4MSV |
Crystal structure of FASL and DcR3 complex |
Summary for 4MSV
| Related | 4EN0 3MHD 4J6G 4KGG 4KGQ 3K51 |
|---|---|
| Descriptor | Tumor necrosis factor receptor superfamily member 6B, Tumor necrosis factor ligand superfamily member 6, MAGNESIUM ION, ... (5 entities in total) |
| Functional Keywords | fasl, dcr3, tnf, tnfr, tnf6, structural genomics, psi-biology, new york structural genomics, research consortium, nysgrc, immunity, tnf supe cd95l, fas ligand, membrane, atoms-to-animals: the immune function network, ifn, jelly-roll fold, bind tnf receptor fas, protein structure initiative, new york structural genomics research consortium, cd95l, tnf superfamily, secreted protein, cytokine, immune system |
| Biological source | Homo sapiens (human) |
| Cellular location | Cell membrane; Single-pass type II membrane protein. Tumor necrosis factor ligand superfamily member 6, soluble form: Secreted . FasL intracellular domain: Nucleus P48023 Secreted O95407 |
| Total number of polymer chains | 2 |
| Total molecular weight | 36505.79 |
| Authors | Liu, W.,Ramagopal, U.A.,Zhan, C.,Bonanno, J.B.,Bhosle, R.C.,Nathenson, S.G.,Almo, S.C.,Atoms-to-Animals: The Immune Function Network (IFN),New York Structural Genomics Research Consortium (NYSGRC) (deposition date: 2013-09-18, release date: 2013-11-27, Last modification date: 2016-11-16) |
| Primary citation | Liu, W.,Ramagopal, U.,Cheng, H.,Bonanno, J.B.,Toro, R.,Bhosle, R.,Zhan, C.,Almo, S.C. Crystal Structure of the Complex of Human FasL and Its Decoy Receptor DcR3. Structure, 24:2016-2023, 2016 PubMed: 27806260 (PDB entries with the same primary citation) DOI: 10.1016/j.str.2016.09.009  Import into Mendeley |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
Download full validation report
More Asymmetric unit images
More Biological unit images
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (4msv.pdb1.gz [147.7 KB])
> Structural details
Entity
| Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| B | Tumor necrosis factor receptor superfamily member 6B | polymer | 174 | 19044.3 | 1 | Homo sapiens (human)@PDBj | Decoy receptor 3, DcR3, Decoy receptor for Fas ligand, M68 | |
| A | Tumor necrosis factor ligand superfamily member 6 | polymer | 152 | 17345.1 | 1 | Homo sapiens (human)@PDBj | Apoptosis antigen ligand, APTL, CD95 ligand, CD95-L, Fas antigen ligand, Fas ligand, FasL, Tumor necrosis factor ligand superfamily member 6, membrane form, Tumor necrosis factor ligand superfamily member 6, soluble form, Receptor-binding FasL ectodomain, Soluble Fas ligand, sFasL, ADAM10-processed FasL form, APL, FasL intracellular domain, FasL ICD, SPPL2A-processed FasL form, SPA | |
| MAGNESIUM ION | non-polymer | 24.3 | 1 | |||||
| GLYCEROL | non-polymer | 92.1 | 1 | |||||
| water | water | 18.0 | 63 |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 2 |
| Total molecular weight | 36389.4 | |
| Non-Polymers* | Number of molecules | 2 |
| Total molecular weight | 116.4 | |
| All* | Total molecular weight | 36505.8 |
> Experimental details
Refinement Statistics
| Experimental method: | X-RAY DIFFRACTION (2.5 Å) |
| Cell axes | 126.909 | 126.909 | 205.729 |
| Cell angles | 90.00 | 90.00 | 120.00 |
| Spacegroup | H 3 2 | ||
| Resolution limits | 48.52 - 2.50 | ||
| the highest resolution shell value | 2.561 - 2.496 | ||
| R-factor | 0.18914 | ||
| R-work | 0.18744 | ||
| the highest resolution shell value | 0.294 | ||
| R-free | 0.22075 | ||
| the highest resolution shell value | 0.390 | ||
| RMSD bond length | 0.022 | ||
| RMSD bond angle | 2.036 | ||
Data Collection Statistics
| Resolution limits | 50.00 - 2.50 |
| the highest resolution shell value | - |
| Number of reflections | 22326 |
| Rmerge_l_obs | 0.116 |
| the highest resolution shell value | 0.826 |
| Completeness | 100.0 |
| Redundancy | 7.3 |
| the highest resolution shell value | 7 |
Crystallization Conditions
| crystal ID | method | pH | pH range | temperature | unit |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 290 |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
Crystallization Reagents in Literatures*
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
Annotated Information is extracted from Literature Info*
> Functional details
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005615 | cellular_component | extracellular space |
| B | 0005887 | cellular_component | integral component of plasma membrane |
| B | 0004872 | molecular_function | receptor activity |
| B | 0005031 | molecular_function | tumor necrosis factor-activated receptor activity |
| B | 0097190 | biological_process | apoptotic signaling pathway |
| B | 0006955 | biological_process | immune response |
| B | 0006954 | biological_process | inflammatory response |
| B | 0007275 | biological_process | multicellular organism development |
| B | 0043066 | biological_process | negative regulation of apoptotic process |
| B | 0042127 | biological_process | regulation of cell proliferation |
| B | 0032496 | biological_process | response to lipopolysaccharide |
| B | 0033209 | biological_process | tumor necrosis factor-mediated signaling pathway |
| A | 0005901 | cellular_component | caveola |
