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- PDB-7nwu: Co-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII -

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Basic information

Entry
Database: PDB / ID: 7nwu
TitleCo-crystal structure of UPF3B-RRM-NOPS-L with UPF2-MIF4GIII
Components
  • Regulator of nonsense transcripts 2
  • Regulator of nonsense transcripts 3B
KeywordsRNA BINDING PROTEIN / nonsense mediated mRNA decay neurological development x-linked intellectual disability up-frameshift proteins
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 / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / centriolar satellite / mRNA transport ...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 / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / centriolar satellite / mRNA transport / animal organ regeneration / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / positive regulation of neuron differentiation / mRNA Splicing - Major Pathway / positive regulation of translation / liver development / brain development / cytoplasmic ribonucleoprotein granule / Regulation of expression of SLITs and ROBOs / neuron projection development / mRNA binding / neuronal cell body / nucleolus / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
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 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 ...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 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA-binding domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Regulator of nonsense transcripts 3B / Regulator of nonsense transcripts 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsPowers, K.T. / Bufton, J.C. / Szeto, J.A. / Schaffitzel, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210701/Z/18/Z United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation.
Authors: Bufton, J.C. / Powers, K.T. / Szeto, J.A. / Toelzer, C. / Berger, I. / Schaffitzel, C.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of nonsense transcripts 3B
B: Regulator of nonsense transcripts 2
C: Regulator of nonsense transcripts 3B
D: Regulator of nonsense transcripts 2
E: Regulator of nonsense transcripts 3B
F: Regulator of nonsense transcripts 2
G: Regulator of nonsense transcripts 3B
H: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,44211
Polymers176,7728
Non-polymers6713
Water2,882160
1
A: Regulator of nonsense transcripts 3B
B: Regulator of nonsense transcripts 2
C: Regulator of nonsense transcripts 3B
D: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6245
Polymers88,3864
Non-polymers2381
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Regulator of nonsense transcripts 3B
F: Regulator of nonsense transcripts 2
G: Regulator of nonsense transcripts 3B
H: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8186
Polymers88,3864
Non-polymers4332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.593, 130.593, 267.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c

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Components

#1: Protein
Regulator of nonsense transcripts 3B / Nonsense mRNA reducing factor 3B / Up-frameshift suppressor 3 homolog B / hUpf3B / Up-frameshift ...Nonsense mRNA reducing factor 3B / Up-frameshift suppressor 3 homolog B / hUpf3B / Up-frameshift suppressor 3 homolog on chromosome X / hUpf3p-X


Mass: 14541.423 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPF3B, RENT3B, UPF3X / Plasmid: pPROEX HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BZI7
#2: Protein
Regulator of nonsense transcripts 2 / Nonsense mRNA reducing factor 2 / Up-frameshift suppressor 2 homolog / hUpf2


Mass: 29651.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPF2, KIAA1408, RENT2 / Plasmid: pPROEX HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HAU5
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.65 % / Description: Flat plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M Ca acetate 0.1M MES 15% PEG 400 P 41 2 2 / Temp details: 20C

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2020
RadiationMonochromator: cPGM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.309→30 Å / Num. obs: 80565 / % possible obs: 99.94 % / Redundancy: 14.2 % / Biso Wilson estimate: 53.53 Å2 / Rpim(I) all: 0.061 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRpim(I) allDiffraction-ID% possible all
2.5-2.5514.4145290.8091100
12.75-3014.139.16780.01192.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uw4

1uw4


Resolution: 2.6→30 Å / SU ML: 0.3521 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9337
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2559 3567 4.97 %
Rwork0.2167 68166 -
obs0.2187 71733 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12043 0 45 160 12248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003912382
X-RAY DIFFRACTIONf_angle_d0.536316768
X-RAY DIFFRACTIONf_chiral_restr0.0411826
X-RAY DIFFRACTIONf_plane_restr0.00342146
X-RAY DIFFRACTIONf_dihedral_angle_d10.11951653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.31411340.28552687X-RAY DIFFRACTION99.86
2.64-2.670.3231350.2762680X-RAY DIFFRACTION99.96
2.67-2.710.33071570.26912670X-RAY DIFFRACTION100
2.71-2.760.30091420.26722684X-RAY DIFFRACTION99.93
2.76-2.80.33681410.27622664X-RAY DIFFRACTION99.93
2.8-2.850.36261460.28762705X-RAY DIFFRACTION99.96
2.85-2.90.351450.27662668X-RAY DIFFRACTION99.93
2.9-2.960.3251390.26862693X-RAY DIFFRACTION99.96
2.96-3.020.34141450.25472682X-RAY DIFFRACTION99.96
3.02-3.080.31711560.24862695X-RAY DIFFRACTION99.96
3.08-3.150.31641260.24442695X-RAY DIFFRACTION100
3.15-3.230.28251310.24732726X-RAY DIFFRACTION100
3.23-3.320.36411490.25052693X-RAY DIFFRACTION99.96
3.32-3.420.31511370.23822735X-RAY DIFFRACTION99.97
3.42-3.530.27641470.22592699X-RAY DIFFRACTION100
3.53-3.650.23731390.20572716X-RAY DIFFRACTION99.93
3.65-3.80.22391440.19862712X-RAY DIFFRACTION99.93
3.8-3.970.22511530.2052725X-RAY DIFFRACTION99.97
3.97-4.180.21341460.18422736X-RAY DIFFRACTION100
4.18-4.440.19781510.18172743X-RAY DIFFRACTION100
4.44-4.780.21481420.17952751X-RAY DIFFRACTION100
4.78-5.260.23831440.19962772X-RAY DIFFRACTION100
5.26-6.020.26371350.23142802X-RAY DIFFRACTION99.93
6.02-7.560.30011290.22892850X-RAY DIFFRACTION99.97
7.57-300.1811540.17292983X-RAY DIFFRACTION99.46

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