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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20118 | ||||||||||||||||||
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Title | Full length HIV-1 Env AMC011 in complex with PGT151 Fab | ||||||||||||||||||
![]() | Full length AMC011 HIV-1 Env in complex with PGT151 Fab | ||||||||||||||||||
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Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||||||||
![]() | Rantalainen K / Torrents de la Pena A / Ward AB | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Similarities and differences between native HIV-1 envelope glycoprotein trimers and stabilized soluble trimer mimetics. Authors: Alba Torrents de la Peña / Kimmo Rantalainen / Christopher A Cottrell / Joel D Allen / Marit J van Gils / Jonathan L Torres / Max Crispin / Rogier W Sanders / Andrew B Ward / ![]() ![]() ![]() Abstract: The HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, ...The HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, such as SOSIP trimers, have taken a central role in HIV-1 vaccine research aimed at inducing bNAbs. We therefore performed a direct and thorough comparison of a full-length unmodified Env trimer containing the transmembrane domain and the cytoplasmic tail, with the sequence matched soluble SOSIP trimer, both based on an early Env sequence (AMC011) from an HIV+ individual that developed bNAbs. The structures of the full-length AMC011 trimer bound to either bNAb PGT145 or PGT151 were very similar to the structures of SOSIP trimers. Antigenically, the full-length and SOSIP trimers were comparable, but in contrast to the full-length trimer, the SOSIP trimer did not bind at all to non-neutralizing antibodies, most likely as a consequence of the intrinsic stabilization of the SOSIP trimer. Furthermore, the glycan composition of full-length and SOSIP trimers was similar overall, but the SOSIP trimer possessed slightly less complex and less extensively processed glycans, which may relate to the intrinsic stabilization as well as the absence of the membrane tether. These data provide insights into how to best use and improve membrane-associated full-length and soluble SOSIP HIV-1 Env trimers as immunogens. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 152 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.5 KB 24.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.5 KB | Display | ![]() |
Images | ![]() | 123.8 KB | ||
Masks | ![]() | 163.6 MB | ![]() | |
Others | ![]() ![]() | 129 MB 129 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6olpMC ![]() 9378C ![]() 6nijC 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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Map
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Annotation | Full length AMC011 HIV-1 Env in complex with PGT151 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Full length AMC011 HIV-1 Env in complex with PGT151 Fab - half map 2
File | emd_20118_half_map_1.map | ||||||||||||
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Annotation | Full length AMC011 HIV-1 Env in complex with PGT151 Fab - half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Full length AMC011 HIV-1 Env in complex with PGT151 Fab - half map 1
File | emd_20118_half_map_2.map | ||||||||||||
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Annotation | Full length AMC011 HIV-1 Env in complex with PGT151 Fab - half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : PGT151 Fab in complex with full length AMC011 HIV-1 Env
Entire | Name: PGT151 Fab in complex with full length AMC011 HIV-1 Env |
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Components |
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-Supramolecule #1: PGT151 Fab in complex with full length AMC011 HIV-1 Env
Supramolecule | Name: PGT151 Fab in complex with full length AMC011 HIV-1 Env type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: AMC011 Glycoprotein 120
Supramolecule | Name: AMC011 Glycoprotein 120 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: AMC011 Glycoprotein 41
Supramolecule | Name: AMC011 Glycoprotein 41 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #4: PGT151 Fab
Supramolecule | Name: PGT151 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 56.973098 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRVKEIRKNY QHLWKWGIML LGILMICSAA EQLWVTVYYG VPVWKEATTT LFCASDARAY DTEVHNVWAT HACVPTDPNP QEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPCV KLTPLCVTLN CTDLRNATNT NATNTTSSSR GTMEGGEIKN C SFNITTSM ...String: MRVKEIRKNY QHLWKWGIML LGILMICSAA EQLWVTVYYG VPVWKEATTT LFCASDARAY DTEVHNVWAT HACVPTDPNP QEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPCV KLTPLCVTLN CTDLRNATNT NATNTTSSSR GTMEGGEIKN C SFNITTSM RDKVQKEYAL FYKLDVVPIK NDNTSYRLIS CNTSVITQAC PKVSFEPIPI HYCAPAGFAI LKCNDKKFNG TG PCTNVST VQCTHGIRPV VSTQLLLNGS LAEEEVVIRS ANFTDNAKII IVQLNKSVEI NCTRPNNNTR KSIHIGPGRA FYT TGEIIG DIRQAHCNIS GTKWNDTLKQ IVVKLKEQFG NKTIVFNHSS GGDPEIVMHS FNCGGEFFYC NSTQLFNSTW NDTT GSNYT GTIVLPCRIK QIVNMWQEVG KAMYAPPIKG QIRCSSNITG LILIRDGGKN RSENTEIFRP GGGDMRDNWR SELYK YKVV KIEPLGIAPT KAKRRVVQRE KR |
-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: ![]() ![]() |
Molecular weight | Theoretical: 39.677762 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RLLLSGIVQQ QNNLLRAIEA QQHLLQLTVW GIKQLQARVL AVERYLKDQQ LLGIWGCSG KLICTTAVPW NTSWSNKSYN QIWNNMTWME WEREIDNYTS LIYTLIEDSQ NQQEKNEQEL LELDKWASLW N WFDITKWL ...String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RLLLSGIVQQ QNNLLRAIEA QQHLLQLTVW GIKQLQARVL AVERYLKDQQ LLGIWGCSG KLICTTAVPW NTSWSNKSYN QIWNNMTWME WEREIDNYTS LIYTLIEDSQ NQQEKNEQEL LELDKWASLW N WFDITKWL WYIKIFIMIV GGLIGLRIVF TVLSIVNRIR QGYSPLSFQT PLPTPRGPDR PEGIEEEGGE RDRDRSDRLV TG FLALIWV DLRSLCLFSY HRLRDLLLIV TRIVELLGRR GWGVLKYWWN LLQYWSQELR NSAVSLLNAT AIAVAEGTDR VIE VSQRAF RAILHVPVRI RQGLERALV |
-Macromolecule #3: Immunoglobulin G PGT151 Fab, Heavy chain
Macromolecule | Name: Immunoglobulin G PGT151 Fab, Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.087438 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF ...String: RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DK |
-Macromolecule #4: Immunoglobulin G PGT151 Fab, Light chain
Macromolecule | Name: Immunoglobulin G PGT151 Fab, Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.057809 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String: DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C |
-Macromolecule #15: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 15 / Number of copies: 41 / 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 | 6 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
Details: Detergent removed with biobeads prior to grid preparation | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 0 No wait Blot time 6 sec. |
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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 - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 3076 / Average exposure time: 8.0 sec. / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-6olp: |