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- PDB-3d9k: Snapshots of the RNA processing factor SCAF8 bound to different p... -

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Basic information

Entry
Database: PDB / ID: 3d9k
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
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: 2.2 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 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq / 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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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
Y: CTD-PEPTIDE
Z: CTD-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,30113
Polymers37,4364
Non-polymers8659
Water1,49583
1
B: RNA-binding protein 16
Z: CTD-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1026
Polymers18,7182
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-51 kcal/mol
Surface area8370 Å2
MethodPISA
2
A: RNA-binding protein 16
Y: CTD-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1987
Polymers18,7182
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-58 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.450, 56.450, 106.270
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: 16940.648 Da / Num. of mol.: 2
Fragment: CTD INTERACTING DOMAIN OF SCAF8, UNP residues 1-136
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: 1777.412 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: PEPTIDE DERIVED FROM THE CONSERVED REPEAT SEQUENCE IN RNA POLYMERASE II CTD
References: UniProt: P24928*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
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: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 25, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 16475 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 36.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 18.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 1955 / Rsym value: 0.33 / % possible all: 92.6

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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: 2.2→19.89 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.634 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.283 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25161 847 5 %RANDOM
Rwork0.18976 ---
obs0.19284 16046 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2--1.62 Å20 Å2
3----3.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 45 83 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222540
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9853450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1035306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13424.649114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59615.126476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6481511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021843
X-RAY DIFFRACTIONr_nbd_refined0.1970.21230
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.22
X-RAY DIFFRACTIONr_mcbond_it0.5391.51548
X-RAY DIFFRACTIONr_mcangle_it0.8822461
X-RAY DIFFRACTIONr_scbond_it1.39631120
X-RAY DIFFRACTIONr_scangle_it2.1424.5980
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 67 -
Rwork0.211 1205 -
obs-1205 100 %
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)
12.73670.16591.1642.95480.91726.3668-0.0357-0.14740.2311-0.148-0.18650.039-0.2054-0.15850.2221-0.2294-0.034-0.01-0.1717-0.0052-0.168643.91434.310516.4277
22.6073-0.46480.37672.94771.32197.4888-0.12610.0708-0.148-0.00960.1931-0.1109-0.3031-0.1135-0.067-0.2042-0.0486-0.0311-0.21140.0081-0.145923.806514.3726-9.7758
385.6712-35.32159.914944.6655-17.34256.9837-0.47731.7098-0.62920.9722-2.89470.39620.7451.97333.3720.3887-0.2790.05310.44650.05950.406831.18770.938113.5174
416.1062-11.453210.238228.089213.971729.15340.1614-1.5022-1.32811.3461-2.01012.310.4171-2.4131.84870.0597-0.21930.08110.33850.13880.394610.95711.7657-5.4595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1382 - 138
2X-RAY DIFFRACTION2BB1 - 1411 - 141
3X-RAY DIFFRACTION3YC-1 - 46 - 11
4X-RAY DIFFRACTION4ZD1 - 91 - 9

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