[English] 日本語
Yorodumi
- EMDB-23149: Cryo-electron microscopy reconstruction of antibody DH898.1 Fab-d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23149
TitleCryo-electron microscopy reconstruction of antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV Env SOSIP trimer CH848 10.17
Map dataFinal sharpened, locally filtered, map of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer
Sample
  • Complex: Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
    • Complex: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
      • Protein or peptide: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664
    • Complex: Antibody DH898.1 Fragment antigen binding (Fab) dimer
      • Protein or peptide: Antibody DH898.1 Fragment antigen binding (Fab) heavy chain
      • Protein or peptide: Antibody DH898.1 Fragment antigen binding (Fab) light chain
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsEdwards RJ / Acharya P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI140897 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145687 United States
CitationJournal: bioRxiv / Year: 2020
Title: Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques
Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N ...Authors: Williams WB / Meyerhoff RR / Edwards RJ / Li H / Nicely NI / Henderson R / Zhou Y / Janowska K / Mansouri K / Manne K / Stalls V / Hsu AL / Borgnia MJ / Stewart-Jones G / Lee MS / Bronkema N / Perfect J / Moody MA / Wiehe K / Bradley T / Kepler TB / Alam SM / Foulger A / Bonsignori M / LaBranche CC / Montefiori DC / Seaman M / Santra S / Francica JR / Lynn GM / Aussedat B / Walkowicz WE / Laga R / Kelso G / Saunders KO / Fera D / Kwong PD / Seder RA / Bartesaghi A / Shaw GM / Acharya P / Haynes BF
History
DepositionDec 17, 2020-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23149.png

Downloads & links

-
Map

FileDownload / File: emd_23149.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal sharpened, locally filtered, map of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer
Voxel sizeX=Y=Z: 1.0665 Å
Density
Contour LevelBy AUTHOR: 0.55 / Movie #1: 0.55
Minimum - Maximum-0.5400671 - 1.9104918
Average (Standard dev.)0.026924657 (±0.11468069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.02298 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.066496093751.066496093751.06649609375
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.023273.023273.023
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.5401.9100.027

-
Supplemental data

-
Mask #1

Fileemd_23149_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_23149_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unmodified final map of antibody DH898.1 Fab-dimer bound...

Fileemd_23149_additional_1.map
AnnotationUnmodified final map of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local resolution ofof antibody DH898.1 Fab-dimer bound to...

Fileemd_23149_additional_2.map
AnnotationLocal resolution ofof antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer, at the 0.5 FSC level.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map A of antibody DH898.1 Fab-dimer bound to...

Fileemd_23149_half_map_1.map
AnnotationHalf-map A of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map B of antibody DH898.1 Fab-dimer bound to...

Fileemd_23149_half_map_2.map
AnnotationHalf-map B of antibody DH898.1 Fab-dimer bound to HIV Env CH848 10.17 SOSIP trimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV...

EntireName: Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
Components
  • Complex: Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
    • Complex: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
      • Protein or peptide: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664
    • Complex: Antibody DH898.1 Fragment antigen binding (Fab) dimer
      • Protein or peptide: Antibody DH898.1 Fragment antigen binding (Fab) heavy chain
      • Protein or peptide: Antibody DH898.1 Fragment antigen binding (Fab) light chain

-
Supramolecule #1: Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV...

SupramoleculeName: Antibody DH898.1 Fab-dimer bound near the CD4 binding site of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 94 KDa

-
Supramolecule #2: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer

SupramoleculeName: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: CH848 10.17
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

-
Supramolecule #3: Antibody DH898.1 Fragment antigen binding (Fab) dimer

SupramoleculeName: Antibody DH898.1 Fragment antigen binding (Fab) dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: Composed of two heavy chains and two light chains
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

