[English] 日本語
Yorodumi
- PDB-6mev: Structure of JMJD6 bound to Mono-Methyl Arginine. -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / membraneless 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 / signaling receptor activity / retina development in camera-type eye / heart development / T cell differentiation in thymus / 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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more