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Yorodumi- PDB-2xra: crystal structure of the HK20 Fab in complex with a gp41 mimetic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xra | ||||||
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Title | crystal structure of the HK20 Fab in complex with a gp41 mimetic 5- Helix | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIBODY / MONOCLONAL CELLS / NEUTRALIZATION TESTS | ||||||
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 | SYNTHETIC CONSTRUCT (others) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Sabin, C. / Corti, D. / Buzon, V. / Seaman, M.S. / Lutje Hulsik, D. / Hinz, A. / Vanzetta, F. / Agatic, G. / Silacci, C. / Langedijk, J.P.M. ...Sabin, C. / Corti, D. / Buzon, V. / Seaman, M.S. / Lutje Hulsik, D. / Hinz, A. / Vanzetta, F. / Agatic, G. / Silacci, C. / Langedijk, J.P.M. / Mainetti, L. / Scarlatti, G. / Sallusto, F. / Weiss, R. / Lanzavecchia, A. / Weissenhorn, W. | ||||||
Citation | Journal: PLoS Pathog. / Year: 2010 Title: Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41. Authors: Sabin, C. / Corti, D. / Buzon, V. / Seaman, M.S. / Lutje Hulsik, D. / Hinz, A. / Vanzetta, F. / Agatic, G. / Silacci, C. / Mainetti, L. / Scarlatti, G. / Sallusto, F. / Weiss, R. / ...Authors: Sabin, C. / Corti, D. / Buzon, V. / Seaman, M.S. / Lutje Hulsik, D. / Hinz, A. / Vanzetta, F. / Agatic, G. / Silacci, C. / Mainetti, L. / Scarlatti, G. / Sallusto, F. / Weiss, R. / Lanzavecchia, A. / Weissenhorn, W. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Structural Basis for HIV-1 Neutralization by a Gp41 Fusion Intermediate-Directed Antibody. Authors: Luftig, M.A. / Mattu, M. / Di Giovine, P. / Geleziunas, R. / Hrin, R. / Barbato, G. / Bianchi, E. / Miller, M.D. / Pessi, A. / Carfi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xra.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xra.ent.gz | 106.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xra_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 2xra_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 2xra_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 2xra_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/2xra ftp://data.pdbj.org/pub/pdb/validation_reports/xr/2xra | HTTPS FTP |
-Related structure data
Related structure data | 2cmrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 25721.725 Da / Num. of mol.: 1 Fragment: 5-HELIX INNER-CORE MIMETIC COMPRISED OF REPEATS OF RESIDUES 543-582 AND 625-662 Source method: isolated from a genetically manipulated source Details: SEQUENCE DERIVED FROM UNIPROT AC P04578 WHERE THREE REGIONS EACH EQUIVALENT TO AA 543-582 ARE INTERSPERSED BY TWO DIFFERENT REGIONS (EACH EQUIVALENT TO AA 625-662). LINKERS GGSGG AND GSSGG ...Details: SEQUENCE DERIVED FROM UNIPROT AC P04578 WHERE THREE REGIONS EACH EQUIVALENT TO AA 543-582 ARE INTERSPERSED BY TWO DIFFERENT REGIONS (EACH EQUIVALENT TO AA 625-662). LINKERS GGSGG AND GSSGG JOIN THE REGIONS AND ALTERNATE STARTING WITH GGSGG. A Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI BL21(DE3) / Variant (production host): Gold / References: UniProt: P04578 |
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#2: Antibody | Mass: 23609.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: MEMORY B-LYMPHOCYTE / Tissue: BLOOD |
#3: Antibody | Mass: 23630.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: MEMORY B-LYMPHOCYTE / Tissue: BLOOD |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.05 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5, 0.2 M AMMONIUM SULPHATE, 25% PEG 3350 (W/V) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9765 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→37 Å / Num. obs: 28254 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / % possible all: 89.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CMR Resolution: 2.3→37.63 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.729 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED LOOPS REGIONS OF GP41-5HB WERE NOT MODELED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.977 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→37.63 Å
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Refine LS restraints |
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