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Yorodumi- EMDB-41417: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with bro... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41417 | |||||||||
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Title | Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing bi-specific antibody CAP256L-R27 targeting the CD4-binding site and the V2-apex | |||||||||
Map data | cryo-EM density of bi-specific antibody CAP256L-R27 in complex with HIV-1 Env BG505 DS-SOSIP | |||||||||
Sample |
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Keywords | HIV-1 Envelope / bi-specific / antibody / nanobody / VHH / llama / BG505 DS-SOSIP / neutralization / CAP256 / R27 / immunization / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.61 Å | |||||||||
Authors | Zhou T / Morano NC / Roark RS / Kwong PD / Xu J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing bi-specific antibody CAP256L-R27 targeting the CD4-binding site and the V2-apex Authors: Xu J / Zhou T | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41417.map.gz | 237.1 MB | EMDB map data format | |
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Header (meta data) | emd-41417-v30.xml emd-41417.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
Images | emd_41417.png | 115.9 KB | ||
Masks | emd_41417_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-41417.cif.gz | 6.9 KB | ||
Others | emd_41417_additional_1.map.gz emd_41417_half_map_1.map.gz emd_41417_half_map_2.map.gz | 450.4 MB 442.3 MB 442.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41417 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41417 | HTTPS FTP |
-Validation report
Summary document | emd_41417_validation.pdf.gz | 990 KB | Display | EMDB validaton report |
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Full document | emd_41417_full_validation.pdf.gz | 989.6 KB | Display | |
Data in XML | emd_41417_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_41417_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41417 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41417 | HTTPS FTP |
-Related structure data
Related structure data | 8tniMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41417.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | cryo-EM density of bi-specific antibody CAP256L-R27 in complex with HIV-1 Env BG505 DS-SOSIP | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41417_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened cryo-EM map of bi-specific antibody CAP256L-R27 in...
File | emd_41417_additional_1.map | ||||||||||||
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Annotation | Sharpened cryo-EM map of bi-specific antibody CAP256L-R27 in complex with HIV-1 Env BG505 DS-SOSIP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map of bi-specific antibody CAP256L-R27 in...
File | emd_41417_half_map_1.map | ||||||||||||
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Annotation | cryo-EM half map of bi-specific antibody CAP256L-R27 in complex with HIV-1 Env BG505 DS-SOSIP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map of bi-specific antibody CAP256L-R27 in...
File | emd_41417_half_map_2.map | ||||||||||||
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Annotation | cryo-EM half map of bi-specific antibody CAP256L-R27 in complex with HIV-1 Env BG505 DS-SOSIP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex between HIV-1 Env BG505 DS-SOSIP and Bi-specific antibody...
Entire | Name: Complex between HIV-1 Env BG505 DS-SOSIP and Bi-specific antibody CAP256L-R27 |
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Components |
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-Supramolecule #1: Complex between HIV-1 Env BG505 DS-SOSIP and Bi-specific antibody...
Supramolecule | Name: Complex between HIV-1 Env BG505 DS-SOSIP and Bi-specific antibody CAP256L-R27 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 405 KDa |
-Macromolecule #1: HIV-1 BG505 DS-SOSIP gp120
Macromolecule | Name: HIV-1 BG505 DS-SOSIP 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: 54.086324 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 SACTQACPKV 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 CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #2: HIV-1 BG505 DS-SOSIP gp41
Macromolecule | Name: HIV-1 BG505 DS-SOSIP 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 UniProtKB: Envelope glycoprotein gp160 |
-Macromolecule #3: Light chain of bi-specific antibody CAP256L-R27
Macromolecule | Name: Light chain of bi-specific antibody CAP256L-R27 / 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: 36.949734 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGGG LVQPGGSLRL SCVASGFDLE NYSIGWFRQA PGKAREGVAC LSKNSGIGHS VKGRFTISRD GDSNTWFLQM GALEAEDTA VYTCATYNRA CANYVTIWPE FRGQGTQVTV SSGGSGGGGS GGGGSGGQSV LTQPPSVSAA PGQKVTISCS G NTSNIGNN ...String: QVQLQESGGG LVQPGGSLRL SCVASGFDLE NYSIGWFRQA PGKAREGVAC LSKNSGIGHS VKGRFTISRD GDSNTWFLQM GALEAEDTA VYTCATYNRA CANYVTIWPE FRGQGTQVTV SSGGSGGGGS GGGGSGGQSV LTQPPSVSAA PGQKVTISCS G NTSNIGNN FVSWYQQRPG RAPQLLIYET DKRPSGIPDR FSASKSGTSG TLAITGLQTG DEADYYCATW AASLSSARVF GT GTQVIVL GQPKVNPTVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK QSNNKYAASS YLS LTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS |
-Macromolecule #4: Heavy chain of bi-specific antibody CAP256L-R27
Macromolecule | Name: Heavy chain of bi-specific antibody CAP256L-R27 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.863039 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVESGGG VVQPGTSLRL SCAASQFRFD GYGMHWVRQA PGKGLEWVAS ISHDGIKKYH AEKVWGRFTI SRDNSKNTLY LQMNSLRPE DTALYYCAKD LREDECEEWW SD(TYS)(TYS)DFGAQL PCAKSRGGLV GIADNWGQGT MVTVSSASTK GPS VFPLAP ...String: QVQLVESGGG VVQPGTSLRL SCAASQFRFD GYGMHWVRQA PGKGLEWVAS ISHDGIKKYH AEKVWGRFTI SRDNSKNTLY LQMNSLRPE DTALYYCAKD LREDECEEWW SD(TYS)(TYS)DFGAQL PCAKSRGGLV GIADNWGQGT MVTVSSASTK GPS VFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNH KPSNT KVDKKVEPKS |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 32 / 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
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
Details | Purified complex by FPLC and concentrated to final concentration. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 100.0 K |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 58.06 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 103000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 82.9 |
Output model | PDB-8tni: |