[English] 日本語
Yorodumi
- EMDB-25676: The Envelope Glycoprotein SIVmac239.K180S SOSIP trimer in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25676
TitleThe Envelope Glycoprotein SIVmac239.K180S SOSIP trimer in complex with 3 copies of the neutralizing antibody K11
Map data
Sample
  • Complex: SIVmac239.K180S SOSIP trimer in complex with 3 copies of K11 IgG
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: K11 IgG heavy chain
    • Protein or peptide: K11 IgG light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSIV / Env / vaccine / neutralizing antibody / glycoprotein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell endosome membrane / membrane => GO:0016020 / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesSimian immunodeficiency virus / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBerndsen ZT / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
Bill & Melinda Gates FoundationOPP1196345/INV-008813 United States
CitationJournal: Nat Commun / Year: 2022
Title: Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus.
Authors: Fangzhu Zhao / Zachary T Berndsen / Nuria Pedreño-Lopez / Alison Burns / Joel D Allen / Shawn Barman / Wen-Hsin Lee / Srirupa Chakraborty / Sandrasegaram Gnanakaran / Leigh M Sewall / ...Authors: Fangzhu Zhao / Zachary T Berndsen / Nuria Pedreño-Lopez / Alison Burns / Joel D Allen / Shawn Barman / Wen-Hsin Lee / Srirupa Chakraborty / Sandrasegaram Gnanakaran / Leigh M Sewall / Gabriel Ozorowski / Oliver Limbo / Ge Song / Peter Yong / Sean Callaghan / Jessica Coppola / Kim L Weisgrau / Jeffrey D Lifson / Rebecca Nedellec / Thomas B Voigt / Fernanda Laurino / Johan Louw / Brandon C Rosen / Michael Ricciardi / Max Crispin / Ronald C Desrosiers / Eva G Rakasz / David I Watkins / Raiees Andrabi / Andrew B Ward / Dennis R Burton / Devin Sok /
Abstract: SIVmac239 infection of macaques is a favored model of human HIV infection. However, the SIVmac239 envelope (Env) trimer structure, glycan occupancy, and the targets and ability of neutralizing ...SIVmac239 infection of macaques is a favored model of human HIV infection. However, the SIVmac239 envelope (Env) trimer structure, glycan occupancy, and the targets and ability of neutralizing antibodies (nAbs) to protect against SIVmac239 remain unknown. Here, we report the isolation of SIVmac239 nAbs that recognize a glycan hole and the V1/V4 loop. A high-resolution structure of a SIVmac239 Env trimer-nAb complex shows many similarities to HIV and SIVcpz Envs, but with distinct V4 features and an extended V1 loop. Moreover, SIVmac239 Env has a higher glycan shield density than HIV Env that may contribute to poor or delayed nAb responses in SIVmac239-infected macaques. Passive transfer of a nAb protects macaques from repeated intravenous SIVmac239 challenge at serum titers comparable to those described for protection of humans against HIV infection. Our results provide structural insights for vaccine design and shed light on antibody-mediated protection in the SIV model.
History
DepositionDec 9, 2021-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_25676.png

Downloads & links

-
Map

FileDownload / File: emd_25676.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.81242543 - 1.465525
Average (Standard dev.)-0.00023646058 (±0.03984898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 345.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_25676_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_25676_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_25676_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SIVmac239.K180S SOSIP trimer in complex with 3 copies of K11 IgG

EntireName: SIVmac239.K180S SOSIP trimer in complex with 3 copies of K11 IgG
Components
  • Complex: SIVmac239.K180S SOSIP trimer in complex with 3 copies of K11 IgG
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: K11 IgG heavy chain
    • Protein or peptide: K11 IgG light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: SIVmac239.K180S SOSIP trimer in complex with 3 copies of K11 IgG

SupramoleculeName: SIVmac239.K180S SOSIP trimer in complex with 3 copies of K11 IgG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Simian immunodeficiency virus

