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- PDB-6mev: Structure of JMJD6 bound to Mono-Methyl Arginine. -

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Basic information

Entry
Database: PDB / ID: 6mev
TitleStructure of JMJD6 bound to Mono-Methyl Arginine.
ComponentsBifunctional arginine demethylase and lysyl-hydroxylase JMJD6
KeywordsTRANSCRIPTION / Jumonji / Arginine / Methyl / endopeptidase / exopeptidase
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 / 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 / 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 / Up-down Bundle / Sandwich ...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 / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Chem-NMM / Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, S. / Zhang, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5T32AI007405-28 (MPI) United States
CitationJournal: Elife / Year: 2020
Title: JMJD6 cleaves MePCE to release positive transcription elongation factor b (P-TEFb) in higher eukaryotes.
Authors: Lee, S. / Liu, H. / Hill, R. / Chen, C. / Hong, X. / Crawford, F. / Kingsley, M. / Zhang, Q. / Liu, X. / Chen, Z. / Lengeling, A. / Bernt, K.M. / Marrack, P. / Kappler, J. / Zhou, Q. / Li, C. ...Authors: Lee, S. / Liu, H. / Hill, R. / Chen, C. / Hong, X. / Crawford, F. / Kingsley, M. / Zhang, Q. / Liu, X. / Chen, Z. / Lengeling, A. / Bernt, K.M. / Marrack, P. / Kappler, J. / Zhou, Q. / Li, C.Y. / Xue, Y. / Hansen, K. / Zhang, G.
History
DepositionSep 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
B: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
C: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
D: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
E: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
F: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
G: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
H: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,92328
Polymers320,5558
Non-polymers2,36820
Water12,070670
1
A: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4604
Polymers40,0691
Non-polymers3903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2713
Polymers40,0691
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2713
Polymers40,0691
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2713
Polymers40,0691
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4604
Polymers40,0691
Non-polymers3903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2713
Polymers40,0691
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4604
Polymers40,0691
Non-polymers3903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4604
Polymers40,0691
Non-polymers3903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.547, 141.906, 149.263
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40069.379 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD6, KIAA0585, PTDSR / Production host: Escherichia coli (E. coli)
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
#2: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-NMM / (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid / L-NMMA / Methylarginine


Type: L-peptide linking / Mass: 188.228 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H16N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate pH 5.6 1.0M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.987 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→64 Å / Num. obs: 127739 / % possible obs: 99 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.2198 / Net I/σ(I): 8.36
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 1.542 / Num. unique all: 12429 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→64 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2872 1999 -
Rwork0.2291 --
obs0.2557 127739 99 %
Refinement stepCycle: LAST / Resolution: 2.6→64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22475 0 140 670 23285
LS refinement shellResolution: 2.6→2.693 Å
RfactorNum. reflection
Rfree0.3466 -
Rwork0.313 -
obs-12429

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