+Open data
-Basic information
Entry | Database: PDB / ID: 5l0p | ||||||
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Title | Symmetry-based assembly of a two-dimensional protein lattice | ||||||
Components | Transcription factor ETV6, Transcription factor ETV6, Transcription factor ETV6, Ferric uptake regulation protein chimera | ||||||
Keywords | DE NOVO PROTEIN / design / lattice / 2D / assembly | ||||||
Function / homology | Function and homology information Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Faham, S. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Symmetry based assembly of a 2 dimensional protein lattice. Authors: Poulos, S. / Agah, S. / Jallah, N. / Faham, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l0p.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l0p.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 5l0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l0p_validation.pdf.gz | 426 KB | Display | wwPDB validaton report |
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Full document | 5l0p_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 5l0p_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 5l0p_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/5l0p ftp://data.pdbj.org/pub/pdb/validation_reports/l0/5l0p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40559.727 Da / Num. of mol.: 1 Fragment: 3 x TelSAM (UNP residues 47-124) + FUR (UNP residues 3-83) with connecting linkers Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: ETV6, TEL, TEL1, fur / Production host: Escherichia coli (E. coli) / References: UniProt: P41212, UniProt: P45599 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.99 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, pH 8.0, 3.5 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 20782 / % possible obs: 93.9 % / Redundancy: 4.8 % / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.283 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1JI7 & 2FU4 Resolution: 2.3→50 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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LS refinement shell | Resolution: 2.3→2.36 Å /
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