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Yorodumi- PDB-5t3s: HIV gp140 trimer MD39-10MUTA in complex with Fabs PGT124 and 35022 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t3s | |||||||||
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Title | HIV gp140 trimer MD39-10MUTA in complex with Fabs PGT124 and 35022 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 neutralizing antibody | |||||||||
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 | Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | |||||||||
Authors | Stanfield, R.L. / Wilson, I.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Immunity / Year: 2016 Title: HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies. Authors: Steichen, J.M. / Kulp, D.W. / Tokatlian, T. / Escolano, A. / Dosenovic, P. / Stanfield, R.L. / McCoy, L.E. / Ozorowski, G. / Hu, X. / Kalyuzhniy, O. / Briney, B. / Schiffner, T. / Garces, F. ...Authors: Steichen, J.M. / Kulp, D.W. / Tokatlian, T. / Escolano, A. / Dosenovic, P. / Stanfield, R.L. / McCoy, L.E. / Ozorowski, G. / Hu, X. / Kalyuzhniy, O. / Briney, B. / Schiffner, T. / Garces, F. / Freund, N.T. / Gitlin, A.D. / Menis, S. / Georgeson, E. / Kubitz, M. / Adachi, Y. / Jones, M. / Mutafyan, A.A. / Yun, D.S. / Mayer, C.T. / Ward, A.B. / Burton, D.R. / Wilson, I.A. / Irvine, D.J. / Nussenzweig, M.C. / Schief, W.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t3s.cif.gz | 608.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t3s.ent.gz | 506.6 KB | Display | PDB format |
PDBx/mmJSON format | 5t3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t3s_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 5t3s_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 5t3s_validation.xml.gz | 54.4 KB | Display | |
Data in CIF | 5t3s_validation.cif.gz | 74 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/5t3s ftp://data.pdbj.org/pub/pdb/validation_reports/t3/5t3s | HTTPS FTP |
-Related structure data
Related structure data | 5cezS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Envelope glycoprotein ... , 2 types, 2 molecules GB
#1: Protein | Mass: 54151.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): 293S / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6 |
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#2: Protein | Mass: 17134.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): 293S / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6 |
-Antibody , 4 types, 4 molecules LHDE
#3: Antibody | Mass: 23056.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human) |
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#4: Antibody | Mass: 25460.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human) |
#5: Antibody | Mass: 25783.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human) |
#6: Antibody | Mass: 23318.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human) |
-Sugars , 7 types, 17 molecules
#7: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 | ||||||||||
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#8: 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 #9: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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 #10: Polysaccharide | Source method: isolated from a genetically manipulated source #11: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 #12: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 #13: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.39 Å3/Da / Density % sol: 71.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.1 / Details: 5% Peg6000 0.1M citric acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→50.01 Å / Num. obs: 17067 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 106 Å2 / CC1/2: 0.76 / Rmerge(I) obs: 0.213 / Net I/σ(I): 4.75 |
Reflection shell | Resolution: 4.5→4.58 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.63 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CEZ Resolution: 4.5→50.01 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.835 / SU B: 281.642 / SU ML: 1.373 / Cross valid method: THROUGHOUT / ESU R Free: 1.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 187.769 Å2
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Refinement step | Cycle: 1 / Resolution: 4.5→50.01 Å
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