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Yorodumi- PDB-6mpx: Twelve chloride ions induce formation and stabilize the NC1 hexam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mpx | |||||||||
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Title | Twelve chloride ions induce formation and stabilize the NC1 hexamer of collagen IV assembled from transition state trimers | |||||||||
Components | fusion protein of non-collagenous domains of collagen type IV | |||||||||
Keywords | STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information retinal blood vessel morphogenesis / collagen type IV trimer / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / glomerular basement membrane development / Collagen chain trimerization / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization ...retinal blood vessel morphogenesis / collagen type IV trimer / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / glomerular basement membrane development / Collagen chain trimerization / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization / extracellular matrix structural constituent conferring tensile strength / 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 / Assembly of collagen fibrils and other multimeric structures / extracellular matrix structural constituent / neuromuscular junction development / branching involved in blood vessel morphogenesis / 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 / negative regulation of angiogenesis / extracellular matrix organization / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Bauer, R. / Boudko, S.P. / Hudson, B.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: A chloride ring is an ancient evolutionary innovation mediating the assembly of the collagen IV scaffold of basement membranes. Authors: Pedchenko, V. / Bauer, R. / Pokidysheva, E.N. / Al-Shaer, A. / Forde, N.R. / Fidler, A.L. / Hudson, B.G. / Boudko, S.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mpx.cif.gz | 290 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mpx.ent.gz | 228.8 KB | Display | PDB format |
PDBx/mmJSON format | 6mpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mpx_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 6mpx_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6mpx_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 6mpx_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/6mpx ftp://data.pdbj.org/pub/pdb/validation_reports/mp/6mpx | HTTPS FTP |
-Related structure data
Related structure data | 1li1S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 76309.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A1, COL4A2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02462, UniProt: P08572 |
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-Non-polymers , 7 types, 461 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-P6G / | #7: Chemical | ChemComp-GOL / #8: 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: 2.55 Å3/Da / Density % sol: 51.75 % / Mosaicity: 0.63 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: .085 M HEPES (pH 7.5), 1.68 M ammonium sulfate, and 1.5% (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→85.673 Å / Num. all: 62515 / Num. obs: 62515 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 28.9 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.129 / Rsym value: 0.122 / Net I/av σ(I): 3.6 / Net I/σ(I): 9.5 / Num. measured all: 558146 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LI1 Resolution: 1.9→39.893 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.23 Å2 / Biso mean: 35.159 Å2 / Biso min: 17.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→39.893 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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Refinement TLS params. | Method: refined / Origin x: 20.6292 Å / Origin y: 24.2647 Å / Origin z: 17.6963 Å
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Refinement TLS group | Selection details: (chain A and resseq 4:676) |