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- PDB-3ldb: Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment. -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ldb | ||||||
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Title | Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment. | ||||||
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![]() | IMMUNE SYSTEM / JMJ6D / ALPHA-KETOGLUTARATE / Fab Fragments | ||||||
Function / homology | ![]() peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine / histone H3R2 demethylase activity / peptidyl-lysine 5-dioxygenase activity / histone H4R3 demethylase activity / protein demethylase activity / recognition of apoptotic cell / negative regulation of protein homooligomerization / oxidative RNA demethylation / oxidative RNA demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor ...peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine / histone H3R2 demethylase activity / peptidyl-lysine 5-dioxygenase activity / histone H4R3 demethylase activity / protein demethylase activity / recognition of apoptotic cell / negative regulation of protein homooligomerization / oxidative RNA demethylation / oxidative RNA demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / macrophage activation / non-membrane-bounded organelle assembly / transcription regulator activator activity / regulation of mRNA splicing, via spliceosome / sprouting angiogenesis / Protein hydroxylation / P-TEFb complex binding / histone demethylase activity / erythrocyte development / phagocytosis / RNA splicing / kidney development / lung development / HDMs demethylate histones / protein homooligomerization / mRNA processing / retina development in camera-type eye / signaling receptor activity / heart development / T cell differentiation in thymus / single-stranded RNA binding / cell surface receptor signaling pathway / chromatin remodeling / ribonucleoprotein complex / iron ion binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hong, X. / Zang, J. / White, J. / Kappler, J.W. / Wang, C. / Zhang, G. | ||||||
![]() | ![]() Title: Interaction of JMJD6 with single-stranded RNA. Authors: Hong, X. / Zang, J. / White, J. / Wang, C. / Pan, C.H. / Zhao, R. / Murphy, R.C. / Dai, S. / Henson, P. / Kappler, J.W. / Hagman, J. / Zhang, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.4 KB | Display | ![]() |
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PDB format | ![]() | 132.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.2 KB | Display | ![]() |
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Full document | ![]() | 531 KB | Display | |
Data in XML | ![]() | 32.8 KB | Display | |
Data in CIF | ![]() | 43.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ld8SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39437.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6NYC1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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-Antibody , 2 types, 2 molecules BC
#2: Antibody | Mass: 24100.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell: hybridoma / Production host: ![]() |
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#3: Antibody | Mass: 24007.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell: hybridoma / Production host: ![]() |
-Non-polymers , 5 types, 28 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HG.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-AKG / | #7: Chemical | ChemComp-FE / | #8: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.02 Å3/Da / Density % sol: 75.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Bis(2-hydroxyethyl)-amino-tris(hydroxymethyl)-methane, 2.1 M Ammonium Sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.61→99 Å / Num. all: 54702 / Num. obs: 48696 / % possible obs: 89 % / Biso Wilson estimate: 66.1 Å2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 3LD8, JMJD6, and Fab Fragment Resolution: 2.7→47.28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3487182.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.7914 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→47.28 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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