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- PDB-3ulh: Crystal structure of a RNA binding domain of THO complex subunit ... -

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Basic information

Entry
Database: PDB / ID: 3ulh
TitleCrystal structure of a RNA binding domain of THO complex subunit 4 protein (THOC4) from Homo sapiens at 2.54 A resolution
ComponentsTHO complex subunit 4
KeywordsRNA BINDING PROTEIN / nuclear protein / RNA binding / THO complex / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


transcription export complex / C5-methylcytidine-containing RNA reader activity / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / mRNA export from nucleus ...transcription export complex / C5-methylcytidine-containing RNA reader activity / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / mRNA export from nucleus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / osteoblast differentiation / nuclear speck / mRNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily ...Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / THO complex subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.54 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a RNA binding domain of THO complex subunit 4 protein (THOC4) from Homo sapiens at 2.54 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionNov 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THO complex subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8503
Polymers11,6601
Non-polymers1902
Water46826
1
A: THO complex subunit 4
hetero molecules

A: THO complex subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6996
Polymers23,3192
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_545-x+1/4,z-1/4,y+1/41
Buried area2140 Å2
ΔGint-9 kcal/mol
Surface area8390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.152, 101.152, 101.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-201-

PO4

21A-201-

PO4

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein THO complex subunit 4 / Tho4 / Ally of AML-1 and LEF-1 / Transcriptional coactivator Aly/REF / bZIP-enhancing factor BEF


Mass: 11659.740 Da / Num. of mol.: 1 / Fragment: RNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALY, BC052302, BEF, THOC4 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q86V81
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 78-183 OF THE TARGET SEQUENCE.

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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: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25.0% Glycerol, 0.6M di-sodium hydrogen phosphate, 0.6M potassium dihydrogen phosphate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796,0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
30.97941
ReflectionResolution: 2.54→29.2 Å / Num. all: 6271 / Num. obs: 6271 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rsym value: 0.086 / Net I/σ(I): 16.6
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.54-2.6110.32.245954471.136100
2.61-2.6810.3343724250.849100
2.68-2.7610.2444504370.604100
2.76-2.8410.34.941234020.499100
2.84-2.9310.26.641354070.352100
2.93-3.0410.18.838573810.245100
3.04-3.151011.938163810.171100
3.15-3.281014.636863690.127100
3.28-3.439.916.235273550.113100
3.43-3.599.819.833413400.085100
3.59-3.799.822.831213180.071100
3.79-4.029.727.529453050.059100
4.02-4.299.530.527972950.06100
4.29-4.649.332.425372740.061100
4.64-5.08931.723142560.067100
5.08-5.688.430.719652340.06999.9
5.68-6.569.129.619392120.064100
6.56-8.039.231.217121860.048100
8.03-11.368.636.813231540.041100
11.36-29.27.430.9687930.0494.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.54→29.2 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 11.829 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. PHOSPHATE (PO4) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 289 4.6 %RANDOM
Rwork0.1812 ---
obs0.1819 6245 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 140.62 Å2 / Biso mean: 64.6075 Å2 / Biso min: 38.72 Å2
Refinement stepCycle: LAST / Resolution: 2.54→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 10 26 668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019672
X-RAY DIFFRACTIONr_bond_other_d0.0010.02450
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.988911
X-RAY DIFFRACTIONr_angle_other_deg0.91331099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.958589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27724.37532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99315109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.689155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
X-RAY DIFFRACTIONr_bond_it2.9453.228672
X-RAY DIFFRACTIONr_bond_other0.653.386450
X-RAY DIFFRACTIONr_angle_it4.8614.76908
X-RAY DIFFRACTIONr_angle_others2.9785.0031099
X-RAY DIFFRACTIONr_torsion_it9.0269.74235
LS refinement shellResolution: 2.541→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 15 -
Rwork0.347 349 -
all-364 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 21.315 Å / Origin y: 9.835 Å / Origin z: 34.297 Å
111213212223313233
T0.3207 Å2-0.0265 Å2-0.0042 Å2-0.2449 Å20.0316 Å2--0.1967 Å2
L4.6916 °20.0133 °2-1.4523 °2-2.9984 °2-0.8582 °2--7.3375 °2
S0.2874 Å °0.1811 Å °0.003 Å °0.0967 Å °-0.3135 Å °-0.2137 Å °0.0721 Å °0.3183 Å °0.0261 Å °

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