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- EMDB-20511: Structure of full-length, fully glycosylated, non-modified HIV-1 ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20511 | |||||||||
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Title | Structure of full-length, fully glycosylated, non-modified HIV-1 gp160 bound to PG16 Fab | |||||||||
![]() | Full-length, fully glycosylated, non-modified HIV-1 gp160 bound to PG16 Fab | |||||||||
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Function / homology | ![]() host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.2 Å | |||||||||
![]() | Pan J / Chen B / Harrison SC | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structure of Full-length HIV-1 Env Bound With the Fab of Antibody PG16. Authors: Junhua Pan / Hanqin Peng / Bing Chen / Stephen C Harrison / ![]() Abstract: The HIV-1 envelope protein (Env) is the target of neutralizing antibodies and the template for vaccine immunogen design. The dynamic conformational equilibrium of trimeric Env influences its ...The HIV-1 envelope protein (Env) is the target of neutralizing antibodies and the template for vaccine immunogen design. The dynamic conformational equilibrium of trimeric Env influences its antigenicity and potential immunogenicity. Antibodies that bind at the trimer apex stabilize a "closed" conformation characteristic of the most difficult to neutralize isolates. A goal of vaccine development is therefore to mimic the closed conformation in a designed immunogen. A disulfide-stabilized, trimeric Env ectodomain-the "SOSIP" construct-has many of the relevant properties; it is also particularly suitable for structure determination. Some single-molecule studies have, however, suggested that the SOSIP trimer is not a good representation of Env on the surface of a virion or an infected cell. We isolated Env (fully cleaved to gp120 and gp41) from the surface of expressing cells using tagged, apex-binding Fab PG16 and determined the structure of the PG16-Env complex by cryo-EM to an overall resolution of 4.6 Å. Placing the only purification tag on the Fab ensured that the isolated Env was continuously stabilized in its closed, native conformation. The Env structure in this complex corresponds closely to the SOSIP structures determined by both x-ray crystallography and cryo-EM. Although the membrane-interacting elements are not resolved in our reconstruction, we can make inferences about the connection between ectodomain and membrane-proximal external region (MPER) by reference to the published cryo-tomography structure of an Env "spike" and the NMR structure of the MPER-transmembrane segment. We discuss these results in view of the conflicting interpretations in the literature. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.9 KB 20.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 57.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pwuMC ![]() 6ulcC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Full-length, fully glycosylated, non-modified HIV-1 gp160 bound to PG16 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : HIV-1 GP160 trimer:PG16 Fab complex
Entire | Name: HIV-1 GP160 trimer:PG16 Fab complex |
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Components |
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-Supramolecule #1: HIV-1 GP160 trimer:PG16 Fab complex
Supramolecule | Name: HIV-1 GP160 trimer:PG16 Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: recombinant protein complex |
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Molecular weight | Theoretical: 530 KDa |
-Supramolecule #2: HIV-1 envelope glycoprotein GP160 (mature)
Supramolecule | Name: HIV-1 envelope glycoprotein GP160 (mature) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: mature envelope glycoprotein GP160 (i.e. cleaved form consisting of receptor binding domain GP120 and fusogenic domain GP41) |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: Antibody PG16 Fab
