[English] 日本語
Yorodumi- PDB-6mnr: Rhesus macaque anti-HIV V3 antibody DH753 with gp120 V3 ZAM18 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mnr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Rhesus macaque anti-HIV V3 antibody DH753 with gp120 V3 ZAM18 peptide | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / HIV-1 gp120 V3 antibody | |||||||||
Function / homology | Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / viral envelope / Immunoglobulin-like / Sandwich / Mainly Beta / Envelope glycoprotein Function and homology information | |||||||||
Biological species | Macaca mulatta (Rhesus monkey) Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å | |||||||||
Authors | Nicely, N.I. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Difficult-to-neutralize global HIV-1 isolates are neutralized by antibodies targeting open envelope conformations. Authors: Han, Q. / Jones, J.A. / Nicely, N.I. / Reed, R.K. / Shen, X. / Mansouri, K. / Louder, M. / Trama, A.M. / Alam, S.M. / Edwards, R.J. / Bonsignori, M. / Tomaras, G.D. / Korber, B. / ...Authors: Han, Q. / Jones, J.A. / Nicely, N.I. / Reed, R.K. / Shen, X. / Mansouri, K. / Louder, M. / Trama, A.M. / Alam, S.M. / Edwards, R.J. / Bonsignori, M. / Tomaras, G.D. / Korber, B. / Montefiori, D.C. / Mascola, J.R. / Seaman, M.S. / Haynes, B.F. / Saunders, K.O. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6mnr.cif.gz | 186.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6mnr.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 6mnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mnr_validation.pdf.gz | 456.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6mnr_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 6mnr_validation.xml.gz | 18 KB | Display | |
Data in CIF | 6mnr_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/6mnr ftp://data.pdbj.org/pub/pdb/validation_reports/mn/6mnr | HTTPS FTP |
-Related structure data
Related structure data | 6mnqC 6mnsC 5iieS 5jr1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein/peptide , 1 types, 1 molecules P
#1: Protein/peptide | Mass: 2394.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: A0A0K0KAD3 |
---|
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24036.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) |
---|---|
#3: Antibody | Mass: 22795.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) |
-Non-polymers , 3 types, 88 molecules
#4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium sulfate decahydrate, 20% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 23370 / % possible obs: 100 % / Redundancy: 7.9 % / Rpim(I) all: 0.035 / Rsym value: 0.073 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1154 / Rpim(I) all: 0.237 / Rsym value: 0.525 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBs 5JR1, 5IIE Resolution: 2.201→43.41 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.58
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.201→43.41 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|