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Yorodumi- PDB-1tji: Crystal Structure of the broadly neutralizing anti-HIV-1 antibody... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tji | ||||||
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Title | Crystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a gp41 17mer epitope | ||||||
Components |
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Keywords | Viral protein/Immune system / 2F5 / antibody / gp41 / HIV-1 / neutralizing / membrane-proximal / Viral protein-Immune system COMPLEX | ||||||
Function / homology | Function and homology information Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER METHOD / Resolution: 2.2 Å | ||||||
Authors | Ofek, G. / Tang, M. / Sambor, A. / Katinger, H. / Mascola, J.R. / Wyatt, R. / Kwong, P.D. | ||||||
Citation | Journal: J.Virol. / Year: 2004 Title: Structure and mechanistic analysis of the Anti-Human Immunodeficiency Virus type 1 antibody 2F5 in complex with its gp41 epitope Authors: Ofek, G. / Tang, M. / Sambor, A. / Katinger, H. / Mascola, J.R. / Wyatt, R. / Kwong, P.D. | ||||||
History |
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Remark 999 | SEQUENCE THERE ARE CURRENTLY NO SEQUENCE DATABASE MATCHES FOR CHAINS L AND H. CHAINS L AND H ARE ...SEQUENCE THERE ARE CURRENTLY NO SEQUENCE DATABASE MATCHES FOR CHAINS L AND H. CHAINS L AND H ARE NUMBERED IN KABAT FORMAT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tji.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tji.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 1tji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tji ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tji | HTTPS FTP |
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-Related structure data
Related structure data | 1tjgC 1tjhSC C: citing same article (ref.) S: Starting model for refinement |
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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/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 2131.364 Da / Num. of mol.: 1 / Fragment: Transmembrane Glycoprotein (residues 653-659) / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in the human immunodeficiency virus (HIV-1; Strain JRFL). References: UniProt: P04580 |
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-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23362.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: Heteromyeloma cell line fused with peripheral blood mononuclear cells Cell line (production host): CB-F7 / Production host: Cricetulus griseus (Chinese hamster) |
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#2: Antibody | Mass: 25286.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: Heteromyeloma cell line fused with peripheral blood mononuclear cells Cell line (production host): CB-F7 / Production host: Cricetulus griseus (Chinese hamster) |
-Non-polymers , 3 types, 562 molecules
#4: Chemical | #5: Chemical | ChemComp-IPA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.296 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 293 K / pH: 5.6 Details: 20% PEG 4000, 20% Isopropanol, 0.125 M NaCitrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 31, 2003 |
Radiation | Monochromator: SI (220) / 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: 32958 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.126 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.95 / Rsym value: 0.494 / % possible all: 75.5 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER METHOD Starting model: PDB ENTRY 1TJH Resolution: 2.2→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 332712.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.29 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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