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Yorodumi- EMDB-9166: Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 anti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9166 | |||||||||
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Title | Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding fragment | |||||||||
Map data | Cryo-EM of BG505.SOSIP.664 in complex with BF520.1-Fab | |||||||||
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 / virion membrane / structural molecule activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Williams JA / Lee KK / Overbaugh J | |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage. Authors: Cassandra A Simonich / Laura Doepker / Duncan Ralph / James A Williams / Amrit Dhar / Zak Yaffe / Lauren Gentles / Christopher T Small / Brian Oliver / Vladimir Vigdorovich / Vidya Mangala ...Authors: Cassandra A Simonich / Laura Doepker / Duncan Ralph / James A Williams / Amrit Dhar / Zak Yaffe / Lauren Gentles / Christopher T Small / Brian Oliver / Vladimir Vigdorovich / Vidya Mangala Prasad / Ruth Nduati / D Noah Sather / Kelly K Lee / Frederick A Matsen Iv / Julie Overbaugh / Abstract: HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine ...HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. Here we reconstruct the developmental lineage of BF520.1, an infant-derived HIV-specific broadly neutralizing antibody (bnAb), using computational methods developed specifically for this purpose. We find that the BF520.1 inferred naive precursor binds HIV Env. We also show that heterologous cross-clade neutralizing activity evolved in the infant within six months of infection and that, ultimately, only 2% SHM is needed to achieve the full breadth of the mature antibody. Mutagenesis and structural analyses reveal that, for this infant bnAb, substitutions in the kappa chain were critical for activity, particularly in CDRL1. Overall, the developmental pathway of this infant antibody includes features distinct from adult antibodies, including several that may be amenable to better vaccine responses. | |||||||||
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_9166.map.gz | 1.4 MB | EMDB map data format | |
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Header (meta data) | emd-9166-v30.xml emd-9166.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9166_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_9166.png | 39.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9166 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9166 | HTTPS FTP |
-Validation report
Summary document | emd_9166_validation.pdf.gz | 355.2 KB | Display | EMDB validaton report |
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Full document | emd_9166_full_validation.pdf.gz | 354.7 KB | Display | |
Data in XML | emd_9166_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | emd_9166_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9166 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9166 | HTTPS FTP |
-Related structure data
Related structure data | 6mn7MC M: atomic model generated by this map C: citing same article (ref.) |
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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_9166.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM of BG505.SOSIP.664 in complex with BF520.1-Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 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 : Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664
Entire | Name: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664 |
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Components |
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-Supramolecule #1: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664
Supramolecule | Name: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
-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: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 53.278301 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG R |
-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: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 17.146482 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD |
-Macromolecule #3: BF520.1 Fab variable region
Macromolecule | Name: BF520.1 Fab variable region / 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: 25.974941 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE MKMPGASVKV SCKASGYTFT GNYIHWVRQA PGQGLEWMGW IAPHSGDTSY AQRFQGRVTM TGDTSLSTAY MELSRLRSD DTAVYYCARG PFPNYYGPGS YWGGLDFWGQ GTLVSVSSEI VMTQSPATLS VSLGERATLS CRTSQNVAYN F AWYQQKPG ...String: QVQLVQSGAE MKMPGASVKV SCKASGYTFT GNYIHWVRQA PGQGLEWMGW IAPHSGDTSY AQRFQGRVTM TGDTSLSTAY MELSRLRSD DTAVYYCARG PFPNYYGPGS YWGGLDFWGQ GTLVSVSSEI VMTQSPATLS VSLGERATLS CRTSQNVAYN F AWYQQKPG QAPRLLIYEA SSRATGTPAR FSGSGFGTEF TLTISSMQSE DFAVYYCQQY NNWPSPFTFG PGTKVHIK |
-Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 9 / 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
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |