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Yorodumi- EMDB-23424: Cryo-EM map of Q23.17_DS-SOSIP in complex with Glycan276-Dependen... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23424 | |||||||||
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Title | Cryo-EM map of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab | |||||||||
Map data | Cryo-EM map of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 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 / host cell plasma membrane / structural molecule activity / virion membrane / 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 | Manne K / Acharya P | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Rep / Year: 2021 Title: Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies. Authors: Christopher A Cottrell / Kartik Manne / Rui Kong / Shuishu Wang / Tongqing Zhou / Gwo-Yu Chuang / Robert J Edwards / Rory Henderson / Katarzyna Janowska / Megan Kopp / Bob C Lin / Mark K ...Authors: Christopher A Cottrell / Kartik Manne / Rui Kong / Shuishu Wang / Tongqing Zhou / Gwo-Yu Chuang / Robert J Edwards / Rory Henderson / Katarzyna Janowska / Megan Kopp / Bob C Lin / Mark K Louder / Adam S Olia / Reda Rawi / Chen-Hsiang Shen / Justin D Taft / Jonathan L Torres / Nelson R Wu / Baoshan Zhang / Nicole A Doria-Rose / Myron S Cohen / Barton F Haynes / Lawrence Shapiro / Andrew B Ward / Priyamvada Acharya / John R Mascola / Peter D Kwong / Abstract: Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To ...Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition. | |||||||||
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_23424.map.gz | 117.1 MB | EMDB map data format | |
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Header (meta data) | emd-23424-v30.xml emd-23424.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
Images | emd_23424.png | 84.7 KB | ||
Others | emd_23424_additional_1.map.gz emd_23424_half_map_1.map.gz emd_23424_half_map_2.map.gz | 115.6 MB 115.8 MB 115.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23424 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23424 | HTTPS FTP |
-Validation report
Summary document | emd_23424_validation.pdf.gz | 705.5 KB | Display | EMDB validaton report |
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Full document | emd_23424_full_validation.pdf.gz | 705.1 KB | Display | |
Data in XML | emd_23424_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | emd_23424_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23424 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23424 | HTTPS FTP |
-Related structure data
Related structure data | 7llkMC 7lg6C 7ll1C 7ll2C 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_23424.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.00065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryo-EM sharpened-map of Q23.17 DS-SOSIP in complex with Glycan276-Dependent...
File | emd_23424_additional_1.map | ||||||||||||
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Annotation | Cryo-EM sharpened-map of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map B Q23.17 DS-SOSIP in complex with...
File | emd_23424_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM half map B Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map A Q23.17 DS-SOSIP in complex with...
File | emd_23424_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM half map A Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Trimeric HIV-1 Env in complex with VRC33.01 Fab
Entire | Name: Trimeric HIV-1 Env in complex with VRC33.01 Fab |
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Components |
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-Supramolecule #1: Trimeric HIV-1 Env in complex with VRC33.01 Fab
Supramolecule | Name: Trimeric HIV-1 Env in complex with VRC33.01 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) |
-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: 53.62793 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AENLWVTVYY GVPVWRDADT TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSACTQAC ...String: AENLWVTVYY GVPVWRDADT TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSACTQAC PKVSFEPIPI HYCAPAGFAI LKCKDEGFNG TGLCKNVSTV QCTHGIKPVV STQLLLNGSL AEKNITIRSE NI TNNAKII IVQLVQPVTI KCIRPNNNTR KSIRIGPGQA FYATGDIIGD IRQAHCNVSR SRWNKTLQEV AEKLRTYFGN KTI IFANSS GGDLEITTHS FNCGGEFFYC NTSGLFNSTW YVNSTWNDTD STQESNDTIT LPCRIKQIIN MWQRAGQCMY APPI PGVIK CESNITGLLL TRDGGKDNNV NETFRPGGGD MRDNWRSELY KYKVVKIEPL GVAPTRCKRR VVERRRRRR |
-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: 17.211594 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QNNLPRAPEA QQHLLKLTVW GIKQLQARVL AVERYLEVQQ LLGIWGCSG KLICCTNVPW NSSWSNKSLD EIWNNMTWLQ WDKEINNYTQ LIYRLIEESQ FQQEINEVEL LALD |
-Macromolecule #3: 179NC75 Fab Heavy chain
Macromolecule | Name: 179NC75 Fab Heavy chain / 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: 25.897457 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EMRLEESGGA LVKPGGSLRL SCVASGFKLS EWSLMWVRQA PGKGLQWVSS ISLNQDYISY AGSVRGRFDV FRDRTQTSLL LNMNKLKTE DTGVYFCARV HAWRYFDWVN RRSPVEKVLS IDLWGRGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE ...String: EMRLEESGGA LVKPGGSLRL SCVASGFKLS EWSLMWVRQA PGKGLQWVSS ISLNQDYISY AGSVRGRFDV FRDRTQTSLL LNMNKLKTE DTGVYFCARV HAWRYFDWVN RRSPVEKVLS IDLWGRGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK |
-Macromolecule #4: 179NC75 Fab Light chain
Macromolecule | Name: 179NC75 Fab Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.042402 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SVTSGATQPP SVSVSKGETA RITCSGVELS SQYVSWYRQR PGQSPVLVMF HNNSRASRIP ERFSASDSGD TATLTIAGAQ DVDEAEYYC QTWDSKNYVT FGGGTKLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS ...String: SVTSGATQPP SVSVSKGETA RITCSGVELS SQYVSWYRQR PGQSPVLVMF HNNSRASRIP ERFSASDSGD TATLTIAGAQ DVDEAEYYC QTWDSKNYVT FGGGTKLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS |
-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: 10 / 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: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: Blot for 2.5 S before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 93.15 K / Max: 93.15 K |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |