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Yorodumi- EMDB-8717: Cryo-EM reconstruction of B41 SOSIP.664 in complex with fragment ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8717 | |||||||||
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Title | Cryo-EM reconstruction of B41 SOSIP.664 in complex with fragment antigen binding of b12 | |||||||||
Map data | Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12 | |||||||||
Sample |
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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 | |||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Pallesen J / Ozorowski G / de Val N / Ward AB | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2017 Title: Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. Authors: Gabriel Ozorowski / Jesper Pallesen / Natalia de Val / Dmitry Lyumkis / Christopher A Cottrell / Jonathan L Torres / Jeffrey Copps / Robyn L Stanfield / Albert Cupo / Pavel Pugach / John P ...Authors: Gabriel Ozorowski / Jesper Pallesen / Natalia de Val / Dmitry Lyumkis / Christopher A Cottrell / Jonathan L Torres / Jeffrey Copps / Robyn L Stanfield / Albert Cupo / Pavel Pugach / John P Moore / Ian A Wilson / Andrew B Ward / Abstract: For many enveloped viruses, binding to a receptor(s) on a host cell acts as the first step in a series of events culminating in fusion with the host cell membrane and transfer of genetic material for ...For many enveloped viruses, binding to a receptor(s) on a host cell acts as the first step in a series of events culminating in fusion with the host cell membrane and transfer of genetic material for replication. The envelope glycoprotein (Env) trimer on the surface of HIV is responsible for receptor binding and fusion. Although Env can tolerate a high degree of mutation in five variable regions (V1-V5), and also at N-linked glycosylation sites that contribute roughly half the mass of Env, the functional sites for recognition of receptor CD4 and co-receptor CXCR4/CCR5 are conserved and essential for viral fitness. Soluble SOSIP Env trimers are structural and antigenic mimics of the pre-fusion native, surface-presented Env, and are targets of broadly neutralizing antibodies. Thus, they are attractive immunogens for vaccine development. Here we present high-resolution cryo-electron microscopy structures of subtype B B41 SOSIP Env trimers in complex with CD4 and antibody 17b, or with antibody b12, at resolutions of 3.7 Å and 3.6 Å, respectively. We compare these to cryo-electron microscopy reconstructions of B41 SOSIP Env trimers with no ligand or in complex with either CD4 or the CD4-binding-site antibody PGV04 at 5.6 Å, 5.2 Å and 7.4 Å resolution, respectively. Consequently, we present the most complete description yet, to our knowledge, of the CD4-17b-induced intermediate and provide the molecular basis of the receptor-binding-induced conformational change required for HIV-1 entry into host cells. Both CD4 and b12 induce large, previously uncharacterized conformational rearrangements in the gp41 subunits, and the fusion peptide becomes buried in a newly formed pocket. These structures provide key details on the biological function of the type I viral fusion machine from HIV-1 as well as new templates for inhibitor 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_8717.map.gz | 60 MB | EMDB map data format | |
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Header (meta data) | emd-8717-v30.xml emd-8717.xml | 29.1 KB 29.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8717_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_8717.png | 69.7 KB | ||
Others | emd_8717_additional.map.gz emd_8717_half_map_1.map.gz emd_8717_half_map_2.map.gz | 59.9 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8717 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8717 | HTTPS FTP |
-Validation report
Summary document | emd_8717_validation.pdf.gz | 702.3 KB | Display | EMDB validaton report |
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Full document | emd_8717_full_validation.pdf.gz | 701.9 KB | Display | |
Data in XML | emd_8717_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_8717_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8717 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8717 | HTTPS FTP |
-Related structure data
Related structure data | 5vn8MC 8713C 8714C 8715C 8716C 8729C 8730C 5vn3C 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_8717.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryo-EM model of B41 SOSIP.664 in complex with...
File | emd_8717_additional.map | ||||||||||||
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Annotation | Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12, additional map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM model of B41 SOSIP.664 in complex with...
File | emd_8717_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12, half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM model of B41 SOSIP.664 in complex with...
