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Yorodumi- PDB-1hzh: CRYSTAL STRUCTURE OF THE INTACT HUMAN IGG B12 WITH BROAD AND POTE... -
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-Basic information
Entry | Database: PDB / ID: 1hzh | |||||||||
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Title | CRYSTAL STRUCTURE OF THE INTACT HUMAN IGG B12 WITH BROAD AND POTENT ACTIVITY AGAINST PRIMARY HIV-1 ISOLATES: A TEMPLATE FOR HIV VACCINE DESIGN | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin / antibody / b12 | |||||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / antigen binding / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Potential therapeutics for SARS / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Saphire, E.O. / Burton, D.R. / Wilson, I.A. | |||||||||
Citation | Journal: Science / Year: 2001 Title: Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design. Authors: Saphire, E.O. / Parren, P.W. / Pantophlet, R. / Zwick, M.B. / Morris, G.M. / Rudd, P.M. / Dwek, R.A. / Stanfield, R.L. / Burton, D.R. / Wilson, I.A. | |||||||||
History |
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Remark 999 | Sequence The Genbank database sequence (AAA52919) is the correct match for the variable portion of ...Sequence The Genbank database sequence (AAA52919) is the correct match for the variable portion of the heavy chain except that the N-terminus has been changed from LEQSGAE to QVQLVQSGAE in the process of cloning from the recombinant Fab fragment to the IgG. The constant domains of the heavy chains H and K have the same sequence as all human IgG1 antibodies. The variable region of the light chain matches the Genbank database sequence (AAA52920) except that the N-terminus was changed in cloning to the IgG from ELTQAPG to EIVLTQSPG; the constant domains of the light chains L and M have the same sequence as all human kappa light chains. The authors maintain that the sequence of L and M, residue ALA 34 (residue number 35 in seqres) should be an ALA and not ARG (residue 33 -in the sequence database). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 1hzh.cif.gz | 262.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hzh.ent.gz | 215.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hzh_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1hzh_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1hzh_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 1hzh_validation.cif.gz | 74.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/1hzh ftp://data.pdbj.org/pub/pdb/validation_reports/hz/1hzh | HTTPS FTP |
-Related structure data
Related structure data | 1cbvS 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
#1: Antibody | Mass: 50473.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5, UniProt: P01857*PLUS #2: Antibody | Mass: 23707.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q8TCD0, UniProt: P01834*PLUS #3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: 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: 4.11 Å3/Da / Density % sol: 69.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: NH4SO4, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Details: Saphire, E.O., (2001) Acta Crystallogr., D57, 168. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 18, 1999 Details: 58 cm long, Pt-coated, fused silica, vertical focus |
Radiation | Monochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.65 Å / Num. obs: 187712 / % possible obs: 94.4 % / Observed criterion σ(I): -2 / Redundancy: 2.9 % / Biso Wilson estimate: 65.9 Å2 / Rsym value: 0.072 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3113 / Rsym value: 0.626 / % possible all: 95.5 |
Reflection | *PLUS Num. obs: 63686 / Num. measured all: 187712 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 95.5 % / Num. unique obs: 3113 / Num. measured obs: 8424 / Rmerge(I) obs: 0.626 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBV human Fc coordinates (unpublished) Resolution: 2.7→29.65 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 433076.48 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.44 Å2 / ksol: 0.301 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.225 / Rfactor Rfree: 0.272 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 90.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.381 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.352 |