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Yorodumi- PDB-8txn: Adaptive mechanism of collagen IV scaffold assembly in Drosophila... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8txn | |||||||||
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Title | Adaptive mechanism of collagen IV scaffold assembly in Drosophila: crystal structure of recombinant NC1 hexamer | |||||||||
Components | Collagen alpha-1(IV) chain, Collagen IV - chain Viking, Collagen alpha-1(IV) chain | |||||||||
Keywords | STRUCTURAL PROTEIN / collagen IV / trimerization domain / hexamer assembly / basement membrane | |||||||||
Function / homology | Function and homology information oviduct morphogenesis / post-embryonic digestive tract morphogenesis / Collagen degradation / Collagen biosynthesis and modifying enzymes / Assembly of collagen fibrils and other multimeric structures / Collagen chain trimerization / anterior Malpighian tubule development / Malpighian tubule morphogenesis / collagen type IV trimer / somatic muscle development ...oviduct morphogenesis / post-embryonic digestive tract morphogenesis / Collagen degradation / Collagen biosynthesis and modifying enzymes / Assembly of collagen fibrils and other multimeric structures / Collagen chain trimerization / anterior Malpighian tubule development / Malpighian tubule morphogenesis / collagen type IV trimer / somatic muscle development / dorsal closure / intestinal epithelial structure maintenance / extracellular matrix structural constituent conferring tensile strength / basement membrane organization / cardiac muscle cell development / extracellular matrix structural constituent / basement membrane / extracellular matrix organization / collagen-containing extracellular matrix / extracellular space / membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Boudko, S.P. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Collagen IV of basement membranes: IV. Adaptive mechanism of collagen IV scaffold assembly in Drosophila. Authors: Summers, J.A. / Yarbrough, M. / Liu, M. / McDonald, W.H. / Hudson, B.G. / Pastor-Pareja, J.C. / 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 | 8txn.cif.gz | 650.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8txn.ent.gz | 469.1 KB | Display | PDB format |
PDBx/mmJSON format | 8txn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/8txn ftp://data.pdbj.org/pub/pdb/validation_reports/tx/8txn | HTTPS FTP |
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-Related structure data
Related structure data | 8tysC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 79694.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: residues 1550-1779 of the alpha-1(IV) chain, follwed by residues 1510-1739 of the Viking chain, followed by residues 1550-1779 of the alpha-1(IV) chain Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: Col4a1, Cg25C, DCg1, CG4145, vkg, 1209, 6072, alpha(IV)2/vkg, col4a2, ColIV, colIV, ColIValpha2, Coll IV, Coll IValpha2, coll-IV, coll. IV, collagen-IV, CT25584, DmColA2, Dmel\CG16858, l(2) ...Gene: Col4a1, Cg25C, DCg1, CG4145, vkg, 1209, 6072, alpha(IV)2/vkg, col4a2, ColIV, colIV, ColIValpha2, Coll IV, Coll IValpha2, coll-IV, coll. IV, collagen-IV, CT25584, DmColA2, Dmel\CG16858, l(2)01209, veg, Vkg, VkgC, CG16858, Dmel_CG16858, Col4a1 Plasmid: pcDNA-CVC / Cell line (production host): expiCHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08120, UniProt: Q9VMV5 |
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-Non-polymers , 9 types, 885 molecules
#2: Chemical | ChemComp-PGE / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Chemical | #9: Chemical | ChemComp-PO4 / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 1.93 Å3/Da / Density % sol: 36.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Na/K phosphate, 0.2 M sodium chloride, and 26 % (w/v) PEG 1,000 |
-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: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→52.05 Å / Num. obs: 114327 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.092 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 11 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 5634 / Rrim(I) all: 0.589 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→51.69 Å / SU ML: 0.1357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.46 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→51.69 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -46.1722433371 Å / Origin y: 5.28789600051 Å / Origin z: -0.777609654235 Å
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Refinement TLS group | Selection details: all |