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Yorodumi- PDB-1li1: The 1.9-A crystal structure of the noncollagenous (NC1) domain of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1li1 | ||||||
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Title | The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / basement membrane / collagen IV / NC1 domain / covalent cross-link / protein-protein interaction | ||||||
Function / homology | Function and homology information collagen type IV trimer / retinal blood vessel morphogenesis / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization ...collagen type IV trimer / retinal blood vessel morphogenesis / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Laminin interactions / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / NCAM1 interactions / blood vessel morphogenesis / Scavenging by Class A Receptors / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / branching involved in blood vessel morphogenesis / neuromuscular junction development / endodermal cell differentiation / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / epithelial cell differentiation / extracellular matrix organization / negative regulation of angiogenesis / response to activity / cellular response to amino acid stimulus / brain development / angiogenesis / collagen-containing extracellular matrix / molecular adaptor activity / endoplasmic reticulum lumen / DNA-templated transcription / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Than, M.E. / Henrich, S. / Huber, R. / Ries, A. / Mann, K. / Kuhn, K. / Timpl, R. / Bourenkov, G.P. / Bartunik, H.D. / Bode, W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link. Authors: Than, M.E. / Henrich, S. / Huber, R. / Ries, A. / Mann, K. / Kuhn, K. / Timpl, R. / Bourenkov, G.P. / Bartunik, H.D. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1li1.cif.gz | 286.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1li1.ent.gz | 241 KB | Display | PDB format |
PDBx/mmJSON format | 1li1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/1li1 ftp://data.pdbj.org/pub/pdb/validation_reports/li/1li1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological relevant hexamer [alpha 1(IV)]4, [alpha 2(IV)]2 corresponds to the asymmetric unit of this pdb entry. |
-Components
#1: Protein | Mass: 25356.871 Da / Num. of mol.: 4 / Fragment: noncollagenous domain 1 / Source method: isolated from a natural source / Details: placenta / Source: (natural) Homo sapiens (human) / References: UniProt: P02462 #2: Protein | Mass: 25114.551 Da / Num. of mol.: 2 / Fragment: noncollagenous domain 1 / Source method: isolated from a natural source / Details: placenta / Source: (natural) Homo sapiens (human) / References: UniProt: P08572 #3: Chemical | ChemComp-ACT / #4: 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: 3.47 Å3/Da / Density % sol: 64.57 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: MES, sodium acetate, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / PH range low: 7.5 / PH range high: 7.1 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 27, 2001 / Details: mirror |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.95 Å / Num. obs: 155867 / % possible obs: 96.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.9 Å2 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 97.6 |
Reflection | *PLUS Num. measured all: 441349 / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 97.6 % / Rmerge(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→19.95 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.4937 Å2 / ksol: 0.351246 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.277 |