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Yorodumi- PDB-2ls8: Solution structure of human C-type lectin domain family 4 member D -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ls8 | ||||||
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Title | Solution structure of human C-type lectin domain family 4 member D | ||||||
Components | C-type lectin domain family 4 member D | ||||||
Keywords | IMMUNE SYSTEM / STRUCTURAL GENOMICS / New York Structural Genomics Research Consortium / NYSGRC / PSI-Biology | ||||||
Function / homology | Function and homology information positive regulation of myeloid dendritic cell activation / T cell differentiation involved in immune response / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor activity / immunoglobulin receptor binding / Dectin-2 family / mannose binding / tertiary granule membrane / ficolin-1-rich granule membrane ...positive regulation of myeloid dendritic cell activation / T cell differentiation involved in immune response / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor activity / immunoglobulin receptor binding / Dectin-2 family / mannose binding / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / carbohydrate binding / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / defense response to bacterium / external side of plasma membrane / Neutrophil degranulation / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulating annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Harris, R. / Gaudette, J. / Bandaranayake, A.D. / Banu, R. / Bonanno, J.B. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chaparro, R. ...Harris, R. / Gaudette, J. / Bandaranayake, A.D. / Banu, R. / Bonanno, J.B. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chaparro, R. / Evans, B. / Garforth, S. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Lim, S. / Love, J. / Matikainen, B. / Patel, H. / Seidel, R.D. / Smith, B. / Stead, M. / Girvin, M.E. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Solution structure of human C-type lectin domain family 4 member D Authors: Harris, R. / Gaudette, J. / Bandaranayake, A.D. / Banu, R. / Bonanno, J.B. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chaparro, R. / Evans, B. / Garforth, S. / Gizzi, A. / ...Authors: Harris, R. / Gaudette, J. / Bandaranayake, A.D. / Banu, R. / Bonanno, J.B. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chaparro, R. / Evans, B. / Garforth, S. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Lim, S. / Love, J. / Matikainen, B. / Patel, H. / Seidel, R.D. / Smith, B. / Stead, M. / Girvin, M.E. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ls8.cif.gz | 881.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ls8.ent.gz | 757.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ls8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/2ls8 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/2ls8 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18610.725 Da / Num. of mol.: 1 / Fragment: UNP residues 84-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4D, CLECSF8, MCL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8WXI8 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 10 / pH: 4.5 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulating annealing / Software ordinal: 1 / Details: Refinement in a box of water | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2310 / NOE intraresidue total count: 668 / NOE long range total count: 671 / NOE medium range total count: 349 / NOE sequential total count: 558 / Disulfide bond constraints total count: 9 / Hydrogen bond constraints total count: 72 / Protein other angle constraints total count: 6 / Protein phi angle constraints total count: 81 / Protein psi angle constraints total count: 80 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: 20 structures for lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |