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- PDB-7ssc: TRL345 lineage ancestor I8 Fab bound to an HCMV gB-derived peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ssc | ||||||
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Title | TRL345 lineage ancestor I8 Fab bound to an HCMV gB-derived peptide | ||||||
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![]() | IMMUNE SYSTEM/VIRAL PROTEIN / immunoglobulin / fusion protein / HCMV / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | ![]() host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Sponholtz, M.R. / McLellan, J.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A single, improbable B cell receptor mutation confers potent neutralization against cytomegalovirus. Authors: Jenks, J.A. / Amin, S. / Sponholtz, M.R. / Kumar, A. / Wrapp, D. / Venkatayogi, S. / Tu, J.J. / Karthigeyan, K. / Valencia, S.M. / Connors, M. / Harnois, M.J. / Hora, B. / Rochat, E. / ...Authors: Jenks, J.A. / Amin, S. / Sponholtz, M.R. / Kumar, A. / Wrapp, D. / Venkatayogi, S. / Tu, J.J. / Karthigeyan, K. / Valencia, S.M. / Connors, M. / Harnois, M.J. / Hora, B. / Rochat, E. / McLellan, J.S. / Wiehe, K. / Permar, S.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.3 KB | Display | ![]() |
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PDB format | ![]() | 154.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6uoeS ![]() 6zfoS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23568.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23315.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein/peptide | Mass: 1783.959 Da / Num. of mol.: 1 / Fragment: antigenic domain-2 (UNP residues 65-79) / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M magnesium chloride hexahydrate, 25% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 18, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→66.88 Å / Num. obs: 48200 / % possible obs: 97.9 % / Redundancy: 6 % / Biso Wilson estimate: 13.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.028 / Rrim(I) all: 0.07 / Net I/σ(I): 17.2 / Num. measured all: 287280 / Scaling rejects: 175 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6UOE, 6ZFO Resolution: 1.8→56.39 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.62 Å2 / Biso mean: 18.1973 Å2 / Biso min: 4.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→56.39 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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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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