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Yorodumi- PDB-3se9: Crystal structure of broadly and potently neutralizing antibody V... -
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-Basic information
Entry | Database: PDB / ID: 3se9 | ||||||
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Title | Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with HIV-1 gp120 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HIV / GP120 / ANTIBODY / VRC-PG04 / NEUTRALIZATION / VACCINE / ENVELOPE GLYCOPROTEIN / 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 / 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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kwong, P.D. / Zhou, T. | ||||||
Citation | Journal: Science / Year: 2011 Title: Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Authors: Wu, X. / Zhou, T. / Zhu, J. / Zhang, B. / Georgiev, I. / Wang, C. / Chen, X. / Longo, N.S. / Louder, M. / McKee, K. / O'Dell, S. / Perfetto, S. / Schmidt, S.D. / Shi, W. / Wu, L. / Yang, Y. ...Authors: Wu, X. / Zhou, T. / Zhu, J. / Zhang, B. / Georgiev, I. / Wang, C. / Chen, X. / Longo, N.S. / Louder, M. / McKee, K. / O'Dell, S. / Perfetto, S. / Schmidt, S.D. / Shi, W. / Wu, L. / Yang, Y. / Yang, Z.Y. / Yang, Z. / Zhang, Z. / Bonsignori, M. / Crump, J.A. / Kapiga, S.H. / Sam, N.E. / Haynes, B.F. / Simek, M. / Burton, D.R. / Koff, W.C. / Doria-Rose, N.A. / Connors, M. / Mullikin, J.C. / Nabel, G.J. / Roederer, M. / Shapiro, L. / Kwong, P.D. / Mascola, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3se9.cif.gz | 458.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3se9.ent.gz | 395.2 KB | Display | PDB format |
PDBx/mmJSON format | 3se9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3se9_validation.pdf.gz | 520 KB | Display | wwPDB validaton report |
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Full document | 3se9_full_validation.pdf.gz | 532.7 KB | Display | |
Data in XML | 3se9_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 3se9_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/3se9 ftp://data.pdbj.org/pub/pdb/validation_reports/se/3se9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24644.771 Da / Num. of mol.: 1 / Fragment: Antigen binding fragement of heavy chain Source method: isolated from a genetically manipulated source Details: Co-transfection of both heavy and light chain plasmids Source: (gene. exp.) Homo sapiens (human) / Gene: antibody VRC-PG04 heavy chain / Plasmid: CMVR derived plasmids for IgG1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 23073.822 Da / Num. of mol.: 1 / Fragment: antibody light chain Source method: isolated from a genetically manipulated source Details: Co-transfection of both heavy and light chain plasmids Source: (gene. exp.) Homo sapiens (human) / Gene: antibody VRC-PG04 light chain / Plasmid: CMVR derived plasmids for IgG1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 11 molecules G
#1: Protein | Mass: 39211.434 Da / Num. of mol.: 1 / Fragment: Core gp120 with trancations Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Gene: gp120 / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 584 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-BU3 / ( | #9: Chemical | ChemComp-TRS / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 9.9% PEG 4000, 9.0 % isopropanol, 100 mM Li2SO4, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 67230 / Num. obs: 59364 / % possible obs: 88.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→23.734 Å / SU ML: 0.51 / σ(F): 1.93 / Phase error: 25.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.269 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→23.734 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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