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- PDB-3d9o: Snapshots of the RNA processing factor SCAF8 bound to different p... -

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Basic information

Entry
Database: PDB / ID: 3d9o
TitleSnapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
Components
  • CTD-PEPTIDE
  • RNA-binding protein 16
KeywordsTRANSCRIPTION / SCAF8 / RNA POLYMERASE II CTD INTERACTING DOMAIN / ARM REPEATS / PHOSPHO-CTD / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / RNA polymerase core enzyme binding / microfibril binding / mRNA cleavage factor complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis ...negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / RNA polymerase core enzyme binding / microfibril binding / mRNA cleavage factor complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of DNA-templated transcription, elongation / 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 / termination of RNA polymerase II transcription / 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 / RNA polymerase II complex binding / 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 / nuclear matrix / DNA-directed RNA polymerase / Dual incision in TC-NER / 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 / mRNA binding / ubiquitin protein ligase binding / regulation of DNA-templated transcription / magnesium ion binding / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SCAF8, RNA recognition motif / : / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic ...SCAF8, RNA recognition motif / : / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
AMMONIUM ION / DNA-directed RNA polymerase II subunit RPB1 / SR-related and CTD-associated factor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsBecker, R. / Loll, B. / Meinhart, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II.
Authors: Becker, R. / Loll, B. / Meinhart, A.
History
DepositionMay 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 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: RNA-binding protein 16
B: RNA-binding protein 16
Z: CTD-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,39011
Polymers35,7783
Non-polymers6128
Water2,288127
1
B: RNA-binding protein 16
Z: CTD-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9246
Polymers18,6182
Non-polymers3064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-41 kcal/mol
Surface area8230 Å2
MethodPISA
2
A: RNA-binding protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4665
Polymers17,1601
Non-polymers3064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.444, 57.444, 107.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein RNA-binding protein 16 / RNA-binding motif protein 16


Mass: 17160.238 Da / Num. of mol.: 2
Fragment: CTD INTERACTING DOMAIN OF SCAF8, UNP residues 1-136
Mutation: N15M, Y17M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM16, KIAA1116 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9UPN6
#2: Protein/peptide CTD-PEPTIDE


Mass: 1457.496 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PEPTIDE DERIVED FROM THE CONSERVED REPEAT SEQUENCE IN RNA POLYMERASE II CTD
References: UniProt: P24928*PLUS
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.2M Li2SO4, 1.6M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23561 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 36.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 17.4
Reflection shellResolution: 2→2.2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 11086 / Rsym value: 0.38 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345SOFTWAREdata collection
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Pdb entry 3D9J

3d9j


Resolution: 2→40.76 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.13 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.189 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23994 1177 5 %RANDOM
Rwork0.2044 ---
obs0.20613 22384 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.719 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 32 127 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222456
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9763323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5635299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40924.673107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89815478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2181511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021785
X-RAY DIFFRACTIONr_nbd_refined0.1950.21155
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.29
X-RAY DIFFRACTIONr_mcbond_it0.7711.51517
X-RAY DIFFRACTIONr_mcangle_it0.93222409
X-RAY DIFFRACTIONr_scbond_it1.58531064
X-RAY DIFFRACTIONr_scangle_it2.3334.5906
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 88 -
Rwork0.23 1650 -
obs-1650 99.54 %
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)
12.81630.46610.53534.09731.47917.0404-0.03670.12770.3551-0.4633-0.38430.1616-0.30380.23910.421-0.18120.0174-0.0438-0.14410.0345-0.124644.50553.852916.8574
22.8419-0.41050.4984.08312.12416.2585-0.1591-0.1167-0.19210.13110.2058-0.2916-0.05110.0137-0.0468-0.2456-0.0069-0.0318-0.1924-0.0038-0.151324.474714.7122-10.1054
33.857213.2018-2.553546.1449-5.260114.29510.2617-0.8204-0.88861.7485-0.79931.7034-0.3664-1.61370.5375-0.0642-0.02950.03330.2230.04160.075412.9099.0271-7.8068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1382 - 138
2X-RAY DIFFRACTION2BB1 - 1401 - 140
3X-RAY DIFFRACTION3ZC-1 - 76 - 14

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