File | emd_8717_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12, half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 Env B41 SOSIP.664 in complex with b12 fragment antigen binding
Entire | Name: HIV-1 Env B41 SOSIP.664 in complex with b12 fragment antigen binding |
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Components |
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-Supramolecule #1: HIV-1 Env B41 SOSIP.664 in complex with b12 fragment antigen binding
Supramolecule | Name: HIV-1 Env B41 SOSIP.664 in complex with b12 fragment antigen binding type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 570 KDa |
-Supramolecule #2: HIV-1 Env B41 SOSIP.664
Supramolecule | Name: HIV-1 Env B41 SOSIP.664 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
-Supramolecule #3: b12 fragment
Supramolecule | Name: b12 fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
-Macromolecule #1: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / 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: 57.702469 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEI VLGNVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCNNV NTNNTNNSTN ATISDWEKME T GEMKNCSF ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEI VLGNVTENFN MWKNNMVEQM HEDIISLWDQ SLKPCVKLTP LCVTLNCNNV NTNNTNNSTN ATISDWEKME T GEMKNCSF NVTTSIRDKI KKEYALFYKL DVVPLENKNN INNTNITNYR LINCNTSVIT QACPKVSFEP IPIHYCAPAG FA ILKCNSK TFNGSGPCTN VSTVQCTHGI RPVVSTQLLL NGSLAEEEIV IRSENITDNA KTIIVQLNEA VEINCTRPNN NTR KSIHIG PGRAFYATGD IIGNIRQAHC NISKARWNET LGQIVAKLEE QFPNKTIIFN HSSGGDPEIV THSFNCGGEF FYCN TTPLF NSTWNNTRTD DYPTGGEQNI TLQCRIKQII NMWQGVGKAM YAPPIRGQIR CSSNITGLLL TRDGGRDQNG TETFR PGGG NMRDNWRSEL YKYKVVKIEP LGIAPTACKR RV |
-Macromolecule #2: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / 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: 17.357824 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGLGAFILG FLGAAGSTMG AASMALTVQA RLLLSGIVQQ QNNLLRAPEA QQHMLQLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KIICCTNVPW NDSWSNKTIN EIWDNMTWMQ WEKEIDNYTQ HIYTLLEVSQ IQQEKNEQEL LELD |
-Macromolecule #3: b12 Fab heavy chain
Macromolecule | Name: b12 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: 24.910846 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE VKKPGASVKV SCQASGYRFS NFVIHWVRQA PGQRFEWMGW INPYNGNKEF SAKFQDRVTF TADTSANTAY MELRSLRSA DTAVYYCARV GPYSWDDSPQ DNYYMDVWGK GTTVIVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String: QVQLVQSGAE VKKPGASVKV SCQASGYRFS NFVIHWVRQA PGQRFEWMGW INPYNGNKEF SAKFQDRVTF TADTSANTAY MELRSLRSA DTAVYYCARV GPYSWDDSPQ DNYYMDVWGK GTTVIVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKAEPK SC |
-Macromolecule #4: b12 Fab light chain
Macromolecule | Name: b12 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: 23.707354 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGERAT FSCRSSHSIR SRRVAWYQHK PGQAPRLVIH GVSNRASGIS DRFSGSGSGT DFTLTITRVE PEDFALYYC QVYGASSYTF GQGTKLERKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: EIVLTQSPGT LSLSPGERAT FSCRSSHSIR SRRVAWYQHK PGQAPRLVIH GVSNRASGIS DRFSGSGSGT DFTLTITRVE PEDFALYYC QVYGASSYTF GQGTKLERKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLRSPVTK SFNRGEC |
-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: 33 / 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
Concentration | 5 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: DDM was added to a final concentration of 0.06 mM prior to vitrification | ||||||||||||
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER Details: 3 uL of sample applied to a holey carbon grid on glow discharged face and blotted manually on sample side until filter paper detached from grid, followed by immediate plunging. | ||||||||||||
Details | B41 SOSIP.664 was incubated with a 6X molar excess of 17b Fab overnight at room temperature, purified by size exclusion chromatography, and concentrated prior to grid application |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 0.000131 µm / Digitization - Frames/image: 1-50 / Number real images: 1300 / Average exposure time: 10.0 sec. / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 38168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Homology model of B41 SOSIP.664 created using PDB 5CEZ as initial model. b12 coordinates taken from PDB 2NY7. Performed fragment based refinement using Rosetta, followed by relaxed refinement in Rosetta. Modeled glycans using Chimera and performed final refinements using Phenix. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: EMRinger |
Output model | PDB-5vn8: |