[English] 日本語
Yorodumi- PDB-6cbp: Crystal structure of the single chain variable fragment of the DH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cbp | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the single chain variable fragment of the DH270.6 bnAb in complex with the Man9-V3 glycopeptide | ||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||
Keywords | IMMUNE SYSTEM / FAB fragment / HIV-1 / antibody / glycopeptide | ||||||||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å | ||||||||||||||||||||||||
Authors | Fera, D. / Harrison, S.C. | ||||||||||||||||||||||||
Funding support | United States, 7items
| ||||||||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: HIV envelope V3 region mimic embodies key features of a broadly neutralizing antibody lineage epitope. Authors: Fera, D. / Lee, M.S. / Wiehe, K. / Meyerhoff, R.R. / Piai, A. / Bonsignori, M. / Aussedat, B. / Walkowicz, W.E. / Ton, T. / Zhou, J.O. / Danishefsky, S. / Haynes, B.F. / Harrison, S.C. | ||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6cbp.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6cbp.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 6cbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cbp_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6cbp_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6cbp_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 6cbp_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/6cbp ftp://data.pdbj.org/pub/pdb/validation_reports/cb/6cbp | HTTPS FTP |
-Related structure data
Related structure data | 6cbjC 5tqaS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein/peptide / Antibody / Non-polymers , 3 types, 97 molecules PA
#1: Protein/peptide | Mass: 3368.745 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q74448 |
---|---|
#2: Antibody | Mass: 27297.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#7: Water | ChemComp-HOH / |
-Sugars , 4 types, 4 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 |
---|---|
#4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-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 |
#5: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose Source method: isolated from a genetically manipulated source |
#6: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.36 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 30% PEG8000, 10 mM CHES, 1 M sodium chloride, pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97925 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2016 |
Radiation | Monochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→60.141 Å / Num. obs: 15878 / % possible obs: 95.09 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.31 Å2 / CC1/2: 0.982 / Net I/σ(I): 7.65 |
Reflection shell | Resolution: 2.17→2.248 Å / Num. unique obs: 5929 / CC1/2: 0.417 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5TQA Resolution: 2.17→60.141 Å / FOM work R set: 0.7661 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.27 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.13 Å2 / Biso mean: 39.92 Å2 / Biso min: 16.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.17→60.141 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 12.8754 Å / Origin y: -21.8135 Å / Origin z: -16.5555 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|