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Yorodumi- EMDB-8182: Broadly neutralizing antibody PGDM21 in complex with BG505 SOSIP.... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8182 | |||||||||
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Title | Broadly neutralizing antibody PGDM21 in complex with BG505 SOSIP.664 Env trimer | |||||||||
Map data | Broadly neutralizing antibody PGDM21 in complex with BG505 SOSIP.664 Env trimer | |||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.0 Å | |||||||||
Authors | Lee JH / Ward AB | |||||||||
Citation | Journal: Immunity / Year: 2016 Title: A Prominent Site of Antibody Vulnerability on HIV Envelope Incorporates a Motif Associated with CCR5 Binding and Its Camouflaging Glycans. Authors: Devin Sok / Matthias Pauthner / Bryan Briney / Jeong Hyun Lee / Karen L Saye-Francisco / Jessica Hsueh / Alejandra Ramos / Khoa M Le / Meaghan Jones / Joseph G Jardine / Raiza Bastidas / ...Authors: Devin Sok / Matthias Pauthner / Bryan Briney / Jeong Hyun Lee / Karen L Saye-Francisco / Jessica Hsueh / Alejandra Ramos / Khoa M Le / Meaghan Jones / Joseph G Jardine / Raiza Bastidas / Anita Sarkar / Chi-Hui Liang / Sachin S Shivatare / Chung-Yi Wu / William R Schief / Chi-Huey Wong / Ian A Wilson / Andrew B Ward / Jiang Zhu / Pascal Poignard / Dennis R Burton / Abstract: The dense patch of high-mannose-type glycans surrounding the N332 glycan on the HIV envelope glycoprotein (Env) is targeted by multiple broadly neutralizing antibodies (bnAbs). This region is ...The dense patch of high-mannose-type glycans surrounding the N332 glycan on the HIV envelope glycoprotein (Env) is targeted by multiple broadly neutralizing antibodies (bnAbs). This region is relatively conserved, implying functional importance, the origins of which are not well understood. Here we describe the isolation of new bnAbs targeting this region. Examination of these and previously described antibodies to Env revealed that four different bnAb families targeted the (324)GDIR(327) peptide stretch at the base of the gp120 V3 loop and its nearby glycans. We found that this peptide stretch constitutes part of the CCR5 co-receptor binding site, with the high-mannose patch glycans serving to camouflage it from most antibodies. GDIR-glycan bnAbs, in contrast, bound both (324)GDIR(327) peptide residues and high-mannose patch glycans, which enabled broad reactivity against diverse HIV isolates. Thus, as for the CD4 binding site, bnAb effectiveness relies on circumventing the defenses of a critical functional region on Env. | |||||||||
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_8182.map.gz | 13.6 MB | EMDB map data format | |
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Header (meta data) | emd-8182-v30.xml emd-8182.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_8182.png | 32.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8182 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8182 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8182.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Broadly neutralizing antibody PGDM21 in complex with BG505 SOSIP.664 Env trimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 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 : BG505 SOSIP.664 trimer in complex with PGDM21 Fab
Entire | Name: BG505 SOSIP.664 trimer in complex with PGDM21 Fab |
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Components |
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-Supramolecule #1: BG505 SOSIP.664 trimer in complex with PGDM21 Fab
Supramolecule | Name: BG505 SOSIP.664 trimer in complex with PGDM21 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: BG505 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4 |
-Macromolecule #1: BG505 SOSIP.664 Trimer
Macromolecule | Name: BG505 SOSIP.664 Trimer / type: protein_or_peptide / ID: 1 Details: This soluble Env sequence is derived from HIV-1 isolate BG505. It contains mutations to generate the N332 N-linked glycosylation site (T332N) and has stabilizing mutations A501C, I559P, and ...Details: This soluble Env sequence is derived from HIV-1 isolate BG505. It contains mutations to generate the N332 N-linked glycosylation site (T332N) and has stabilizing mutations A501C, I559P, and T605C. The construct is truncated at residue 664 of GP41. Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: BG505 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKH NVW ATHACVPTDP NPQEIHLENV TEEFNMWKNN MVEQMHTDII SLWDQSLKPC VKLTPLCVTL QCTNVTNN I TDDMRGELKN CSFNMTTELR DKKQKVYSLF YRLDVVQINE NQGNRSNNSN KEYRLINCNT ...String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKH NVW ATHACVPTDP NPQEIHLENV TEEFNMWKNN MVEQMHTDII SLWDQSLKPC VKLTPLCVTL QCTNVTNN I TDDMRGELKN CSFNMTTELR DKKQKVYSLF YRLDVVQINE NQGNRSNNSN KEYRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EVMIRSENIT NNAKNILVQF NTPVQINCTR PNNNTRKSIR IGPGQAFYAT GDIIGDIRQA HCNVSKATWN ETLGKVVKQL RKHFGNNTII RFANSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAMYAPPIQ GVIRCVSNIT GLILTRDGGS TNSTTETFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTR CKRRVVGRRR RRRAVGIGAV FLGFLGAAGS TMGAASMTLT VQARNLLSGI VQQQSNLLRA PEAQQHLLKL TVWGIKQLQA RVLAVERYLR DQQLLGIWGC SGKLICCTNV PWNSSWSNRN LSEIWDNMTW LQWDKEISNY TQIIYGLLEE SQNQQEKNEQ DLLALD |
-Macromolecule #2: Heavy chain Fab of broadly neutralizing antibody PGDM21
Macromolecule | Name: Heavy chain Fab of broadly neutralizing antibody PGDM21 type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVEWGAR LVKPSETLSL TCGVSGGTLE AYFWTWLRQS PGRE LEWLG EVRFFDYGGT TTNVNPSFKS RFSASLDASK GHISLRLTSV TAADTAVYYC ARR TFWKSD YTGYYHFHMD VWSNGTSVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPV ...String: EVQLVEWGAR LVKPSETLSL TCGVSGGTLE AYFWTWLRQS PGRE LEWLG EVRFFDYGGT TTNVNPSFKS RFSASLDASK GHISLRLTSV TAADTAVYYC ARR TFWKSD YTGYYHFHMD VWSNGTSVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCD |
-Macromolecule #3: Light chain of broadly neutralizing antibody PGDM21
Macromolecule | Name: Light chain of broadly neutralizing antibody PGDM21 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPVS LSVSPGERAT LSCKTSQSLD NKHVAWYQRK PGLAPRLLIY GVSDRATGIP DRFSGSGSGT NFSLTIGRVE PEDLAVYVCQ QYSVSLITFG QGTRLDLKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDS ...String: EIVLTQSPVS LSVSPGERAT LSCKTSQSLD NKHVAWYQRK PGLAPRLLIY GVSDRATGIP DRFSGSGSGT NFSLTIGRVE PEDLAVYVCQ QYSVSLITFG QGTRLDLKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Staining | Type: NEGATIVE / Material: 2% uranyl formate | |||||||||
Grid | Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN |
Temperature | Max: 298.0 K |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / Number real images: 166 / Average electron dose: 25.0 e/Å2 |
-Image processing
Startup model | Type of model: OTHER Details: Common lines model generated from reference-free 2D class averages |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: SPARX / Software - details: sxali3d.py |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Software - details: sxali3d.py / Number images used: 4378 |