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- PDB-2xb2: Crystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b as... -

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Basic information

Entry
Database: PDB / ID: 2xb2
TitleCrystal structure of the core Mago-Y14-eIF4AIII-Barentsz-UPF3b assembly shows how the EJC is bridged to the NMD machinery
Components
  • EUKARYOTIC INITIATION FACTOR 4A-III
  • PROTEIN CASC3
  • PROTEIN MAGO NASHI HOMOLOG
  • PUTATIVE REGULATOR OF NONSENSE TRANSCRIPTS 3B
  • REGULATOR OF NONSENSE TRANSCRIPTS 3B
  • RNA POLY-U-RIBONUCLEOTIDE
  • RNA-BINDING PROTEIN 8A
KeywordsHYDROLASE / EXON JUNCTION COMPLEX / NONSENSE-MEDIATED MRNA DECAY / TRANSLATION / UPF3B
Function / homology
Function and homology information


exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of excitatory postsynaptic potential / intracellular mRNA localization ...exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / regulation of translation at postsynapse, modulating synaptic transmission / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of excitatory postsynaptic potential / intracellular mRNA localization / Deadenylation of mRNA / regulation of mRNA processing / selenocysteine insertion sequence binding / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / mRNA 3'-end processing / embryonic cranial skeleton morphogenesis / U2-type catalytic step 1 spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / RNA Polymerase II Transcription Termination / exploration behavior / regulation of alternative mRNA splicing, via spliceosome / associative learning / centriolar satellite / mRNA transport / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / ribonucleoprotein complex binding / cellular response to brain-derived neurotrophic factor stimulus / positive regulation of neuron differentiation / catalytic step 2 spliceosome / RNA splicing / mRNA Splicing - Major Pathway / positive regulation of translation / response to organic cyclic compound / brain development / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / cytoplasmic stress granule / rRNA processing / RNA stem-loop binding / neuron projection development / regulation of translation / postsynapse / nuclear membrane / RNA helicase activity / negative regulation of translation / RNA helicase / nuclear speck / mRNA binding / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / dendrite / nucleolus / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
UPF3B, RNA recognition motif-like domain / Nonsense-mediated mRNA decay protein 3 / Smg-4/UPF3 family / UPF3 domain / Mago nashi protein / Mago nashi / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / Mago nashi protein ...UPF3B, RNA recognition motif-like domain / Nonsense-mediated mRNA decay protein 3 / Smg-4/UPF3 family / UPF3 domain / Mago nashi protein / Mago nashi / CASC3/Barentsz eIF4AIII binding / CASC3/Barentsz eIF4AIII binding / Btz domain / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / RRM (RNA recognition motif) domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / RNA (> 10) / Protein CASC3 / Eukaryotic initiation factor 4A-III / Protein mago nashi homolog / Regulator of nonsense transcripts 3B / RNA-binding protein 8A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBuchwald, G. / Ebert, J. / Basquin, C. / Sauliere, J. / Jayachandran, U. / Bono, F. / Le Hir, H. / Conti, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Insights Into the Recruitment of the Nmd Machinery from the Crystal Structure of a Core Ejc-Upf3B Complex.
Authors: Buchwald, G. / Ebert, J. / Basquin, C. / Sauliere, J. / Jayachandran, U. / Bono, F. / Le Hir, H. / Conti, E.
History
DepositionApr 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: EUKARYOTIC INITIATION FACTOR 4A-III
C: PROTEIN MAGO NASHI HOMOLOG
D: RNA-BINDING PROTEIN 8A
E: RNA POLY-U-RIBONUCLEOTIDE
F: PUTATIVE REGULATOR OF NONSENSE TRANSCRIPTS 3B
G: REGULATOR OF NONSENSE TRANSCRIPTS 3B
R: RNA POLY-U-RIBONUCLEOTIDE
S: PROTEIN CASC3
T: PROTEIN CASC3
U: REGULATOR OF NONSENSE TRANSCRIPTS 3B
X: EUKARYOTIC INITIATION FACTOR 4A-III
Y: PROTEIN MAGO NASHI HOMOLOG
Z: RNA-BINDING PROTEIN 8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,44617
Polymers207,38513
Non-polymers1,0614
Water00
1
R: RNA POLY-U-RIBONUCLEOTIDE
S: PROTEIN CASC3
U: REGULATOR OF NONSENSE TRANSCRIPTS 3B
X: EUKARYOTIC INITIATION FACTOR 4A-III
Y: PROTEIN MAGO NASHI HOMOLOG
Z: RNA-BINDING PROTEIN 8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0358
Polymers103,5056
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-73.9 kcal/mol
Surface area28380 Å2
MethodPISA
2
A: EUKARYOTIC INITIATION FACTOR 4A-III
C: PROTEIN MAGO NASHI HOMOLOG
D: RNA-BINDING PROTEIN 8A
E: RNA POLY-U-RIBONUCLEOTIDE
G: REGULATOR OF NONSENSE TRANSCRIPTS 3B
T: PROTEIN CASC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0358
Polymers103,5056
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15400 Å2
ΔGint-68.1 kcal/mol
Surface area28670 Å2
MethodPISA
3
F: PUTATIVE REGULATOR OF NONSENSE TRANSCRIPTS 3B


