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- PDB-2gfa: double tudor domain complex structure -

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Basic information

Entry
Database: PDB / ID: 2gfa
Titledouble tudor domain complex structure
Components
  • Jumonji domain-containing protein 2A
  • peptide
KeywordsMETAL BINDING PROTEIN / double tudor domain / tudor tandem / trimethyl histone H3 lysine 4 / jmjc domain containing
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of neuron differentiation / methylated histone binding / negative regulation of autophagy / response to nutrient levels / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #70 / Vcp-like ATPase; Chain A, domain 2 / : / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 ...Vcp-like ATPase; Chain A, domain 2 - #70 / Vcp-like ATPase; Chain A, domain 2 / : / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Zinc finger, RING/FYVE/PHD-type / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHuang, Y. / Fang, J. / Bedford, M.T. / Zhang, Y. / Xu, R.M.
CitationJournal: Science / Year: 2006
Title: Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A
Authors: Huang, Y. / Fang, J. / Bedford, M.T. / Zhang, Y. / Xu, R.M.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Jumonji domain-containing protein 2A
B: Jumonji domain-containing protein 2A
C: peptide
D: peptide


Theoretical massNumber of molelcules
Total (without water)29,3204
Polymers29,3204
Non-polymers00
Water4,414245
1
A: Jumonji domain-containing protein 2A
C: peptide


Theoretical massNumber of molelcules
Total (without water)14,6602
Polymers14,6602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-5 kcal/mol
Surface area7530 Å2
MethodPISA
2
B: Jumonji domain-containing protein 2A
D: peptide


Theoretical massNumber of molelcules
Total (without water)14,6602
Polymers14,6602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-4 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.822, 96.733, 110.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Jumonji domain-containing protein 2A


Mass: 13467.824 Da / Num. of mol.: 2 / Fragment: double tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD2A, JMJD2, KIAA0677 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75164
#2: Protein/peptide peptide


Mass: 1192.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: this sequence occrus naturally in humans
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 24%PEG 4K, 0.1 M Na Cacodylate (pH 7.4), 0.2 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 24003 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Χ2: 1.16 / Net I/σ(I): 16.4
Reflection shellResolution: 1.98→2.05 Å / % possible obs: 95.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.337 / Num. unique obs: 2256 / Χ2: 0.874 / % possible all: 95.1

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å14.99 Å
Translation3.5 Å14.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GF7

2gf7


Resolution: 2.1→50 Å / FOM work R set: 0.747 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1529 7.5 %random
Rwork0.224 ---
all0.27 24003 --
obs0.27 19495 96.2 %-
Solvent computationBsol: 36.574 Å2
Displacement parametersBiso mean: 30.635 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2--11.031 Å20 Å2
3----10.021 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 0 245 2097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1-2.120.3610.266530591
2.12-2.150.259590.26514573
2.15-2.180.301490.253517566
2.18-2.20.292490.271587636
2.2-2.230.354490.263584633
2.23-2.260.317490.255560609
2.26-2.290.298340.252596630
2.29-2.330.316460.235584630
2.33-2.370.321400.255598638
2.37-2.40.29610.256567628
2.4-2.450.257550.253596651
2.45-2.490.273450.259598643
2.49-2.540.307650.248592657
2.54-2.590.316480.277576624
2.59-2.650.286540.284616670
2.65-2.710.313450.25599644
2.71-2.780.307570.259598655
2.78-2.850.318450.259607652
2.85-2.930.343460.236615661
2.93-3.030.32500.239632682
3.03-3.140.308500.23611661
3.14-3.260.257490.202628677
3.26-3.410.277480.211628676
3.41-3.590.275610.207609670
3.59-3.820.258530.209626679
3.82-4.110.198530.174639692
4.11-4.520.246480.186629677
4.52-5.180.198620.166628690
5.18-6.520.249440.222664708
6.52-500.251540.255638692
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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