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- PDB-6q5y: Crystal structure of the SPOC domain of human PHF3 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6q5y
TitleCrystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2Ser5
Components
  • PHD finger protein 3
  • pSer2pSer5
KeywordsTRANSCRIPTION / SPOC domain / PHF3 / Pol II / pSer2Ser5 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 / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...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 / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / PIWI-interacting RNA (piRNA) biogenesis / 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 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 / mRNA Splicing - Major Pathway / Inhibition of DNA recombination at telomere / positive regulation of RNA splicing / TP53 Regulates Transcription of DNA Repair Genes / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / DNA-templated transcription termination / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / DNA-directed RNA polymerase / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-directed RNA polymerase activity / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / transcription by RNA polymerase II / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
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 Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. ...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 Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / 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 / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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: 2.85 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 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Advisory / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_radiation_wavelength / diffrn_source / pdbx_database_proc / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: PHD finger protein 3
D: PHD finger protein 3
E: pSer2pSer5
F: pSer2pSer5


Theoretical massNumber of molelcules
Total (without water)76,3996
Polymers76,3996
Non-polymers00
Water18010
1
A: PHD finger protein 3


Theoretical massNumber of molelcules
Total (without water)18,2111
Polymers18,2111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8880 Å2
MethodPISA
2
B: PHD finger protein 3
F: pSer2pSer5


Theoretical massNumber of molelcules
Total (without water)19,9892
Polymers19,9892
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-9 kcal/mol
Surface area9630 Å2
MethodPISA
3
C: PHD finger protein 3
E: pSer2pSer5


Theoretical massNumber of molelcules
Total (without water)19,9892
Polymers19,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-8 kcal/mol
Surface area8740 Å2
MethodPISA
4
D: PHD finger protein 3


Theoretical massNumber of molelcules
Total (without water)18,2111
Polymers18,2111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.832, 67.832, 178.118
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA1206 - 135412 - 160
21GLNGLNBB1206 - 135412 - 160
12LYSLYSAA1206 - 135212 - 158
22LYSLYSCC1206 - 135212 - 158
13GLNGLNAA1206 - 135412 - 160
23GLNGLNDD1206 - 135412 - 160
14ARGARGBB1206 - 135312 - 159
24ARGARGCC1206 - 135312 - 159
15GLNGLNBB1206 - 135412 - 160
25GLNGLNDD1206 - 135412 - 160
16LYSLYSCC1206 - 135212 - 158
26LYSLYSDD1206 - 135212 - 158

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
PHD finger protein 3


Mass: 18211.150 Da / Num. of mol.: 4
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 pSer2pSer5


Mass: 1777.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24928*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M imidazole-MES pH 6.5, 20% glycerol and 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.262
11K, H, -L20.233
11-K, -H, -L30.251
11-h,-k,l40.254
ReflectionResolution: 2.85→44.53 Å / Num. obs: 21184 / % possible obs: 98.8 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.124 / Rrim(I) all: 0.183 / Net I/σ(I): 6.6
Reflection shellResolution: 2.85→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.432 / Num. unique obs: 3104 / Rpim(I) all: 0.819 / Rrim(I) all: 1.662 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q2V

6q2v


Resolution: 2.85→41.76 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.794 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22689 1017 4.8 %RANDOM
Rwork0.19212 ---
obs0.19394 20123 98.81 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 71.322 Å2
Baniso -1Baniso -2Baniso -3
1-7.47 Å20 Å20 Å2
2--7.47 Å20 Å2
3----14.95 Å2
Refinement stepCycle: 1 / Resolution: 2.85→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4908 0 0 10 4918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135029
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174777
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.6566840
X-RAY DIFFRACTIONr_angle_other_deg1.0611.57411114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9665607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87121.878229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.89615850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5211528
X-RAY DIFFRACTIONr_chiral_restr0.0560.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025429
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021019
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5587.7072449
X-RAY DIFFRACTIONr_mcbond_other4.5557.7072449
X-RAY DIFFRACTIONr_mcangle_it7.27511.5483049
X-RAY DIFFRACTIONr_mcangle_other7.27411.5483050
X-RAY DIFFRACTIONr_scbond_it3.4177.7762580
X-RAY DIFFRACTIONr_scbond_other3.4047.7772577
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4411.6183792
X-RAY DIFFRACTIONr_long_range_B_refined12.26619085
X-RAY DIFFRACTIONr_long_range_B_other12.26619086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A36840.22
12B36840.22
21A37400.21
22C37400.21
31A38290.21
32D38290.21
41B38790.19
42C38790.19
51B39250.19
52D39250.19
61C40040.19
62D40040.19
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 53 -
Rwork0.199 1513 -
obs--99.37 %

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