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Yorodumi- PDB-6mtq: Crystal structure of VRC42.N1 Fab in complex with T117-F MPER scaffold -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mtq | ||||||
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Title | Crystal structure of VRC42.N1 Fab in complex with T117-F MPER scaffold | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Anti-HIV-1 human antibody / MPER / gp41 | ||||||
Function / homology | Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Kwon, Y.D. / Law, W.H. / Veradi, R. / Doria-Rose, N.A. / Kwong, P.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Immunity / Year: 2019 Title: Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual. Authors: Krebs, S.J. / Kwon, Y.D. / Schramm, C.A. / Law, W.H. / Donofrio, G. / Zhou, K.H. / Gift, S. / Dussupt, V. / Georgiev, I.S. / Schatzle, S. / McDaniel, J.R. / Lai, Y.T. / Sastry, M. / Zhang, B. ...Authors: Krebs, S.J. / Kwon, Y.D. / Schramm, C.A. / Law, W.H. / Donofrio, G. / Zhou, K.H. / Gift, S. / Dussupt, V. / Georgiev, I.S. / Schatzle, S. / McDaniel, J.R. / Lai, Y.T. / Sastry, M. / Zhang, B. / Jarosinski, M.C. / Ransier, A. / Chenine, A.L. / Asokan, M. / Bailer, R.T. / Bose, M. / Cagigi, A. / Cale, E.M. / Chuang, G.Y. / Darko, S. / Driscoll, J.I. / Druz, A. / Gorman, J. / Laboune, F. / Louder, M.K. / McKee, K. / Mendez, L. / Moody, M.A. / O'Sullivan, A.M. / Owen, C. / Peng, D. / Rawi, R. / Sanders-Buell, E. / Shen, C.H. / Shiakolas, A.R. / Stephens, T. / Tsybovsky, Y. / Tucker, C. / Verardi, R. / Wang, K. / Zhou, J. / Zhou, T. / Georgiou, G. / Alam, S.M. / Haynes, B.F. / Rolland, M. / Matyas, G.R. / Polonis, V.R. / McDermott, A.B. / Douek, D.C. / Shapiro, L. / Tovanabutra, S. / Michael, N.L. / Mascola, J.R. / Robb, M.L. / Kwong, P.D. / Doria-Rose, N.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mtq.cif.gz | 204.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mtq.ent.gz | 162.2 KB | Display | PDB format |
PDBx/mmJSON format | 6mtq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mtq_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 6mtq_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | 6mtq_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 6mtq_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/6mtq ftp://data.pdbj.org/pub/pdb/validation_reports/mt/6mtq | HTTPS FTP |
-Related structure data
Related structure data | 6mtoC 6mtpSC 6mtrC 6mtsC 6mttC S: Starting model for refinement 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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Unit cell |
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-Components
#1: Antibody | Mass: 23507.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24117.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
#3: Protein | Mass: 18218.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 5% PEG 400, 0.1M Magnesium sulfate, 2M Ammonium sulfate, 0.1M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Nov 17, 2017 |
Radiation | Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 18549 / % possible obs: 97.3 % / Redundancy: 2.9 % / CC1/2: 0.864 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.099 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.7→2.75 Å / Rmerge(I) obs: 0.717 / CC1/2: 0.521 / Rpim(I) all: 0.499 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MTP, VRC42.04 Resolution: 2.7→36.847 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→36.847 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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