-
Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Simian immunodeficiency virus
Molecular weightTheoretical: 60.324441 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGCLGNQLLI AILLLSVYGI YCTLYVTVFY GVPAWRNATI PLFCATKNRD TWGTTQCLPD NGDYSEMALN VTESFDAWNN TVTEQAIED VWQLFETSIK PCVKLSPLCI TMRCNKSETD RWGLTKSITT TASTTSTTAS AKVDMVNETS SCIAQDNCTG L EQEQMISC ...String:
MGCLGNQLLI AILLLSVYGI YCTLYVTVFY GVPAWRNATI PLFCATKNRD TWGTTQCLPD NGDYSEMALN VTESFDAWNN TVTEQAIED VWQLFETSIK PCVKLSPLCI TMRCNKSETD RWGLTKSITT TASTTSTTAS AKVDMVNETS SCIAQDNCTG L EQEQMISC KFNMTGLKRD KSKEYNETWY SADLVCEQGN NTGNESRCYM NHCNTSVIQE SCDKHYWDAI RFRYCAPPGY AL LRCNDTN YSGFMPKCSK VVVSSCTRMM ETQTSTWFGF NGTRAENRTY IYWHGRDNRT IISLNKYYNL TMKCRRPGNK TVL PVTIMS GLVFHSQPIN DRPKQAWCWF GGKWKDAIKE VKQTIVKHPR YTGTNNTDKI NLTAPGGGDP EVTFMWTNCR GEFL YCKMN WFLNWVEDRN TANQKPKEQH KRNYVPCHIR QIINTWHKVG KNVYLPPREG DLTCNSTVTS LIANIDWIDG NQTNI TMSA EVAELYRLEL GDYKLVEITP IGLAPTSCKR YTTGGTSRRR RRR

-
Macromolecule #2: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Simian immunodeficiency virus
Molecular weightTheoretical: 18.1446 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GVFVLGFLGF LATAGSAMGA ASLTLTAQSR TLLAGIVQQQ QQLLDVPKRQ QELLRLTVWG TKNLQTRVTA IEKYLKDQAQ LNAWGCAFR QVCCTTVPWP NASLIPKWNN ETWQEWERKV DFLEENITAL LEEAQIQQEK NMYELQKLNG SGHHHHHHHH

-
Macromolecule #3: K11 IgG heavy chain

MacromoleculeName: K11 IgG heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 53.29077 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DWTWRILFLV AAATGAHSQV QLQESGPGVV RPSQTLSLTC AVSGDTVSSC CFFWTWIRQP PGKGLEWIGN IYSDNDNTNY NPSLKTRIS ISKDMSKNQF SLKLNSLTAT DTAIYYCARE SPSRGNFCYA YLYGNCPLHF DLWGQGVLVT VSSASTKGPS V FPLAPSSR ...String:
DWTWRILFLV AAATGAHSQV QLQESGPGVV RPSQTLSLTC AVSGDTVSSC CFFWTWIRQP PGKGLEWIGN IYSDNDNTNY NPSLKTRIS ISKDMSKNQF SLKLNSLTAT DTAIYYCARE SPSRGNFCYA YLYGNCPLHF DLWGQGVLVT VSSASTKGPS V FPLAPSSR STSESTAALG CLVKDYFPEP VTVSWNSGSL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYVCNVN HK PSNTKVD KRVEIKTCGG GSKPPTCPPC TSPELLGGPS VFLFPPKPKD TLMISRTPEV TCVVVDVSQE DPDVKFNWYV NGA EVHHAQ TKPRETQYNS TYRVVSVLTV THQDWLNGKE YTCKVSNKAL PAPIQKTISK DKGQPREPQV YTLPPSREEL TKNQ VSLTC LVKGFYPSDI VVEWESSGQP ENTYKTTPPV LDSDGSYFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLS LSPG K

-
Macromolecule #4: K11 IgG light chain

MacromoleculeName: K11 IgG light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 25.29315 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETDTLLLWVL LLWVPGSTGD ILLTQSPSSL SGSVGDRVTI TCRASQGINS YLNWYQQKPG KAPKLLIYFA NRLQSGVPSR FSGSGSGTE FTLTISSLQS EDGATYYCQQ YDTFPTFGPG TKLDIKRTVA APSVFIFPPS EDQVKSGTVS VVCLLNNFYP R EASVKWKV ...String:
ETDTLLLWVL LLWVPGSTGD ILLTQSPSSL SGSVGDRVTI TCRASQGINS YLNWYQQKPG KAPKLLIYFA NRLQSGVPSR FSGSGSGTE FTLTISSLQS EDGATYYCQQ YDTFPTFGPG TKLDIKRTVA APSVFIFPPS EDQVKSGTVS VVCLLNNFYP R EASVKWKV DGALKTGNSQ ESVTEQDSKD NTYSLSSTLT LSSTEYQSHK VYACEVTHQG LSSPVTKSFN RGEC

-
Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / 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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 86479
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7t4g:
The Envelope Glycoprotein SIVmac239.K180S SOSIP trimer in complex with 3 copies of the neutralizing antibody K11

+
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