| A | 0060205 | cellular_component | cytoplasmic vesicle lumen |
| A | 0009897 | cellular_component | external side of plasma membrane |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005615 | cellular_component | extracellular space |
| A | 0005887 | cellular_component | integral component of plasma membrane |
| A | 0043202 | cellular_component | lysosomal lumen |
| A | 0005634 | cellular_component | nucleus |
| A | 0048471 | cellular_component | perinuclear region of cytoplasm |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0005125 | molecular_function | cytokine activity |
| A | 0005123 | molecular_function | death receptor binding |
| A | 0005102 | molecular_function | receptor binding |
| A | 0005164 | molecular_function | tumor necrosis factor receptor binding |
| A | 0006919 | biological_process | activation of cysteine-type endopeptidase activity involved in apoptotic process |
| A | 0097296 | biological_process | activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway |
| A | 0006915 | biological_process | apoptotic process |
| A | 0097190 | biological_process | apoptotic signaling pathway |
| A | 1903514 | biological_process | release of sequestered calcium ion into cytosol by endoplasmic reticulum |
| A | 0007267 | biological_process | cell-cell signaling |
| A | 0030644 | biological_process | cellular chloride ion homeostasis |
| A | 0048388 | biological_process | endosomal lumen acidification |
| A | 0097191 | biological_process | extrinsic apoptotic signaling pathway |
| A | 0008625 | biological_process | extrinsic apoptotic signaling pathway via death domain receptors |
| A | 0006955 | biological_process | immune response |
| A | 0006925 | biological_process | inflammatory cell apoptotic process |
| A | 0070266 | biological_process | necroptotic process |
| A | 0097527 | biological_process | necroptotic signaling pathway |
| A | 0016525 | biological_process | negative regulation of angiogenesis |
| A | 1902042 | biological_process | negative regulation of extrinsic apoptotic signaling pathway via death domain receptors |
| A | 0000122 | biological_process | negative regulation of transcription from RNA polymerase II promoter |
| A | 0043065 | biological_process | positive regulation of apoptotic process |
| A | 0008284 | biological_process | positive regulation of cell proliferation |
| A | 2000353 | biological_process | positive regulation of endothelial cell apoptotic process |
| A | 0045742 | biological_process | positive regulation of epidermal growth factor receptor signaling pathway |
| A | 0043123 | biological_process | positive regulation of I-kappaB kinase/NF-kappaB signaling |
| A | 0043525 | biological_process | positive regulation of neuron apoptotic process |
| A | 1902041 | biological_process | regulation of extrinsic apoptotic signaling pathway via death domain receptors |
| A | 0070848 | biological_process | response to growth factor |
| A | 0032496 | biological_process | response to lipopolysaccharide |
| A | 0046666 | biological_process | retinal cell programmed cell death |
| A | 0007165 | biological_process | signal transduction |
| A | 0070231 | biological_process | T cell apoptotic process |
| A | 0006351 | biological_process | transcription, DNA-templated |
Functional Information from PDB Data
| site_id | Number of Residues | Details | ||||||||||||||
| AC1 | 6 | BINDING SITE FOR RESIDUE MG B 301 | ||||||||||||||
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| AC2 | 6 | BINDING SITE FOR RESIDUE GOL A 301 | ||||||||||||||
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Functional Information from PDB atom coordinates for the "HETATM" binding sites
| site_id | Number of Residues | Details | |||||||||||||||
| GOL_4msv_A_301 | 10 | GLYCEROL binding site | |||||||||||||||
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Functional Information from PROSITE/UniProt
| site_id | Number of Residues | Details |
Functional Information from SwissProt/UniProt
| site_id | Number of Residues | Details |
Catalytic Information from CSA
| site_id | Number of Residues | Details |
> Sequence Neighbor
> Downloads
Resources
| File format | File name (file size) | |
| PDB | all | pdb4msv.ent.gz (56.99 KB) |
| all (no-compress) | pdb4msv.ent (242.84 KB) | |
| header only | pdb4msv.ent.gz (8.09 KB) | |
| PDBx/mmCIF | 4msv.cif.gz (73.07 KB) | |
| PDBML | all | 4msv.xml.gz (108.99 KB) |
| no-atom | 4msv-noatom.xml.gz (22.88 KB) | |
| ext-atom | 4msv-extatom.xml.gz (57.76 KB) | |
| PDBMLplus | all | 4msv-plus.xml.gz (111.94 KB) |
| no-atom | 4msv-plus-noatom.xml.gz (25.83 KB) | |
| add only | 4msv-add.xml.gz (2.95 KB) | |
| RDF | 4msv.rdf.gz (43.14 KB) | |
| Structure factors | r4msvsf.ent.gz (595.09 KB) | |
| Biological unit (PDB format) | 4msv.pdb1.gz (147.7 KB) (B,A) *author and software defined assembly, 6 molecule(s) (hexameric) | |
| Validation reports | 4msv_validation.pdf.gz (430.29 KB) | |
| PDF-full | 4msv_full_validation.pdf.gz (432.52 KB) | |
| XML | 4msv_validation.xml.gz (13.12 KB) | |
| PNG | 4msv_multipercentile_validation.png.gz (140.39 KB) | |
| SVG | 4msv_multipercentile_validation.svg.gz (927 B) | |
| Sequence (fasta) | 4msv_seq.txt | |
