[English] 日本語
Yorodumi
- EMDB-41361: CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41361
TitleCRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-e.01 FAB
Map data
Sample
  • Complex: BG505 DS-SOSIP DJ85-e.01 FAB COMPLEX
    • Complex: BG505 DS-SOSIP
      • Protein or peptide: BG505 DS-SOSIP Surface protein gp120
      • Protein or peptide: BG505 DS-SOSIP Transmembrane protein gp41
    • Complex: DJ85-e.01 FAB
      • Protein or peptide: DJ85-e.01 FAB HEAVY CHAIN
      • Protein or peptide: DJ85-e.01 FAB LIGHT CHAIN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsbroadly neutralizing antibody / fusion peptide / HIV-1 / glycoprotein / viral protein / FP-targeting vaccines / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPletnev S / Hoyt F / Fischer E / Kwong P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Broad and potent HIV-1 neutralization in fusion peptide-primed SHIV-boosted macaques.
Authors: Wang H
History
DepositionJul 26, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41361.png

Downloads & links

-
Map

FileDownload / File: emd_41361.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 440 pix.
= 380.028 Å		0.86 Å/pix.
x 440 pix.
= 380.028 Å		0.86 Å/pix.
x 440 pix.
= 380.028 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8637 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.4476262 - 2.1037266
Average (Standard dev.)0.00020323874 (±0.03197218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 380.02798 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_41361_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_41361_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41361_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BG505 DS-SOSIP DJ85-e.01 FAB COMPLEX

EntireName: BG505 DS-SOSIP DJ85-e.01 FAB COMPLEX
Components
  • Complex: BG505 DS-SOSIP DJ85-e.01 FAB COMPLEX
    • Complex: BG505 DS-SOSIP
      • Protein or peptide: BG505 DS-SOSIP Surface protein gp120
      • Protein or peptide: BG505 DS-SOSIP Transmembrane protein gp41
    • Complex: DJ85-e.01 FAB
      • Protein or peptide: DJ85-e.01 FAB HEAVY CHAIN
      • Protein or peptide: DJ85-e.01 FAB LIGHT CHAIN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: BG505 DS-SOSIP DJ85-e.01 FAB COMPLEX

SupramoleculeName: BG505 DS-SOSIP DJ85-e.01 FAB COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

-
Supramolecule #2: BG505 DS-SOSIP

SupramoleculeName: BG505 DS-SOSIP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

-
Supramolecule #3: DJ85-e.01 FAB

SupramoleculeName: DJ85-e.01 FAB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: BG505 DS-SOSIP Surface protein gp120

MacromoleculeName: BG505 DS-SOSIP Surface protein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.086324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SACTQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #2: BG505 DS-SOSIP Transmembrane protein gp41

MacromoleculeName: BG505 DS-SOSIP Transmembrane protein 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

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #3: DJ85-e.01 FAB HEAVY CHAIN

MacromoleculeName: DJ85-e.01 FAB HEAVY CHAIN / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.349178 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVWLRESGPG LVKSSETLSL TCAVSGASVG GNYYWNWIRQ FPGKGLEWMG NVHGGSGNTE YNPSLKGRLT ISRDTSRGHF LLHLDSVTA ADTAVYYCST QYWRHTGYDS SFFDSWGQGA LVTVSSASTK GPSVFPLAPS SRSTSESTAA LGCLVKDYFP E PVTVSWNS ...String:
QVWLRESGPG LVKSSETLSL TCAVSGASVG GNYYWNWIRQ FPGKGLEWMG NVHGGSGNTE YNPSLKGRLT ISRDTSRGHF LLHLDSVTA ADTAVYYCST QYWRHTGYDS SFFDSWGQGA LVTVSSASTK GPSVFPLAPS SRSTSESTAA LGCLVKDYFP E PVTVSWNS GSLTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYVC NVNHKPSNTK VDKRVEIKTC GGLEVLFQ

-
Macromolecule #4: DJ85-e.01 FAB LIGHT CHAIN

MacromoleculeName: DJ85-e.01 FAB LIGHT CHAIN / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.527947 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQMTQSPSS LSASVGDRVS ITCRASEDIT TDLEWYQQKP GKAPNLLIYD VSSLQSGVPS RFSGSRSGTE FTLTINSLQP EDFATYFCL QYNSYPWTFG QGTKVDIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DVQMTQSPSS LSASVGDRVS ITCRASEDIT TDLEWYQQKP GKAPNLLIYD VSSLQSGVPS RFSGSRSGTE FTLTINSLQP EDFATYFCL QYNSYPWTFG QGTKVDIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16274 / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1918671
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8euv

Final reconstructionNumber classes used: 52 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 430214
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 52
FSC plot (resolution estimation)

-
Atomic model buiding 1

SoftwareName: UCSF Chimera (ver. 1.14)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8tl4:
CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-e.01 FAB

+
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