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- EMDB-9062: HIV-1 Envelope Glycoprotein Clone BG505 delCT N332T in complex wi... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9062 | |||||||||
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Title | HIV-1 Envelope Glycoprotein Clone BG505 delCT N332T in complex with broadly neutralizing antibody Fab PGT151 | |||||||||
![]() | HIV-1 Envelope Glycoprotein in complex with broadly neutralizing antibody Fab PGT151 | |||||||||
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Function / homology | ![]() 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 / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Berndsen ZT / Ward AB | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Differential processing of HIV envelope glycans on the virus and soluble recombinant trimer. Authors: Liwei Cao / Matthias Pauthner / Raiees Andrabi / Kimmo Rantalainen / Zachary Berndsen / Jolene K Diedrich / Sergey Menis / Devin Sok / Raiza Bastidas / Sung-Kyu Robin Park / Claire M ...Authors: Liwei Cao / Matthias Pauthner / Raiees Andrabi / Kimmo Rantalainen / Zachary Berndsen / Jolene K Diedrich / Sergey Menis / Devin Sok / Raiza Bastidas / Sung-Kyu Robin Park / Claire M Delahunty / Lin He / Javier Guenaga / Richard T Wyatt / William R Schief / Andrew B Ward / John R Yates / Dennis R Burton / James C Paulson / ![]() Abstract: As the sole target of broadly neutralizing antibodies (bnAbs) to HIV, the envelope glycoprotein (Env) trimer is the focus of vaccination strategies designed to elicit protective bnAbs in humans. ...As the sole target of broadly neutralizing antibodies (bnAbs) to HIV, the envelope glycoprotein (Env) trimer is the focus of vaccination strategies designed to elicit protective bnAbs in humans. Because HIV Env is densely glycosylated with 75-90 N-glycans per trimer, most bnAbs use or accommodate them in their binding epitope, making the glycosylation of recombinant Env a key aspect of HIV vaccine design. Upon analysis of three HIV strains, we here find that site-specific glycosylation of Env from infectious virus closely matches Envs from corresponding recombinant membrane-bound trimers. However, viral Envs differ significantly from recombinant soluble, cleaved (SOSIP) Env trimers, strongly impacting antigenicity. These results provide a benchmark for virus Env glycosylation needed for the design of soluble Env trimers as part of an overall HIV vaccine strategy. | |||||||||
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 | ![]() | 116.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.7 KB 21.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.2 KB | Display | ![]() |
Images | ![]() | 71.4 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Others | ![]() ![]() | 98.5 MB 98.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 800 KB | Display | ![]() |
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Full document | ![]() | 799.6 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6marMC ![]() 9030C 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HIV-1 Envelope Glycoprotein in complex with broadly neutralizing antibody Fab PGT151 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 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: HIV-1 Envelope Glycoprotein in complex with broadly neutralizing...
File | emd_9062_half_map_1.map | ||||||||||||
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Annotation | HIV-1 Envelope Glycoprotein in complex with broadly neutralizing antibody Fab PGT151 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: HIV-1 Envelope Glycoprotein in complex with broadly neutralizing...
File | emd_9062_half_map_2.map | ||||||||||||
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Annotation | HIV-1 Envelope Glycoprotein in complex with broadly neutralizing antibody Fab PGT151 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : HIV-1 Envelope Glycoprotein Clone BG505 delCT N332T in complex wi...
Entire | Name: HIV-1 Envelope Glycoprotein Clone BG505 delCT N332T in complex with broadly neutralizing antibody Fab PGT151 |
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Components |
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-Supramolecule #1: HIV-1 Envelope Glycoprotein Clone BG505 delCT N332T in complex wi...
Supramolecule | Name: HIV-1 Envelope Glycoprotein Clone BG505 delCT N332T in complex with broadly neutralizing antibody Fab PGT151 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Immunoglobulin G PGT151 Fab, Heavy chain
Macromolecule | Name: Immunoglobulin G PGT151 Fab, Heavy chain / type: protein_or_peptide / ID: 1 / 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 #2: Immunoglobulin G PGT151, Light chain
Macromolecule | Name: Immunoglobulin G PGT151, Light chain / type: protein_or_peptide / ID: 2 / 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 #3: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 55.261566 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: METDTLLLWV LLLWVPGSTG DAENLWVTVY YGVPVWKDAE TTLFCASDAK AYETEKHNVW ATHACVPTDP NPQEIHLENV TEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF Y RLDVVQIN ...String: METDTLLLWV LLLWVPGSTG DAENLWVTVY YGVPVWKDAE TTLFCASDAK AYETEKHNVW ATHACVPTDP NPQEIHLENV TEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF Y RLDVVQIN ENQGNRSNNS NKEYRLINCN TSAITQACPK VSFEPIPIHY CAPAGFAILK CKDKKFNGTG PCPSVSTVQC TH GIKPVVS TQLLLNGSLA EEEVMIRSEN ITNNAKNILV QFNTPVQINC TRPNNNTRKS IRIGPGQAFY ATGDIIGDIR QAH CTVSKA TWNETLGKVV KQLRKHFGNN TIIRFANSSG GDLEVTTHSF NCGGEFFYCN TSGLFNSTWI SNTSVQGSNS TGSN DSITL PCRIKQIINM WQRIGQAMYA PPIQGVIRCV SNITGLILTR DGGSTNSTTE TFRPGGGDMR DNWRSELYKY KVVKI EPLG VAPTRAKRRV |
-Macromolecule #4: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.9086 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: VGREKRAVGI GAVFLGFLGA AGSTMGAASM TLTVQARNLL SGIVQQQSNL LRAIEAQQHL LKLTVWGIKQ LQARVLAVER YLRDQQLLG IWGCSGKLIC TTNVPWNSSW SNRNLSEIWD NMTWLQWDKE ISNYTQIIYG LLEESQNQQE KNEQDLLALD K WASLWNWF ...String: VGREKRAVGI GAVFLGFLGA AGSTMGAASM TLTVQARNLL SGIVQQQSNL LRAIEAQQHL LKLTVWGIKQ LQARVLAVER YLRDQQLLG IWGCSGKLIC TTNVPWNSSW SNRNLSEIWD NMTWLQWDKE ISNYTQIIYG LLEESQNQQE KNEQDLLALD K WASLWNWF DISNWLWYIK IFIMIVGGLI GLRIVFAVLS VIHRVRQGGG SGGGWSHPQF EK |
-Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 22 / 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 | 0.18 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2335 / Average exposure time: 9.5 sec. / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |