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Basic information

Entry
Database: PDB / ID: 1uw4
TitleThe structural basis of the interaction between nonsense mediated decay factors UPF2 and UPF3
Components
  • REGULATOR OF NONSENSE TRANSCRIPTS 2
  • UPF3X
KeywordsRNA BINDING PROTEIN / NONSENSE MEDIATED MRNA DECAY PROTEIN / RNA-BINDING PROTEIN / NMD / RNP DOMAIN / MIF4G DOMAIN
Function / homology
Function and homology information


positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / RNA Polymerase II Transcription Termination / telomeric DNA binding / centriolar satellite / mRNA transport / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / mRNA 3'-end processing / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / RNA Polymerase II Transcription Termination / telomeric DNA binding / centriolar satellite / mRNA transport / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / animal organ regeneration / mRNA export from nucleus / positive regulation of neuron differentiation / mRNA Splicing - Major Pathway / liver development / positive regulation of translation / brain development / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / neuron projection development / mRNA binding / neuronal cell body / nucleolus / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
UPF3B, RNA recognition motif-like domain / Nonsense-mediated mRNA decay protein 3 / Smg-4/UPF3 family / UPF3 domain / Up-frameshift suppressor 2, C-terminal / Nonsense-mediated mRNA decay protein Nmd2/UPF2 / Up-frameshift suppressor 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) ...UPF3B, RNA recognition motif-like domain / Nonsense-mediated mRNA decay protein 3 / Smg-4/UPF3 family / UPF3 domain / Up-frameshift suppressor 2, C-terminal / Nonsense-mediated mRNA decay protein Nmd2/UPF2 / Up-frameshift suppressor 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RRM (RNA recognition motif) domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Regulator of nonsense transcripts 3B / Regulator of nonsense transcripts 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsKadlec, J. / Izaurralde, E. / Cusack, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: The Structural Basis for the Interaction between Nonsense-Mediated Mrna Decay Factors Upf2 and Upf3
Authors: Kadlec, J. / Izaurralde, E. / Cusack, S.
History
DepositionJan 29, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF3X
B: REGULATOR OF NONSENSE TRANSCRIPTS 2
C: UPF3X
D: REGULATOR OF NONSENSE TRANSCRIPTS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5176
Polymers80,3614
Non-polymers1562
Water5,657314
1
A: UPF3X
B: REGULATOR OF NONSENSE TRANSCRIPTS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2583
Polymers40,1802
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-10.4 kcal/mol
Surface area21560 Å2
MethodPQS
2
C: UPF3X
D: REGULATOR OF NONSENSE TRANSCRIPTS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2583
Polymers40,1802
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-9.1 kcal/mol
Surface area21670 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.306, 100.178, 153.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2067-

HOH

21D-2079-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9945, -0.104, 0.0131), (-0.1041, 0.9945, -0.0075), (-0.0122, -0.0089, -0.9999)141.4101, 8.2411, 229.6434
2given(-0.9938, -0.1085, 0.0224), (-0.1087, 0.994, -0.0087), (-0.0213, -0.0111, -0.9997)142.37511, 8.8348, 228.99249

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Components

#1: Protein UPF3X / RNA PROCESSING PROTEIN / UPF3B


Mass: 10902.323 Da / Num. of mol.: 2 / Fragment: RRM DOMAIN, RESIDUES 50-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HELA-CELL / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BZI7
#2: Protein REGULATOR OF NONSENSE TRANSCRIPTS 2 / UPF2


Mass: 29278.039 Da / Num. of mol.: 2 / Fragment: MIF4G DOMAIN, RESIDUES 768-1015
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HELA-CELL / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HAU5
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.9 Å3/Da / Density % sol: 57.2 %
Crystal growpH: 6.5
Details: 100 MM AMMONIUM ACETATE, 15 MM MAGNESIUM ACETATE 50 MM SODIUM CACODYLATE 6.5, 8% ISOPROPANOL, pH 6.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMTris1droppH7.0
3100 mM1dropNaCl
410 mMbeta-mercaptoethanol1drop
5100 mMammonium acetate1reservoir
615 mMmagnesium acetate1reservoir
750 mMsodium cacodylate1reservoirpH6.5
88 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393, 0.9792, 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93931
20.97921
30.97951
ReflectionResolution: 1.95→33.7 Å / Num. obs: 79316 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.74
Reflection shellResolution: 1.95→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.3 / % possible all: 98.6
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Redundancy: 4.3 % / Num. measured all: 338871 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.305

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.531 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2379 3 %RANDOM
Rwork0.204 ---
obs0.205 76925 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5657 0 2 314 5973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225827
X-RAY DIFFRACTIONr_bond_other_d0.0020.025295
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.9587890
X-RAY DIFFRACTIONr_angle_other_deg0.8312327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1035680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026373
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021246
X-RAY DIFFRACTIONr_nbd_refined0.1970.21130
X-RAY DIFFRACTIONr_nbd_other0.2170.25699
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0790.23158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4881.53413
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92725574
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.57732414
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5984.52316
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 167
Rwork0.26 5413
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)
10.77870.1350.13480.62230.13410.895-0.0362-0.09720.08170.15920.0251-0.0063-0.11690.01040.01110.15520.0116-0.02990.0689-0.0230.054273.03221.881138.012
21.0661-0.17860.27440.8998-0.29731.1172-0.01790.11240.1373-0.0925-0.01160.0113-0.1465-0.00790.02960.0171-0.0094-0.01930.00740.01810.046265.48721.31192.247
32.1064-0.3078-0.70522.3592-0.55012.6622-0.04110.09260.0729-0.1530.0223-0.5449-0.22210.4320.01880.1583-0.1105-0.07980.2176-0.05340.260994.05621.739127.631
42.17050.1254-0.63782.6050.37392.22660.0077-0.14890.06350.2404-0.04610.6212-0.1705-0.40520.03840.04280.069-0.00760.15360.01010.248444.38119.135102.401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B768 - 1015
2X-RAY DIFFRACTION2D768 - 1015
3X-RAY DIFFRACTION3A50 - 140
4X-RAY DIFFRACTION4C50 - 140
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.12

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