[English] 日本語
Yorodumi
- EMDB-23518: Cryo-EM map of DH851.3 bound to HIV-1 CH505 Env -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23518
TitleCryo-EM map of DH851.3 bound to HIV-1 CH505 Env
Map dataCryoEM map of DH851.3 bound to HIV-1 CH505 Env
Sample
  • Complex: DH851.3 bound to HIV-1 CH505 Env
    • Protein or peptide: DH851.3 light chain
    • Protein or peptide: DH851.3 heavy chain
    • Protein or peptide: DH851.3 heavy chain
    • Protein or peptide: DH851.3 light chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / 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 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsEdwards RJ / Manne K / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145687 United States
Citation
Journal: Cell / Year: 2021
Title: Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.
Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler ...Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler Evangelous / Bhavna Hora / Madison Berry / A Yousef Abuahmad / Jordan Sprenz / Margaret Deyton / Victoria Stalls / Megan Kopp / Allen L Hsu / Mario J Borgnia / Guillaume B E Stewart-Jones / Matthew S Lee / Naomi Bronkema / M Anthony Moody / Kevin Wiehe / Todd Bradley / S Munir Alam / Robert J Parks / Andrew Foulger / Thomas Oguin / Gregory D Sempowski / Mattia Bonsignori / Celia C LaBranche / David C Montefiori / Michael Seaman / Sampa Santra / John Perfect / Joseph R Francica / Geoffrey M Lynn / Baptiste Aussedat / William E Walkowicz / Richard Laga / Garnett Kelsoe / Kevin O Saunders / Daniela Fera / Peter D Kwong / Robert A Seder / Alberto Bartesaghi / George M Shaw / Priyamvada Acharya / Barton F Haynes /
Abstract: Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) ...Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (V) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without V-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgMIgDCD27, thus suggesting that they originated from a pool of antigen-experienced IgM or marginal zone B cells.
#1: Journal: bioRxiv / Year: 2020
Title: Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques
Authors: Acharya P / Williams W / Henderson R / Janowska K / Manne K / Parks R / Deyton M / Sprenz J / Stalls V / Kopp M / Mansouri K / Edwards RJ / Meyerhoff RR / Oguin T / Sempowski G / Saunders K / Haynes BF
History
DepositionFeb 21, 2021-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing 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-7lu9
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23518.png

Downloads & links

-
Map

FileDownload / File: emd_23518.map.gz / Format: CCP4 / Size: 27.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of DH851.3 bound to HIV-1 CH505 Env
Voxel sizeX=Y=Z: 1.0665 Å
Density
Contour LevelBy EMDB: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.4758269 - 0.89355016
Average (Standard dev.)3.658373e-13 (±0.040937867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin9875121
Dimensions223232141
Spacing141223232
CellA: 150.3765 Å / B: 237.82948 Å / C: 247.428 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06649645390071.06649775784751.0665
M x/y/z141223232
origin x/y/z0.0000.0000.000
length x/y/z150.376237.829247.428
α/β/γ90.00090.00090.000
start NX/NY/NZ1219875
NX/NY/NZ141223232
MAP C/R/S321
start NC/NR/NS7598121
NC/NR/NS232223141
D min/max/mean-0.4760.8940.000

-
Supplemental data

-
Half map: CryoEM half-map B of DH851.3 bound to HIV-1 CH505 Env

Fileemd_23518_half_map_1.map
AnnotationCryoEM half-map B of DH851.3 bound to HIV-1 CH505 Env
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CryoEM half-map A of DH851.3 bound to HIV-1 CH505 Env

Fileemd_23518_half_map_2.map
AnnotationCryoEM half-map A of DH851.3 bound to HIV-1 CH505 Env
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : DH851.3 bound to HIV-1 CH505 Env

EntireName: DH851.3 bound to HIV-1 CH505 Env
Components
  • Complex: DH851.3 bound to HIV-1 CH505 Env
    • Protein or peptide: DH851.3 light chain
    • Protein or peptide: DH851.3 heavy chain
    • Protein or peptide: DH851.3 heavy chain
    • Protein or peptide: DH851.3 light chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: DH851.3 bound to HIV-1 CH505 Env

SupramoleculeName: DH851.3 bound to HIV-1 CH505 Env / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Human immunodeficiency virus 1

-
Macromolecule #1: DH851.3 light chain

MacromoleculeName: DH851.3 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.127463 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN ...String:
ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN NKYAASSYLS LTSDQWKSHK SYSCQVTHEG STVEKTVAPA EC

-
Macromolecule #2: DH851.3 heavy chain

MacromoleculeName: DH851.3 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.451617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS ...String:
QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVEIKTCGG

-
Macromolecule #3: DH851.3 heavy chain

MacromoleculeName: DH851.3 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.89093 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS ...String:
QVTLMESGPA LVKVTQTLAV TCTFSGFSIR DSGKGVAWIR QPPGGALEWL TSIYWDDTKY HDTSLKPRLT IFRDTSQTQV ILILTNMAP LDTATYYCGR INNGGGWKDH IDFWGPGLLV TVSSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVE

-
Macromolecule #4: DH851.3 light chain

MacromoleculeName: DH851.3 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 21.824127 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN ...String:
ALTQPPSVSK SLEQSVTISC TGTTTGNSVS WYQCHSGTAP RLLIYDVNKR PSGVSDRFSG SKSHNTASLT IFGLQAEDEA DYYCGSYGS GGSLLFGGGT RLTVLGQP(UNK)K ASPTVTLFPP SSEELQANKA TLVCLISDFY PGVVKVAWKA DGSAVNA GV ETTTPSKQSN NKYAASSYLS LTSDQWKSHK SYSCQVTHEG STVEKTVAP

-
Macromolecule #5: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.134512 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLKAIEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

-
Macromolecule #6: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 51.898062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV ...String:
ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV SFDPIPIHYC APAGYAILKC NNKTFTGTGP CNNVSTVQCT HGIKPVVSTQ LLLNGSLAEG EIIIRSENIT NN VKTIIVH LNESVKIECT RPNNKTRTSI RIGPGQWFYA TGQVIGDIRE AYCNINESKW NETLQRVSKK LKEYFPHKNI TFQ PSSGGD LEITTHSFNC GGEFFYCNTS SLFNRTYMAN STDMANSTET NSTRTITIHC RIKQIINMWQ EVGRAMYAPP IAGN ITCIS NITGLLLTRD GGKNNTETFR PGGGNMKDNW RSELYKYKVV KIEPLGVAPT RCKRRV

-
Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 3 / 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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: blot for 2.5 seconds before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 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
TemperatureMin: 93.15 K / Max: 93.15 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 6058 / Average electron dose: 62.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53398

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7lu9:
Cryo-EM structure of DH851.3 bound to HIV-1 CH505 Env

+
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