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- PDB-3d9j: Snapshots of the RNA processing factor SCAF8 bound to different p... -

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Basic information

Entry
Database: PDB / ID: 3d9j
TitleSnapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
ComponentsRNA-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 / mRNA cleavage factor complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of DNA-templated transcription, elongation / termination of RNA polymerase II transcription / RNA polymerase II complex binding / nuclear matrix / mRNA binding / RNA binding ...negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / RNA polymerase core enzyme binding / mRNA cleavage factor complex / RNA polymerase II C-terminal domain phosphoserine binding / positive regulation of DNA-templated transcription, elongation / termination of RNA polymerase II transcription / RNA polymerase II complex binding / nuclear matrix / mRNA binding / RNA 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 recognition motif / RNA recognition motif ...SCAF8, RNA recognition motif / : / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
AMMONIUM ION / SR-related and CTD-associated factor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein 16
B: RNA-binding protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,42728
Polymers33,8812
Non-polymers1,54526
Water4,143230
1
A: RNA-binding protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,90216
Polymers16,9411
Non-polymers96115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-binding protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,52512
Polymers16,9411
Non-polymers58511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.620, 57.620, 107.150
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: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: H4N
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M citric acid, 2.8 M (NH4)2SO4, 1% (v/v) glycerol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0007 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 1.6→41 Å / Num. obs: 44703 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 29.6 Å2 / Rsym value: 0.04 / Net I/σ(I): 24
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 7158 / Rsym value: 0.271 / % possible all: 94.3

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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 3D9I

3d9i


Resolution: 1.6→40.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.161 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20568 2141 4.7 %RANDOM
Rwork0.17853 ---
obs0.17987 43194 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.831 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2261 0 86 230 2577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222464
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9793324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2945275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12824.779113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2215487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6551511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021741
X-RAY DIFFRACTIONr_nbd_refined0.220.21280
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.221
X-RAY DIFFRACTIONr_mcbond_it0.8671.51445
X-RAY DIFFRACTIONr_mcangle_it1.3722344
X-RAY DIFFRACTIONr_scbond_it2.25931122
X-RAY DIFFRACTIONr_scangle_it3.3284.5980
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 164 -
Rwork0.21 3154 -
obs-3154 98.25 %
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)
11.91880.71871.13682.07651.50415.8147-0.0751-0.01550.1746-0.1597-0.23720.1403-0.2014-0.01710.3123-0.18950.0191-0.031-0.16980.0013-0.15744.79723.995816.7479
21.6602-0.01320.60892.60811.15615.4313-0.1439-0.0136-0.0660.01820.1382-0.2639-0.2290.0590.0056-0.19690.0101-0.0225-0.1764-0.0132-0.145324.486914.7115-10.183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1382 - 138
2X-RAY DIFFRACTION2BB2 - 1412 - 141

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