[English] 日本語
Yorodumi
- EMDB-20500: The HIV-1 Envelope Glycoprotein Clone BG505 SOSIP.664 in Complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20500
TitleThe HIV-1 Envelope Glycoprotein Clone BG505 SOSIP.664 in Complex with Three Copies of the Bovine Broadly Neutralizing Antibody, NC-Cow1, Fragment Antigen Binding Domain
Map dataSingle-Particle Cryo-EM map of The HIV-1 Envelope GLycoprotein Clone BG505 SOSIP.664 in Complex with the Bovine Broadly Neutralizing Antibody, NC-Cow1, Fragment Antigen Binding Domain
Sample
  • Complex: A complex of the HIV-1 Envelope Glycoprotein clone BG505 SOSIP.664 and 3 copies of the bovine Fab NC-Cow1
    • Complex: Envelope Glycoprotein clone BG505 SOSIP.664
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: bovine Fab NC-Cow1
      • Protein or peptide: Broadly Neutralizing Antibody NC-Cow1 Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / 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 / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBerndsen ZT / Ward AB
Funding support United States, 3 items
OrganizationGrant numberCountry
International AIDS Vaccine InitiativeOPP1084519 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI100663 United States
Bill & Melinda Gates FoundationOPP1115782 United States
CitationJournal: Sci Adv / Year: 2020
Title: Structural basis of broad HIV neutralization by a vaccine-induced cow antibody.
Authors: Robyn L Stanfield / Zachary T Berndsen / Ruiqi Huang / Devin Sok / Gabrielle Warner / Jonathan L Torres / Dennis R Burton / Andrew B Ward / Ian A Wilson / Vaughn V Smider /
Abstract: Potent broadly neutralizing antibodies (bnAbs) to HIV have been very challenging to elicit by vaccination in wild-type animals. Here, by x-ray crystallography, cryo-electron microscopy, and site- ...Potent broadly neutralizing antibodies (bnAbs) to HIV have been very challenging to elicit by vaccination in wild-type animals. Here, by x-ray crystallography, cryo-electron microscopy, and site-directed mutagenesis, we structurally and functionally elucidate the mode of binding of a potent bnAb (NC-Cow1) elicited in cows by immunization with the HIV envelope (Env) trimer BG505 SOSIP.664. The exceptionally long (60 residues) third complementarity-determining region of the heavy chain (CDR H3) of NC-Cow1 forms a mini domain (knob) on an extended stalk that navigates through the dense glycan shield on Env to target a small footprint on the gp120 CD4 receptor binding site with no contact of the other CDRs to the rest of the Env trimer. These findings illustrate, in molecular detail, how an unusual vaccine-induced cow bnAb to HIV Env can neutralize with high potency and breadth.
History
DepositionJul 22, 2019-
Header (metadata) releaseFeb 5, 2020-
Map releaseJun 24, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6pw6
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20500.png

Downloads & links

-
Map

FileDownload / File: emd_20500.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-Particle Cryo-EM map of The HIV-1 Envelope GLycoprotein Clone BG505 SOSIP.664 in Complex with the Bovine Broadly Neutralizing Antibody, NC-Cow1, Fragment Antigen Binding Domain
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.08997602 - 0.16736001
Average (Standard dev.)0.0004669091 (±0.007362695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 322.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z322.000322.000322.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0900.1670.000

-
Supplemental data

-
Mask #1

Fileemd_20500_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_20500_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_20500_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A complex of the HIV-1 Envelope Glycoprotein clone BG505 SOSIP.66...

EntireName: A complex of the HIV-1 Envelope Glycoprotein clone BG505 SOSIP.664 and 3 copies of the bovine Fab NC-Cow1
Components
  • Complex: A complex of the HIV-1 Envelope Glycoprotein clone BG505 SOSIP.664 and 3 copies of the bovine Fab NC-Cow1
    • Complex: Envelope Glycoprotein clone BG505 SOSIP.664
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: bovine Fab NC-Cow1
      • Protein or peptide: Broadly Neutralizing Antibody NC-Cow1 Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: A complex of the HIV-1 Envelope Glycoprotein clone BG505 SOSIP.66...

SupramoleculeName: A complex of the HIV-1 Envelope Glycoprotein clone BG505 SOSIP.664 and 3 copies of the bovine Fab NC-Cow1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

-
Supramolecule #2: Envelope Glycoprotein clone BG505 SOSIP.664

SupramoleculeName: Envelope Glycoprotein clone BG505 SOSIP.664 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

-
Supramolecule #3: bovine Fab NC-Cow1

SupramoleculeName: bovine Fab NC-Cow1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Bos taurus (cattle)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

-
Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.945977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK VYSLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NG TGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAF YATGDI IGDIRQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA NSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWI SNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRD NWRS ELYKYKVVKI EPLGVAPTRC KRRVVGRRRR RR

-
Macromolecule #2: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

-
Macromolecule #3: Broadly Neutralizing Antibody NC-Cow1 Heavy Chain

MacromoleculeName: Broadly Neutralizing Antibody NC-Cow1 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 28.928289 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLRESGPS LMKPSQTLSL TCTVSGSKSV GWVRQAPGKA LQWLGSVDTS GNTDYNPGLK SRLSITKDNS KSRISLTVTG MTTEDSATY YCITAHQKTN KKECPEDYTY NPRCPQQYGW SDCDCMGDRF GGYCRQDGCS NYIHRSTYEW YVSAWGQGLL V TVSSASTK ...String:
QVQLRESGPS LMKPSQTLSL TCTVSGSKSV GWVRQAPGKA LQWLGSVDTS GNTDYNPGLK SRLSITKDNS KSRISLTVTG MTTEDSATY YCITAHQKTN KKECPEDYTY NPRCPQQYGW SDCDCMGDRF GGYCRQDGCS NYIHRSTYEW YVSAWGQGLL V TVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SL GTQTYIC NVNHKPSNTK VDKRVEPKSC D

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 36 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.65 mg/mL
BufferpH: 7.4
GridModel: C-flat-2/2 4C / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1506 / Average exposure time: 10.0 sec. / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: Gctf (ver. 2)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationSoftware - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 21427
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5cez

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6pw6:
The HIV-1 Envelope Glycoprotein Clone BG505 SOSIP.664 in Complex with Three Copies of the Bovine Broadly Neutralizing Antibody, NC-Cow1, Fragment Antigen Binding Domain

+
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