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- PDB-8gdx: Crystal structure of JADE1 PZP domain -

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Basic information

Entry
Database: PDB / ID: 8gdx
TitleCrystal structure of JADE1 PZP domain
ComponentsProtein Jade-1
KeywordsTRANSCRIPTION / histone acetylation / transcription activation / Nucleosome / pVHL
Function / homology
Function and homology information


regulation of DNA biosynthetic process / negative regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / histone acetyltransferase complex / ciliary basal body / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / HATs acetylate histones / transcription coactivator activity ...regulation of DNA biosynthetic process / negative regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / histone acetyltransferase complex / ciliary basal body / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / HATs acetylate histones / transcription coactivator activity / regulation of cell cycle / nuclear speck / chromatin remodeling / centrosome / apoptotic process / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Jade-1, PHD finger / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...Jade-1, PHD finger / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsKlein, B.J. / Liu, J. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Guiding the HBO1 complex function through the JADE subunit.
Authors: Gaurav, N. / Kanai, A. / Lachance, C. / Cox, K.L. / Liu, J. / Grzybowski, A.T. / Saksouk, N. / Klein, B.J. / Komata, Y. / Asada, S. / Ruthenburg, A.J. / Poirier, M.G. / Cote, J. / Yokoyama, ...Authors: Gaurav, N. / Kanai, A. / Lachance, C. / Cox, K.L. / Liu, J. / Grzybowski, A.T. / Saksouk, N. / Klein, B.J. / Komata, Y. / Asada, S. / Ruthenburg, A.J. / Poirier, M.G. / Cote, J. / Yokoyama, A. / Kutateladze, T.G.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Jade-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7118
Polymers19,1991
Non-polymers5117
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.439, 81.439, 81.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

21A-513-

HOH

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Components

#1: Protein Protein Jade-1 / Jade family PHD finger protein 1 / PHD finger protein 17


Mass: 19199.365 Da / Num. of mol.: 1 / Fragment: PZP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JADE1, KIAA1807, PHF17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IE81
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 2 M Ammonium sulfate, 0.1 M Sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.74→28.79 Å / Num. obs: 4947 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rpim(I) all: 0.082 / Net I/σ(I): 8.5
Reflection shellResolution: 2.74→2.79 Å / Redundancy: 5 % / Num. unique obs: 230 / Rpim(I) all: 0.298 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ERC

5erc


Resolution: 2.74→28.79 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2687 229 4.67 %
Rwork0.2198 4679 -
obs0.2222 4908 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.71 Å2 / Biso mean: 46.4169 Å2 / Biso min: 15.94 Å2
Refinement stepCycle: final / Resolution: 2.74→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 33 13 1302
Biso mean--78.78 45.17 -
Num. residues----165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.74-3.450.35491070.2575229299
3.45-28.790.23711220.20552387100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.03170.53371.63953.4627-0.44243.4306-0.0609-0.51030.04570.1518-0.10150.2254-0.1614-0.55950.18960.27420.0371-0.00470.3649-0.00430.23573.9296-26.76268.2458
22.46870.94351.86993.0149-0.79482.39080.4718-0.0841-0.54720.3345-0.30620.02680.20850.083-0.09030.2594-0.093-0.03690.40640.03430.38117.6559-16.668810.4349
31.9139-0.4406-0.56292.9027-0.71122.62860.4680.202-0.6527-0.1109-0.30940.36440.25470.1714-0.15120.3044-0.0253-0.08130.41540.00910.339916.3047-19.95540.1901
42.854-0.60330.0525.3899-0.97232.45030.0940.14680.298-0.0862-0.3764-0.6267-0.2190.30920.27550.29-0.091-0.0520.44870.0750.371218.4449-9.6097-1.9498
54.52450.2672-0.70023.93140.19353.69380.02670.1705-0.0567-0.1171-0.11720.0746-0.05020.18960.0560.17770.0424-0.0060.3872-0.01580.30777.4734-8.9848-4.5297
60.3596-0.6766-0.65991.81590.09053.69910.12960.4693-0.76390.188-0.0734-0.4596-0.1875-0.1137-0.02010.2081-0.0441-0.08030.53660.00490.71867.2263-12.2343-12.1492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 203 through 252 )A203 - 252
2X-RAY DIFFRACTION2chain 'A' and (resid 253 through 276 )A253 - 276
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 295 )A277 - 295
4X-RAY DIFFRACTION4chain 'A' and (resid 296 through 332 )A296 - 332
5X-RAY DIFFRACTION5chain 'A' and (resid 333 through 353 )A333 - 353
6X-RAY DIFFRACTION6chain 'A' and (resid 354 through 369 )A354 - 369

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