bs-directed, cross-neutralizing Abs, including one targeting a unique glycan-protein epitope and a bNAb (87% breadth) directed to the gp120:gp41 interface, both resolved by high-resolution cryoelectron microscopy. This study provides proof-of-principle immunogenicity toward eliciting bNAbs by vaccination.
History
DepositionJun 10, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseNov 20, 2019-
UpdateApr 1, 2020-
Current statusApr 1, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20274.png

Downloads & links

-
Map

FileDownload / File: emd_20274.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnegative-stain 3D reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.02496773 - 0.07104748
Average (Standard dev.)0.00023566218 (±0.004520775)
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/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0250.0710.000

-
Supplemental data

-
Half map: half map 1

Fileemd_20274_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_20274_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HIV-1 Env 16055 NFL TD 2CC+ trimer in complex with rabbit antibod...

EntireName: HIV-1 Env 16055 NFL TD 2CC+ trimer in complex with rabbit antibody 1C2 fragment antigen binding
Components
  • Complex: HIV-1 Env 16055 NFL TD 2CC+ trimer in complex with rabbit antibody 1C2 fragment antigen binding
    • Protein or peptide: HIV-1 Env 16055 NFL TD 2CC+ trimer
    • Protein or peptide: Rabbit antibody 1C2 fragment antigen binding heavy chain
    • Protein or peptide: Rabbit antibody 1C2 fragment antigen binding kappa chain

-
Supramolecule #1: HIV-1 Env 16055 NFL TD 2CC+ trimer in complex with rabbit antibod...

SupramoleculeName: HIV-1 Env 16055 NFL TD 2CC+ trimer in complex with rabbit antibody 1C2 fragment antigen binding
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 570 KDa

-
Macromolecule #1: HIV-1 Env 16055 NFL TD 2CC+ trimer

MacromoleculeName: HIV-1 Env 16055 NFL TD 2CC+ trimer / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLANGNLWV TVYYGVPVWK DAETTLFCAS DAKAYEKEKH NVWATHACVP TDPNPQEMVL ENVTENFNMW KNDMVEQMHT DVISLWDQSL KPCVKLTPLC VTLECRQVNT TNATSSVNVT NGEEIKNCSF NATTELRDKK QKVYALFYRL ...String:
MPMGSLQPLA TLYLLGMLVA SVLANGNLWV TVYYGVPVWK DAETTLFCAS DAKAYEKEKH NVWATHACVP TDPNPQEMVL ENVTENFNMW KNDMVEQMHT DVISLWDQSL KPCVKLTPLC VTLECRQVNT TNATSSVNVT NGEEIKNCSF NATTELRDKK QKVYALFYRL DIVPLEEERK GNSSKYRLIN CNTSACTQAC PKVTFDPIPI HYCAPAGYAI LKCNNKTFNG TGPCNNVSTV QCTHGIKPVV STQLLLNGSL AEGEIIIRSE NLTNNVKTII VHLNESVEIV CTRPNNYTRK SIRIGPGQTF YATGDIIGNI RQAYCNISKD DWIRTLQRVG KKLAEHFPRR IINFTSPAGG DLEITTHSFN CRGEFFYCNT SSLFNSTYNP NDTNSNSSSS NSSLDITIPC RIKQIINMWQ RVGQCMYAPP IEGNITCKSN ITGLLLVRDG GVESNETEIF RPGGGDMRNN WRSELYKYKV VEIKPLGIAP TRCKRRVVEG GGGSGGGGSD DDDKAVGLGA VRRGFLGAAG STMGAASITL TVQARQLLSG IVQQQSNLLK APEAQQHLLQ LGVWGIKQLQ TRVLAIERYL KDQQLLGIWG CSGKLICTTA VPWNSSWSNK SHDEIWGNMT WMQWDREIGN YTNTIYRLLE DSQNQQEQNE KDLLACDGGG GSHHHHHHHH

-
Macromolecule #2: Rabbit antibody 1C2 fragment antigen binding heavy chain

MacromoleculeName: Rabbit antibody 1C2 fragment antigen binding heavy chain
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS QCQSLEESGG DLVKPGASLT LTCTASGFSF GWNDYMSWVR QAPGKGLEWI GCIYAGSTRS TYYANWAKGR LTISKTSSTA VTLQMTSLTA ADTATYFCAR GAVTYDGLGG AYLKHFNLWG PGTLVTVSSG QPKAPSVFPL APCCGDTPSS ...String:
MYRMQLLSCI ALSLALVTNS QCQSLEESGG DLVKPGASLT LTCTASGFSF GWNDYMSWVR QAPGKGLEWI GCIYAGSTRS TYYANWAKGR LTISKTSSTA VTLQMTSLTA ADTATYFCAR GAVTYDGLGG AYLKHFNLWG PGTLVTVSSG QPKAPSVFPL APCCGDTPSS TVTLGCLVKG YLPEPVTVTW NSGTLTNGVR TFPSVRQSSG LYSLSSVVSV TSSSQPVTCN VAHPATNTKV DKTVAPSTCS KHHHHHHHH

-
Macromolecule #3: Rabbit antibody 1C2 fragment antigen binding kappa chain

MacromoleculeName: Rabbit antibody 1C2 fragment antigen binding kappa chain
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS AIKMTQTPSS VSAAVGGTVT VNCRASEDIE SYLAWYQQKP GQPPKLLIYD TSKLASGVPS RFKGSGSGTQ FALTISGVQC DDAATYYCLY GYISSDRIDF GFGGGTELVV KGDPVAPSVL IFPPAADQVA TGTVTIVCVA NKYFPDVTVT ...String:
MYRMQLLSCI ALSLALVTNS AIKMTQTPSS VSAAVGGTVT VNCRASEDIE SYLAWYQQKP GQPPKLLIYD TSKLASGVPS RFKGSGSGTQ FALTISGVQC DDAATYYCLY GYISSDRIDF GFGGGTELVV KGDPVAPSVL IFPPAADQVA TGTVTIVCVA NKYFPDVTVT WEVDGTTQTT GIENSKTPQN SADCTYNLSS TLTLTSTQYN SHKEYTCKVT QGTTSVVQSF NRGDC

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
50.0 mMTris
150.0 mMSodium chloride
StainingType: NEGATIVE / Material: uranyl formate
Details: Grids were negatively stained with 2% (w/v) uranyl formate for 50 s

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj


Details: Coordinates for ligand-free SOSIP trimer converted to EM map and low-pass filtered to 40 Angstrom
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 6000
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

+
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