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Yorodumi- PDB-6n1w: Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n1w | |||||||||
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Title | Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody DFPH-a.15 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / HIV-1 Env complex / neutralizing antibody / fusion peptide-directed | |||||||||
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 / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 Macaca mulatta (Rhesus monkey) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Acharya, P. / Kwong, P.D. | |||||||||
Citation | Journal: Cell / Year: 2019 Title: Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization. Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / ...Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Gwo-Yu Chuang / Cara W Chao / Ying Gu / Alexander J Jafari / Mark K Louder / Sijy O'Dell / Ariana P Rowshan / Elise G Viox / Yiran Wang / Chang W Choi / Martin M Corcoran / Angela R Corrigan / Venkata P Dandey / Edward T Eng / Hui Geng / Kathryn E Foulds / Yicheng Guo / Young D Kwon / Bob Lin / Kevin Liu / Rosemarie D Mason / Martha C Nason / Tiffany Y Ohr / Li Ou / Reda Rawi / Edward K Sarfo / Arne Schön / John P Todd / Shuishu Wang / Hui Wei / Winston Wu / / James C Mullikin / Robert T Bailer / Nicole A Doria-Rose / Gunilla B Karlsson Hedestam / Diana G Scorpio / Julie Overbaugh / Jesse D Bloom / Bridget Carragher / Clinton S Potter / Lawrence Shapiro / Peter D Kwong / John R Mascola / Abstract: The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be ...The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6n1w.cif.gz | 715.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n1w.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6n1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n1w_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 6n1w_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 6n1w_validation.xml.gz | 98.9 KB | Display | |
Data in CIF | 6n1w_validation.cif.gz | 154.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/6n1w ftp://data.pdbj.org/pub/pdb/validation_reports/n1/6n1w | HTTPS FTP |
-Related structure data
Related structure data | 9320MC 8977C 9189C 9319C 9359C 6mpgC 6mphC 6mqcC 6mqeC 6mqmC 6mqrC 6mqsC 6n16C 6n1vC 6nf2C 6osyC 6ot1C M: map data used to model this data C: citing same article (ref.) |
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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 2CcADd
#1: Protein | Mass: 52986.969 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: Q2N0S6 #8: Protein | Mass: 17162.525 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: Q2N0S7 |
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-Protein , 2 types, 6 molecules 5Mm8Qq
#4: Protein | Mass: 14838.731 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #7: Protein | Mass: 14506.331 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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-Antibody , 4 types, 12 molecules 3Hh4Ll6Nn7Rr
#2: Antibody | Mass: 24004.799 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) #3: Antibody | Mass: 22962.330 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) #5: Antibody | Mass: 11423.534 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #6: Antibody | Mass: 11386.774 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 , 6 types, 48 molecules
#9: 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 #10: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 #11: Polysaccharide | Source method: isolated from a genetically manipulated source #12: Polysaccharide | Source method: isolated from a genetically manipulated source #13: Polysaccharide | Source method: isolated from a genetically manipulated source #14: Sugar | ChemComp-NAG / |
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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
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Molecular weight | Value: 0.63 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: SPOTITON / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K |
-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 / Calibrated magnification: 22500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 69.98 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 339315 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56291 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.2 Å |