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- PDB-7qg6: Co-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII -

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Basic information

Entry
Database: PDB / ID: 7qg6
TitleCo-crystal structure of UPF3A-RRM-NOPS-L with UPF2-MIF4GIII
Components
  • Regulator of nonsense transcripts 2
  • Regulator of nonsense transcripts 3A
KeywordsRNA BINDING PROTEIN / nonsense mediated mRNA decay neurological development x-linked intellectual disability up-frameshift proteins
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / mRNA transport / animal organ regeneration / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / liver development ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / mRNA transport / animal organ regeneration / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / liver development / positive regulation of translation / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / spermatogenesis / in utero embryonic development / neuron projection / intracellular membrane-bounded organelle / mRNA binding / nucleolus / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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
TRIETHYLENE GLYCOL / Regulator of nonsense transcripts 3A / Regulator of nonsense transcripts 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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
DepositionDec 7, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)234,97112
Polymers234,4868
Non-polymers4864
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, picomolar affinity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-14 kcal/mol
Surface area18380 Å2
MethodPISA
2
C: Regulator of nonsense transcripts 3A
D: Regulator of nonsense transcripts 2
B: Regulator of nonsense transcripts 2
E: Regulator of nonsense transcripts 3A
F: Regulator of nonsense transcripts 2
G: Regulator of nonsense transcripts 3A
H: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,14211
Polymers213,6567
Non-polymers4864
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-16 kcal/mol
Surface area18030 Å2
MethodPISA
3
C: Regulator of nonsense transcripts 3A
D: Regulator of nonsense transcripts 2
B: Regulator of nonsense transcripts 2
E: Regulator of nonsense transcripts 3A
F: Regulator of nonsense transcripts 2
G: Regulator of nonsense transcripts 3A
H: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,14211
Polymers213,6567
Non-polymers4864
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-14 kcal/mol
Surface area18030 Å2
MethodPISA
4
C: Regulator of nonsense transcripts 3A
D: Regulator of nonsense transcripts 2
B: Regulator of nonsense transcripts 2
E: Regulator of nonsense transcripts 3A
F: Regulator of nonsense transcripts 2
G: Regulator of nonsense transcripts 3A
H: Regulator of nonsense transcripts 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,14211
Polymers213,6567
Non-polymers4864
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-11 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.677, 108.579, 119.943
Angle α, β, γ (deg.)90.000, 90.100, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Regulator of nonsense transcripts 3A / Nonsense mRNA reducing factor 3A / Up-frameshift suppressor 3 homolog A / hUpf3


Mass: 20829.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPF3A, RENT3A, UPF3 / Plasmid: pPROEX-HTb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H1J1
#2: Protein
Regulator of nonsense transcripts 2 / Up-frameshift suppressor 2 homolog / hUpf2


Mass: 37791.809 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.94 Å3/Da / Density % sol: 58.11 % / Description: cubic spinel
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium HEPES pH 7.0 10% w/v PEG 4000 10% v/v 2-Propanol
Temp details: 20C

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Data collection

DiffractionMean temperature: 277 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2021
RadiationMonochromator: cPGM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.95→65.25 Å / Num. obs: 41731 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 66.66 Å2 / Rpim(I) all: 0.087 / Net I/σ(I): 7.2
Reflection shellResolution: 2.95→3.02 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2660 / Rpim(I) all: 0.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uw4

1uw4


Resolution: 2.95→65.25 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 2080 4.99 %
Rwork0.2069 39630 -
obs0.2096 41710 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.32 Å2 / Biso mean: 66.928 Å2 / Biso min: 23.2 Å2
Refinement stepCycle: final / Resolution: 2.95→65.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11685 0 31 19 11735
Biso mean--69.17 50.83 -
Num. residues----1458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.020.38781330.320926602793100
3.02-3.090.3751200.288726762796100
3.09-3.180.34931560.27292602275899
3.18-3.270.33121810.26132577275899
3.27-3.380.32461320.24472658279099
3.38-3.50.3121220.241926472769100
3.5-3.640.30271320.22962637276999
3.64-3.80.27661470.22952619276699
3.8-40.24541270.1992673280099
4-4.250.26311350.18552612274799
4.25-4.580.20431360.17312661279799
4.58-5.040.21621450.16682604274999
5.04-5.770.25551640.18922645280999
5.77-7.270.26171290.22242655278499
7.28-65.250.20961210.17262704282598

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