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Yorodumi- PDB-5cin: Crystal Structure of non-neutralizing version of 4E10 (DeltaLoop)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cin | |||||||||
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Title | Crystal Structure of non-neutralizing version of 4E10 (DeltaLoop) with epitope bound | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / BROADLY NEUTRALIZING ANTIBODY / RECOMBINANT FAB / ENV-PEPTIDE / HIV-1 / EPITOPE | |||||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 | Homo sapiens (human) Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Caaveiro, J.M.M. / Rujas, E. / Nieva, J.L. / Tsumoto, K. | |||||||||
Funding support | United States, Japan, 2items
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Citation | Journal: J.Virol. / Year: 2015 Title: Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10 Authors: Rujas, E. / Gulzar, N. / Morante, K. / Tsumoto, K. / Scott, J.K. / Nieva, J.L. / Caaveiro, J.M.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cin.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cin.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 5cin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cin_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
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Full document | 5cin_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 5cin_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 5cin_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/5cin ftp://data.pdbj.org/pub/pdb/validation_reports/ci/5cin | HTTPS FTP |
-Related structure data
Related structure data | 5cilC 5cipC 4wy7S 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: 2187.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 23334.219 Da / Num. of mol.: 1 / Mutation: W100S, W100(B)null, L100(C)null Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle |
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#2: Antibody | Mass: 23106.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle |
-Non-polymers , 3 types, 589 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.99 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM TRSI-HCl, 200mM Ammonium acetate, 30% PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36.1 Å / Num. obs: 59239 / % possible obs: 98.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.3 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WY7 Resolution: 1.7→36.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.616 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.702 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→36.1 Å
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Refine LS restraints |
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