Supramolecule | Name: Antibody PG16 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 97.560695 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRVRGIQRNC QHLWRWGTLI LGMLMICSAA ENLWVTVYYG VPVWKDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPNP QEIYMENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV QLTPLCVTLD CSYNITNNIT NSITNSSVNM REEIKNCSFN M TTELRDKN ...String: MRVRGIQRNC QHLWRWGTLI LGMLMICSAA ENLWVTVYYG VPVWKDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPNP QEIYMENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV QLTPLCVTLD CSYNITNNIT NSITNSSVNM REEIKNCSFN M TTELRDKN RKVYSLFYKL DVVQINNGNN SSNLYRLINC NTSALTQACP KVTFEPIPIR YCAPAGYAIL KCNDKEFNGT GL CKNVSTV QCTHGIRPVV STQLLLNGSL AEGKVMIRSE NITNNVKNII VQLNETVTIN CTRPNNNTRK SVRIGPGQTF YAT GDIIGD IRQAHCNVSG SQWNRALHQV VGQLREYWNT TIIFKNSSGG DLEITTHSFN CGGEFFYCNT SGLFNSNWTH NDTA SMKPN DTITLPCRIK QIINMWQRVG QAIYAPPIQG VIRCESNITG LILTRDGGGN INESQIFRPG GGDMRDNWRS ELYKY KVVR IEPLGVAPTK AKRRVVEREK RAVVELGAVF IGFLGTAGST MGAASITLTV QVRKLLSGIV QQQSNLLRAI EAQQHL LKL TVWGIKQLQA RVLAVERYLR DQQLLGIWGC SGKLICTTNV PWNSSWSNKS EREIWENMTW LQWDKEISNY THIIYEL IE ESQKQQEKNE QELLELDKWA NLWNWFDISN WLWYIKIFIM IVGGLIGLRI VFAVLSVINR VRQGYSPLSF QTLTPNPR D PDRPGRIEGE GGEQDRGRSI RLVSGFLALA WDDLRNLCLS SYHQLRDFIL IVARTVELLG HSSLKGLRLG WEGLKYLGN LLLYWGRELK TSAINLFDTI AIVVAGWTDR VIEVGQRLGR AILNIPRRIR QGLERALL |
-Macromolecule #2: Antibody PG16 Fab heavy chain
Macromolecule | Name: Antibody PG16 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 31.952703 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MEFGLSWVFL VALLRGVQCQ EQLVESGGGV VQPGGSLRLS CLASGFTFHK YGMHWVRQAP GKGLEWVALI SDDGMRKYHS DSMWGRVTI SRDNSKNTLY LQFSSLKVED TAMFFCAREA GGPIWHDDVK YYDFNDGYYN YHYMDVWGKG TTVTVSSAST K GPSVFPLA ...String: MEFGLSWVFL VALLRGVQCQ EQLVESGGGV VQPGGSLRLS CLASGFTFHK YGMHWVRQAP GKGLEWVALI SDDGMRKYHS DSMWGRVTI SRDNSKNTLY LQFSSLKVED TAMFFCAREA GGPIWHDDVK YYDFNDGYYN YHYMDVWGKG TTVTVSSAST K GPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CN VNHKPSN TKVDKRVEPK SCDKASGGGS AWSHPQFEKG GGSGGGSGGS SAWSHPQFEK |
-Macromolecule #3: Antibody PG16 Fab light chain
Macromolecule | Name: Antibody PG16 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.424229 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAWALLLLTL LTQGTGSWAQ SALTQPASVS GSPGQTITIS CNGTSSDVGG FDSVSWYQQS PGKAPKVMVF DVSHRPSGIS NRFSGSKSG NTASLTISGL HIEDEGDYFC SSLTDRSHRI FGGGTKVTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT ...String: MAWALLLLTL LTQGTGSWAQ SALTQPASVS GSPGQTITIS CNGTSSDVGG FDSVSWYQQS PGKAPKVMVF DVSHRPSGIS NRFSGSKSG NTASLTISGL HIEDEGDYFC SSLTDRSHRI FGGGTKVTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT VAWKADSSPV KAGVETTTPS KQSNNKYAAS SYLSLTPEQW KSHKSYSCQV THEGSTVEKT VAPTECSGGS GG HHHHHHH HHH |
-Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 44 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa Details: Quantifoil-Cu R1.2/1.3 200 mesh was glow discharged by Pelilcan EasiGlow for 30 seconds at 20 mA. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK I / Details: 4.2 second blot before plunging. | ||||||||||||
Details | This sample was monodisperse (stoichiometry 3:1). |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 2.5 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 8138 / Average exposure time: 0.125 sec. / Average electron dose: 40.0 e/Å2 Details: image size and sampling interval reported here are for super resolution. The physical pixel size of the camera is 5.0 um and image size is 3838 pixels by 3710 pixels. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 30488 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 300 |
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Output model | ![]() PDB-6pwu: |