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Yorodumi- PDB-7llk: Cryo-EM structure of Q23.17_DS-SOSIP in complex with Glycan276-De... -
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-Basic information
Entry | Database: PDB / ID: 7llk | ||||||
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Title | Cryo-EM structure of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / BG505 DS-SOSIP / Glycan276-Dependent / Glycan276 / 179NC75 Fab / HIV-1 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||
Authors | Manne, K. / Acharya, P. | ||||||
Funding support | United States, 1items
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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
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7llk.cif.gz | 847 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7llk.ent.gz | 735.2 KB | Display | PDB format |
PDBx/mmJSON format | 7llk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7llk_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 7llk_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 7llk_validation.xml.gz | 80.2 KB | Display | |
Data in CIF | 7llk_validation.cif.gz | 117.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/7llk ftp://data.pdbj.org/pub/pdb/validation_reports/ll/7llk | HTTPS FTP |
-Related structure data
Related structure data | 23424MC 7lg6C 7ll1C 7ll2C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Envelope glycoprotein ... , 2 types, 6 molecules EAIFBJ
#1: Protein | Mass: 53627.930 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: O55774 #2: Protein | Mass: 17211.594 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) |
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-Antibody , 2 types, 6 molecules GCKHDL
#3: Antibody | Mass: 25897.457 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 23042.402 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Sugars , 4 types, 42 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Trimeric HIV-1 Env in complex with VRC33.01 Fab / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K / Details: Blot for 2.5 S before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93.15 K / Temperature (min): 93.15 K |
Image recording | Electron dose: 58.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 489824 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6VKN | ||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 130.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||
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