+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21111 | |||||||||
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Title | VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure | |||||||||
Map data | VRC01 Bound BG505 F14 HIV-1 SOSIP Env Trimer | |||||||||
Sample |
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Keywords | Trimer / Complex / Immunogen / HIV-1 / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information immunoglobulin complex / 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 / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response ...immunoglobulin complex / 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 / adaptive immune response / 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 / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Henderson R / Acharya P / Bartesaghi A / Zhou Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements. Authors: Rory Henderson / Maolin Lu / Ye Zhou / Zekun Mu / Robert Parks / Qifeng Han / Allen L Hsu / Elizabeth Carter / Scott C Blanchard / R J Edwards / Kevin Wiehe / Kevin O Saunders / Mario J ...Authors: Rory Henderson / Maolin Lu / Ye Zhou / Zekun Mu / Robert Parks / Qifeng Han / Allen L Hsu / Elizabeth Carter / Scott C Blanchard / R J Edwards / Kevin Wiehe / Kevin O Saunders / Mario J Borgnia / Alberto Bartesaghi / Walther Mothes / Barton F Haynes / Priyamvada Acharya / S Munir Alam / Abstract: The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced ...The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced exposure of the co-receptor binding site and fusion elements. To understand the molecular details of this allostery, here, we introduce Env mutations aimed to prevent CD4-induced rearrangements in the HIV-1 BG505 Env trimer. Binding analysis and single-molecule Förster Resonance Energy Transfer confirm that these mutations prevent CD4-induced transitions of the HIV-1 Env. Structural analysis by single-particle cryo-electron microscopy performed on the BG505 SOSIP mutant Env proteins shows rearrangements in the gp120 topological layer contacts with gp41. Displacement of a conserved tryptophan (W571) from its typical pocket in these Env mutants renders the Env insensitive to CD4 binding. These results reveal the critical function of W571 as a conformational switch in Env allostery and receptor-mediated viral entry and provide insights on Env conformation that are relevant for vaccine design. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21111.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-21111-v30.xml emd-21111.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_21111.png | 57.9 KB | ||
Filedesc metadata | emd-21111.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21111 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21111 | HTTPS FTP |
-Validation report
Summary document | emd_21111_validation.pdf.gz | 346.8 KB | Display | EMDB validaton report |
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Full document | emd_21111_full_validation.pdf.gz | 346.4 KB | Display | |
Data in XML | emd_21111_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | emd_21111_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21111 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21111 | HTTPS FTP |
-Related structure data
Related structure data | 6v8xMC 6v8zC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21111.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | VRC01 Bound BG505 F14 HIV-1 SOSIP Env Trimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08312 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex between VRC01 and BG505 F14 HIV-1 SOSIP Env Trimer
Entire | Name: Complex between VRC01 and BG505 F14 HIV-1 SOSIP Env Trimer |
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Components |
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-Supramolecule #1: Complex between VRC01 and BG505 F14 HIV-1 SOSIP Env Trimer
Supramolecule | Name: Complex between VRC01 and BG505 F14 HIV-1 SOSIP Env Trimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: BG505 F14 HIV-1 SOSIP Env Trimer
Supramolecule | Name: BG505 F14 HIV-1 SOSIP Env Trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-Supramolecule #3: VRC01
Supramolecule | Name: VRC01 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Envelope glycoprotein gp120
Macromolecule | Name: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 52.79184 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNIWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNAITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ...String: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNIWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVK LTPLCVTLQC TNVTNAITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ITQVCPKLSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVLSTQLL LNGSLAEEEV MI RSENITN NAKNILVQFN TPVQINCTRP NNNTRKSIRI GPGQAFYATG DIIGDIRQAH CNVSKATWNE TLGKVVKQLR KHF GNNTII RFANSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAM YAPPI QGVIRCVSNI TGLILTRDGG STNSTTETFR PGGGDMRDNW RSELYKYKVV KIEPLGVAPT RCKRRV UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #2: Envelope glycoprotein gp41
Macromolecule | Name: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 16.44767 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LGFLGAAGST MGAASMTLTV QARNLLSGIV QQQSNLLRAI EAQQHLLKLT VWGIKQLQAR VLAVERYLRD QQLLGIWGCS GKLICCTNV PWNSSWSNRN LSEIWDNMTW LQWDKEISNY TQIIYGLLEE SQNQQEKNEQ DLLALD UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #3: VRC01 Fab Heavy Chain
Macromolecule | Name: VRC01 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.367631 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGGQ MKKPGESMRI SCRASGYEFI DCTLNWIRLA PGKRPEWMGW LKPRGGAVNY ARPLQGRVTM TRDVYSDTAF LELRSLTVD DTAVYFCTRG KNCDYNWDFE HWGRGTPVIV SSPSTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String: QVQLVQSGGQ MKKPGESMRI SCRASGYEFI DCTLNWIRLA PGKRPEWMGW LKPRGGAVNY ARPLQGRVTM TRDVYSDTAF LELRSLTVD DTAVYFCTRG KNCDYNWDFE HWGRGTPVIV SSPSTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK AEPKSC UniProtKB: Ig-like domain-containing protein |
-Macromolecule #4: VRC01 Fab Light Chain
Macromolecule | Name: VRC01 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.930412 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VLTQSPGTLS LSPGETAIIS CRTSQYGSLA WYQQRPGQAP RLVIYSGSTR AAGIPDRFSG SRWGPDYNLT ISNLESGDFG VYYCQQYEF FGQGTKVQVD IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ SGNSQESVTE Q DSKDSTYS ...String: VLTQSPGTLS LSPGETAIIS CRTSQYGSLA WYQQRPGQAP RLVIYSGSTR AAGIPDRFSG SRWGPDYNLT ISNLESGDFG VYYCQQYEF FGQGTKVQVD IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ SGNSQESVTE Q DSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLRSP VTKSFNRGEC UniProtKB: IGK@ protein |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 15 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77632 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |