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- PDB-6ic8: Crystal structure of the SPOC domain of human PHF3 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6ic8
TitleCrystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2
Components
  • PHD finger protein 3
  • TYR-SEP-PRO-THR-SER-PRO-SER-TYR-SEP-PRO-THR
KeywordsPROTEIN BINDING / SPOC domain / PHF3 / pSER2 peptide
Function / homology
Function and homology information


microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex ...microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / mRNA Splicing - Minor Pathway / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II activity / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / promoter-specific chromatin binding / DNA-templated transcription termination / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / kinase binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / transcription by RNA polymerase II / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
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. / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 ...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. / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / Zinc finger, PHD-type / PHD zinc finger / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / PHD finger protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.929 Å
AuthorsGrishkovskaya, I. / Djinovic-Carugo, K. / Slade, D.
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 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 3
B: PHD finger protein 3
C: TYR-SEP-PRO-THR-SER-PRO-SER-TYR-SEP-PRO-THR
D: TYR-SEP-PRO-THR-SER-PRO-SER-TYR-SEP-PRO-THR


Theoretical massNumber of molelcules
Total (without water)39,6574
Polymers39,6574
Non-polymers00
Water1,892105
1
A: PHD finger protein 3
C: TYR-SEP-PRO-THR-SER-PRO-SER-TYR-SEP-PRO-THR


Theoretical massNumber of molelcules
Total (without water)19,8292
Polymers19,8292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-12 kcal/mol
Surface area8070 Å2
MethodPISA
2
B: PHD finger protein 3
D: TYR-SEP-PRO-THR-SER-PRO-SER-TYR-SEP-PRO-THR


Theoretical massNumber of molelcules
Total (without water)19,8292
Polymers19,8292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-9 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.069, 68.019, 99.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHD finger protein 3 /


Mass: 18211.150 Da / Num. of mol.: 2
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: Protein/peptide TYR-SEP-PRO-THR-SER-PRO-SER-TYR-SEP-PRO-THR


Mass: 1617.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24928*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.12 M ethylene glycol mixture, 0.1 M Tris-Bicine buffer pH 8.5, 20% glycerol, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.929→47.471 Å / Num. obs: 27007 / % possible obs: 95.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 41.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Rrim(I) all: 0.078 / Net I/σ(I): 12.9
Reflection shellResolution: 1.929→1.998 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.305 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 1970 / CC1/2: 0.383 / Rpim(I) all: 0.603 / Rrim(I) all: 1.444 / % possible all: 70.6

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Processing

Software
NameVersionClassification
PHENIX(dev_3150: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.929→47.471 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.61
RfactorNum. reflection% reflection
Rfree0.2265 1330 4.93 %
Rwork0.184 --
obs0.1861 27002 95.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.929→47.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 105 2589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072616
X-RAY DIFFRACTIONf_angle_d0.9493570
X-RAY DIFFRACTIONf_dihedral_angle_d7.4432142
X-RAY DIFFRACTIONf_chiral_restr0.06392
X-RAY DIFFRACTIONf_plane_restr0.006452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.929-1.99790.31971030.29251859X-RAY DIFFRACTION70
1.9979-2.07790.31321180.25162412X-RAY DIFFRACTION92
2.0779-2.17250.28381370.23432604X-RAY DIFFRACTION99
2.1725-2.2870.25921340.19832631X-RAY DIFFRACTION99
2.287-2.43030.27291550.22607X-RAY DIFFRACTION99
2.4303-2.61790.2711320.20462665X-RAY DIFFRACTION100
2.6179-2.88130.2311510.20252653X-RAY DIFFRACTION100
2.8813-3.29820.23921310.19652672X-RAY DIFFRACTION99
3.2982-4.1550.20571390.16312722X-RAY DIFFRACTION99
4.155-47.48550.1941300.16362847X-RAY DIFFRACTION99

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