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- PDB-3d9i: Snapshots of the RNA processing factor SCAF8 bound to different p... -

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Basic information

Entry
Database: PDB / ID: 3d9i
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 / SAD / Resolution: 1.907 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_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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)35,38523
Polymers33,8522
Non-polymers1,53321
Water3,423190
1
A: RNA-binding protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,81512
Polymers16,9261
Non-polymers88911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-binding protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,57011
Polymers16,9261
Non-polymers64510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.400, 57.400, 107.490
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: 16925.764 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H4N
#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.: 190 / 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: 52.97 %
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: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 27084 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.04 / Net I/σ(I): 40
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 14.2 / Num. unique all: 5392 / Rsym value: 0.11 / % possible all: 70.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345SOFTWAREdata collection
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.907→19.62 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.365 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21601 1277 4.8 %RANDOM
Rwork0.18105 ---
obs0.18279 25554 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.338 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.907→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 85 190 2535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222466
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9933338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4175307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77824.811106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12815489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2521511
X-RAY DIFFRACTIONr_chiral_restr0.080.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021769
X-RAY DIFFRACTIONr_nbd_refined0.2070.21208
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21702
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.211
X-RAY DIFFRACTIONr_mcbond_it0.7441.51502
X-RAY DIFFRACTIONr_mcangle_it1.11322375
X-RAY DIFFRACTIONr_scbond_it1.89331090
X-RAY DIFFRACTIONr_scangle_it2.8674.5947
LS refinement shellResolution: 1.907→1.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 31 -
Rwork0.19 1786 -
obs-1786 91.72 %
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)
11.53020.4050.68672.28461.25865.9319-0.08760.03930.1189-0.1729-0.23530.168-0.2301-0.01180.3228-0.2110.0072-0.0429-0.1855-0.0008-0.147844.43873.89117.0174
21.7697-0.26580.58773.03011.09185.2002-0.1584-0.049-0.04020.09510.1745-0.2601-0.19610.0108-0.0161-0.21540.0083-0.0252-0.1715-0.0139-0.134824.520314.823-10.1225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1392 - 139
2X-RAY DIFFRACTION2BB1 - 1401 - 140

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