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- PDB-1tjh: Crystal Structure of the broadly neutralizing anti-HIV-1 antibody... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tjh | ||||||
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Title | Crystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a gp41 11mer epitope | ||||||
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![]() | Viral protein/Immune system / 2F5 / antibody / gp41 / HIV-1 / neutralizing / membrane-proximal / Viral protein-Immune system COMPLEX | ||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ofek, G. / Tang, M. / Sambor, A. / Katinger, H. / Mascola, J.R. / Wyatt, R. / Kwong, P.D. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.6 KB | Display | ![]() |
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PDB format | ![]() | 88.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.2 KB | Display | ![]() |
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Full document | ![]() | 480.1 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 37.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tjgSC ![]() 1tjiC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 1398.649 Da / Num. of mol.: 1 / Fragment: Transmembrane Glycoprotein (residues 659-669) / 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.) ![]() Description: Heteromyeloma cell line CB-F7 fused with peripheral blood mononuclear cells Cell line (production host): CB-F7 / Production host: ![]() ![]() |
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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.) ![]() Description: Heteromyeloma cell line CB-F7 fused with peripheral blood mononuclear cells Cell line (production host): CB-F7 / Production host: ![]() ![]() |
-Non-polymers , 3 types, 494 molecules ![](data/chem/img/IPA.gif)
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#4: Chemical | ChemComp-IPA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.327 Å3/Da / Density % sol: 62.3 % |
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Crystal grow | Temperature: 293 K / pH: 5.6 Details: 20% PEG 4000, 20% Isopropanol, 0.1 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 4, 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: 2.1→20 Å / Num. obs: 45339 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.084 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.57 / Rsym value: 0.385 / % possible all: 72.4 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER METHOD Starting model: PDB ENTRY 1TJG Resolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 236355.73 / 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: 84.48 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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