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- PDB-3ldb: Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment. -

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Basic information

Entry
Database: PDB / ID: 3ldb
TitleStructure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.
Components
  • (antibody Fab fragment ...) x 2
  • Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
KeywordsIMMUNE SYSTEM / JMJ6D / ALPHA-KETOGLUTARATE / Fab Fragments
Function / homology
Function and homology information


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 / non-membrane-bounded organelle assembly ...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 / non-membrane-bounded organelle assembly / 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 / transcription regulator activator activity / regulation of mRNA splicing, via spliceosome / sprouting angiogenesis / erythrocyte development / Protein hydroxylation / P-TEFb complex binding / histone demethylase activity / phagocytosis / RNA splicing / kidney development / lung development / protein homooligomerization / HDMs demethylate histones / mRNA processing / retina development in camera-type eye / signaling receptor activity / T cell differentiation in thymus / heart development / single-stranded RNA binding / cell surface receptor signaling pathway / chromatin remodeling / iron ion binding / ribonucleoprotein complex / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Monooxygenase - #270 / Monooxygenase / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Immunoglobulins / Up-down Bundle ...Monooxygenase - #270 / Monooxygenase / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / : / Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
Similarity search - Component
Biological speciesHomo sapiens (human)
Cricetulus migratorius (Armenian hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHong, X. / Zang, J. / White, J. / Kappler, J.W. / Wang, C. / Zhang, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
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
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
B: antibody Fab fragment light chain
C: antibody Fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,43431
Polymers87,5453
Non-polymers2,88928
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.381, 138.381, 183.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 / Histone arginine demethylase JMJD6 / Peptide-lysine 5-dioxygenase JMJD6 / Lysyl-hydroxylase JMJD6 / ...Histone arginine demethylase JMJD6 / Peptide-lysine 5-dioxygenase JMJD6 / Lysyl-hydroxylase JMJD6 / JmjC domain-containing protein 6 / Jumonji domain-containing protein 6 / Phosphatidylserine receptor / Protein PTDSR


Mass: 39437.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD6, JMJD6 (1-403), KIAA0585, PTDSR / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
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 antibody Fab fragment light chain


Mass: 24100.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus migratorius (Armenian hamster)
Cell: hybridoma / Production host: Cricetulus migratorius (Armenian hamster)
#3: Antibody antibody Fab fragment heavy chain


Mass: 24007.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus migratorius (Armenian hamster)
Cell: hybridoma / Production host: Cricetulus migratorius (Armenian hamster)

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Non-polymers , 5 types, 28 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#7: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 5.02 Å3/Da / Density % sol: 75.5 %
Crystal growTemperature: 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

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONALS 8.2.221
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 10, 2005
ADSC QUANTUM 3152CCDOct 10, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→99 Å / Num. all: 54702 / Num. obs: 48696 / % possible obs: 89 % / Biso Wilson estimate: 66.1 Å2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3LD8, JMJD6, and Fab Fragment

3ld8


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
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2024 5 %RANDOM
Rwork0.25 ---
obs0.25 40520 81.7 %-
all-55302 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.7914 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 83.5 Å2
Baniso -1Baniso -2Baniso -3
1-10.72 Å20 Å20 Å2
2--10.72 Å20 Å2
3----21.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.86 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 138 0 6210
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.971.5
X-RAY DIFFRACTIONc_mcangle_it7.842
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.152.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.454 135 4.5 %
Rwork0.427 2861 -
obs--36.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3gol.pargol.top
X-RAY DIFFRACTION4akg.parakg.top
X-RAY DIFFRACTION5water_rep.paramwater_rep.top

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