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Yorodumi- PDB-5t29: Crystal structure of 10E8 Fab light chain mutant3, against the MP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t29 | |||||||||
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Title | Crystal structure of 10E8 Fab light chain mutant3, against the MPER region of the HIV-1 Env, in complex with the MPER epitope scaffold T117v2 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 GP41 MPER / 10E8 FAB / LIPID MEMBRANE | |||||||||
Function / homology | Function and homology information Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | |||||||||
Authors | Irimia, A. / Wilson, I.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: PLoS Pathog. / Year: 2017 Title: Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design. Authors: Irimia, A. / Serra, A.M. / Sarkar, A. / Jacak, R. / Kalyuzhniy, O. / Sok, D. / Saye-Francisco, K.L. / Schiffner, T. / Tingle, R. / Kubitz, M. / Adachi, Y. / Stanfield, R.L. / Deller, M.C. / ...Authors: Irimia, A. / Serra, A.M. / Sarkar, A. / Jacak, R. / Kalyuzhniy, O. / Sok, D. / Saye-Francisco, K.L. / Schiffner, T. / Tingle, R. / Kubitz, M. / Adachi, Y. / Stanfield, R.L. / Deller, M.C. / Burton, D.R. / Schief, W.R. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t29.cif.gz | 246.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t29.ent.gz | 197.8 KB | Display | PDB format |
PDBx/mmJSON format | 5t29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t29_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
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Full document | 5t29_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 5t29_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 5t29_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/5t29 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/5t29 | HTTPS FTP |
-Related structure data
Related structure data | 5sy8C 5t5bC 5t6lC 5t80C 5t85C 5tfwC 3lf6S 4g6fS 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
-Protein , 1 types, 1 molecules O
#3: Protein | Mass: 18643.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: PET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 STAR |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 25447.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-15*05 / Plasmid: PHCMV3 / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 22934.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV3-19*01 / Plasmid: PHCMV3 / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) |
-Non-polymers , 3 types, 146 molecules
#4: Chemical | ChemComp-PO4 / |
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#5: Chemical | ChemComp-PEG / |
#6: 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: 2.44 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M PO4-citrate pH 4.2, 40% PEG 600 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.025→36.56 Å / Num. obs: 36193 / % possible obs: 92.1 % / Redundancy: 2.5 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.081 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.5 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G6F, 3LF6 Resolution: 2.03→36.56 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.45 Details: The ligand named PEG is a fragment of polyethylene glycol 600 from the crystallization buffer
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→36.56 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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