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- PDB-6q2v: Crystal structure of SPOC domain of human PHD-finger protein 3 (PHF3) -

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Basic information

Entry
Database: PDB / ID: 6q2v
TitleCrystal structure of SPOC domain of human PHD-finger protein 3 (PHF3)
ComponentsPHD finger protein 3
KeywordsTRANSCRIPTION / SPOC domain / PHF3
Function / homology
Function and homology information


DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / 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
PHD finger protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.594 Å
AuthorsGrishkovskaya, I. / Slade, D. / Djinovic-Carugo, K.
Citation
Journal: Nat Commun / Year: 2021
Title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC
Authors: Appel, L.M. / Franke, V. / Bruno, M. / Grishkovskaya, I. / Kasiliauskaite, A. / Kaufmann, T. / Schoeberl, U.E. / Puchinger, M.G. / Kostrhon, S. / Ebenwaldner, C. / Sebesta, M. / Beltzung, E. ...Authors: Appel, L.M. / Franke, V. / Bruno, M. / Grishkovskaya, I. / Kasiliauskaite, A. / Kaufmann, T. / Schoeberl, U.E. / Puchinger, M.G. / Kostrhon, S. / Ebenwaldner, C. / Sebesta, M. / Beltzung, E. / Mechtler, K. / Lin, G. / Vlasova, A. / Leeb, M. / Pavri, R. / Stark, A. / Akalin, A. / Stefl, R. / Bernecky, C. / Djinovic-Carugo, K. / Slade, D.
#1: Journal: Biorxiv / Year: 2020
Title: PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC
Authors: Appel, L.M. / Franke, V. / Bruno, M. / Grishkovskaya, I. / Kasiliauskaite, A. / Schoeberl, U.E. / Puchinger, M.G. / Kostrhon, S. / Beltzung, E. / Mechtler, K. / Lin, G. / Vlasova, A. / Leeb, ...Authors: Appel, L.M. / Franke, V. / Bruno, M. / Grishkovskaya, I. / Kasiliauskaite, A. / Schoeberl, U.E. / Puchinger, M.G. / Kostrhon, S. / Beltzung, E. / Mechtler, K. / Lin, G. / Vlasova, A. / Leeb, M. / Pavri, R. / Stark, A. / Akalin, A. / Stefl, R. / Bernecky, C. / Djinovic-Carugo, K. / Slade, D.
History
DepositionDec 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 3
B: PHD finger protein 3
C: PHD finger protein 3
D: PHD finger protein 3
E: PHD finger protein 3
F: PHD finger protein 3
G: PHD finger protein 3
H: PHD finger protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,37410
Polymers147,1908
Non-polymers1842
Water88349
1
A: PHD finger protein 3


Theoretical massNumber of molelcules
Total (without water)18,3991
Polymers18,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHD finger protein 3


Theoretical massNumber of molelcules
Total (without water)18,3991
Polymers18,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHD finger protein 3


Theoretical massNumber of molelcules
Total (without water)18,3991
Polymers18,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PHD finger protein 3


Theoretical massNumber of molelcules
Total (without water)18,3991
Polymers18,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: PHD finger protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4912
Polymers18,3991
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: PHD finger protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4912
Polymers18,3991
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: PHD finger protein 3


Theoretical massNumber of molelcules
Total (without water)18,3991
Polymers18,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: PHD finger protein 3


Theoretical massNumber of molelcules
Total (without water)18,3991
Polymers18,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.745, 69.306, 127.215
Angle α, β, γ (deg.)90.000, 100.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PHD finger protein 3


Mass: 18398.732 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF3, KIAA0244 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92576
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: containing 0.2 M MgCl2, 0.1M Bis-Tris pH 5.5, 25%PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97863 Å / Relative weight: 1
ReflectionResolution: 2.59→48.78 Å / Num. obs: 32812 / % possible obs: 87.8 % / Redundancy: 6 % / Biso Wilson estimate: 51.7 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.069 / Rrim(I) all: 0.126 / Net I/σ(I): 10.5
Reflection shellResolution: 2.59→2.71 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.867 / Num. unique obs: 2252 / Rpim(I) all: 0.79 / Rrim(I) all: 1.17 / % possible all: 50.3

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Processing

Software
NameVersionClassification
PHENIXdev_3150refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.594→48.779 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.81
RfactorNum. reflection% reflection
Rfree0.259 1606 4.9 %
Rwork0.2059 --
obs0.2085 32757 87.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.97 Å2 / Biso mean: 54.5584 Å2 / Biso min: 19.37 Å2
Refinement stepCycle: final / Resolution: 2.594→48.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9353 0 12 49 9414
Biso mean--52.56 45.82 -
Num. residues----1174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.594-2.67770.3682720.33291535160748
2.6777-2.77340.3854860.31061969205561
2.7734-2.88440.36461090.28012346245572
2.8844-3.01570.31381480.25872743289186
3.0157-3.17460.31291690.25223168333798
3.1746-3.37350.31941710.242831763347100
3.3735-3.63390.27191670.210532283395100
3.6339-3.99940.25771630.186831983361100
3.9994-4.57780.20511700.168232403410100
4.5778-5.7660.23361710.165232603431100
5.766-48.78780.22311800.20283288346899

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