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- PDB-4r4f: Crystal structure of non-neutralizing, A32-like antibody 2.2c in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r4f | ||||||
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Title | Crystal structure of non-neutralizing, A32-like antibody 2.2c in complex with HIV-1 YU2 gp120 | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM/INHIBITOR / HIV-1 attachment protein / Membrane / VIRAL PROTEIN-IMMUNE SYSTEM-INHIBITOR complex | ||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Acharya, P. / Kwong, P.D. | ||||||
![]() | ![]() Title: Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection. Authors: Acharya, P. / Tolbert, W.D. / Gohain, N. / Wu, X. / Yu, L. / Liu, T. / Huang, W. / Huang, C.C. / Kwon, Y.D. / Louder, R.K. / Luongo, T.S. / McLellan, J.S. / Pancera, M. / Yang, Y. / Zhang, B. ...Authors: Acharya, P. / Tolbert, W.D. / Gohain, N. / Wu, X. / Yu, L. / Liu, T. / Huang, W. / Huang, C.C. / Kwon, Y.D. / Louder, R.K. / Luongo, T.S. / McLellan, J.S. / Pancera, M. / Yang, Y. / Zhang, B. / Flinko, R. / Foulke, J.S. / Sajadi, M.M. / Kamin-Lewis, R. / Robinson, J.E. / Martin, L. / Kwong, P.D. / Guan, Y. / DeVico, A.L. / Lewis, G.K. / Pazgier, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 340.4 KB | Display | ![]() |
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PDB format | ![]() | 280.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 512.9 KB | Display | ![]() |
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Full document | ![]() | 539.7 KB | Display | |
Data in XML | ![]() | 33.8 KB | Display | |
Data in CIF | ![]() | 44.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h8wC ![]() 4r4bC ![]() 4r4hC ![]() 4r4nC ![]() 4jzzS C: citing same article ( S: Starting model for refinement |
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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
-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 22839.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Antibody | Mass: 23576.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein / Protein/peptide / Sugars , 3 types, 10 molecules AR

#1: Protein | Mass: 41695.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#4: Protein/peptide | |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 5 molecules 


#6: Chemical | #7: Chemical | |
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-Details
Compound details | THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) ...THE CD4-MIMETIC MINIPROTEI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 70.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% MPD, 1.5 M lithium sulfate and 100 mM Imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 11, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. all: 19484 / Num. obs: 16141 / % possible obs: 85.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2 / % possible all: 59.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JZZ Resolution: 3.514→35.754 Å / SU ML: 0.69 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 43.05 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.514→35.754 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | S33: -0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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