-
Macromolecule #1: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664

MacromoleculeName: HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: CH848.3.D0949.10.17
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLI CSNATVKNGT VEEMKNCSFN TTTEIRDKEK KEYALFYKPD IVPLSETNNT SEYRLINCNT SACTQACPKV ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLI CSNATVKNGT VEEMKNCSFN TTTEIRDKEK KEYALFYKPD IVPLSETNNT SEYRLINCNT SACTQACPKV TFEPIPIHYC APAGYAILKC NDETFNGTGP CSNVSTVQCT HGIRPVVSTQ LLLNGSLAEK EIVIRSENLT NNAKIIIVHL HTPVEIVCTR PNNNTRKSVR IGPGQTFYAT GDIIGDIKQA HCNISEEKWN DTLQKVGIEL QKHFPNKTIK YNQSAGGDME ITTHSFNCGG EFFYCNTSNL FNGTYNGTYI STNSSANSTS TITLQCRIKQ IINMWQGVGR CMYAPPIAGN ITCRSNITGL LLTRDGGTNS NETETFRPAG GDMRDNWRSE LYKYKVVKIE PLGVAPTRCK RRVVGRRRRR RAVGIGAVFL GFLGAAGSTM GAASMTLTVQ ARNLLSGIVQ QQSNLLRAPE AQQHLLKLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

-
Macromolecule #2: Antibody DH898.1 Fragment antigen binding (Fab) heavy chain

MacromoleculeName: Antibody DH898.1 Fragment antigen binding (Fab) heavy chain
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey) / Strain: DH898.1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QDLLLQSGAE VREPGASVTV SCQASNYTFP DYYIHWVRLV PGQGLEWLGE MKPKVGVTNV SKKIRDRLFM TADTSTDTAY MVLSALTPGD TAIYYCTRLE PDFLSGWAHW GKGVLVTVSP ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS WNSGSLTSGV ...String:
QDLLLQSGAE VREPGASVTV SCQASNYTFP DYYIHWVRLV PGQGLEWLGE MKPKVGVTNV SKKIRDRLFM TADTSTDTAY MVLSALTPGD TAIYYCTRLE PDFLSGWAHW GKGVLVTVSP ASTKGPSVFP LAPSSRSTSE STAALGCLVK DYFPEPVTVS WNSGSLTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YVCNVNHKPS NTKVDKRVE

-
Macromolecule #3: Antibody DH898.1 Fragment antigen binding (Fab) light chain

MacromoleculeName: Antibody DH898.1 Fragment antigen binding (Fab) light chain
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey) / Strain: DH898.1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQTPLS LSVTPGEPAS LSCRSSASLL HGNGNTYLHW YLRKAGQSPQ LLIFGGSKRV PGISDRFIGS GAGTNFTLKI SSVEADDVGF YYCAQGVAFP WTFGQGTKVE IKRAVAAPSV FIFPPSEDQV KSGTVSVVCL LNNFYPREAS VKWKVDGVLK TGNSQESVTE ...String:
EIVMTQTPLS LSVTPGEPAS LSCRSSASLL HGNGNTYLHW YLRKAGQSPQ LLIFGGSKRV PGISDRFIGS GAGTNFTLKI SSVEADDVGF YYCAQGVAFP WTFGQGTKVE IKRAVAAPSV FIFPPSEDQV KSGTVSVVCL LNNFYPREAS VKWKVDGVLK TGNSQESVTE QDSKDNTYSL SSTLTLSNTD YQSHNVYACE VTHQGLSSPV TKSFNRGE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
5.0 mMHEPES buffer
150.0 mMsodium chlorideNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP
Details: 2.5 microliter of smaple applied to grid and incubated for 30 seconds in chamber, blotted for 2.5 seconds, and plunge frozen in liquid ethane.
DetailsFor the DH898.1-bound complex, purified HIV-1 Env was mixed with 6-fold molar excess of recombinantly expressed and purified DH898.1 Fab to obtain a final Env concentration of 1.5 mg/ml, and incubated for 2 hours at room temperature.

-
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 / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3230 / Average exposure time: 4.0 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1655400
Details: Particles were picked using Blob Picker on 500 micrographs with a minimum and maximum particle diameter of 150 and 250 angstroms for circular blobs, yielding 259,587 particles, which were ...Details: Particles were picked using Blob Picker on 500 micrographs with a minimum and maximum particle diameter of 150 and 250 angstroms for circular blobs, yielding 259,587 particles, which were extracted with a 320-pixel box size and subjected to 2D class averaging with 100 classes. From these, seven classes were chosen for template picking applied to the full final micrograph set, yielding 1,655,400 particles
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Startup modelType of model: INSILICO MODEL / In silico model: ab initio generated directly from data.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 31168 / Software - Name: cryoSPARC (ver. 2.15.0) / Details: Ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 59012
FSC plot (resolution estimation)

+
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