  • defined by author&software
  • 375 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3751
Polymers3751
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.800, 134.800, 227.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.1978, -0.10023, 0.97511), (-0.11426, -0.99034, -0.07862), (0.97356, -0.09586, -0.20734)44.98475, -45.14456, -61.1079
2given(0.1978, -0.10023, 0.97511), (-0.11426, -0.99034, -0.07862), (0.97356, -0.09586, -0.20734)44.98475, -45.14456, -61.1079
3given(0.1978, -0.10023, 0.97511), (-0.11426, -0.99034, -0.07862), (0.97356, -0.09586, -0.20734)44.98475, -45.14456, -61.1079
4given(0.1978, -0.10023, 0.97511), (-0.11426, -0.99034, -0.07862), (0.97356, -0.09586, -0.20734)44.98475, -45.14456, -61.1079

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Components

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Protein , 5 types, 10 molecules AXCYDZGUST

#1: Protein EUKARYOTIC INITIATION FACTOR 4A-III / EIF4AIII / EUKARYOTIC TRANSLATION INITIATION FACTOR 4A ISOFORM 3 / ATP-DEPENDENT RNA HELICASE EIF4A- ...EIF4AIII / EUKARYOTIC TRANSLATION INITIATION FACTOR 4A ISOFORM 3 / ATP-DEPENDENT RNA HELICASE EIF4A-3 / ATP-DEPENDENT RNA HELICASE DDX48 / DEAD BOX PROTEIN 48 / EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34 / NUCLEAR MATRIX PROTEIN 265 / NMP 265


Mass: 46930.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P38919, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein PROTEIN MAGO NASHI HOMOLOG / MAGO


Mass: 17189.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61326
#3: Protein RNA-BINDING PROTEIN 8A / RNA-BINDING MOTIF PROTEIN 8A / Y14 / RIBONUCLEOPROTEIN RBM8A / RNA-BINDING PROTEIN Y14 / BINDER OF ...RNA-BINDING MOTIF PROTEIN 8A / Y14 / RIBONUCLEOPROTEIN RBM8A / RNA-BINDING PROTEIN Y14 / BINDER OF OVCA1-1 / BOV-1


Mass: 10313.474 Da / Num. of mol.: 2 / Fragment: RRM, RESIDUES 66-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5S9
#6: Protein REGULATOR OF NONSENSE TRANSCRIPTS 3B / UPF3B / NONSENSE MRNA REDUCING FACTOR 3B / UP-FRAMESHIFT SUPPRESSOR 3 HOMOLOG B / UP-FRAMESHIFT ...UPF3B / NONSENSE MRNA REDUCING FACTOR 3B / UP-FRAMESHIFT SUPPRESSOR 3 HOMOLOG B / UP-FRAMESHIFT SUPPRESSOR 3 HOMOLOG ON CHROMOSOME X / HUPF3P-X


Mass: 6809.521 Da / Num. of mol.: 2 / Fragment: C-TERMINAL EJC BINDING REGION, RESIDUES 411-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BZI7
#7: Protein PROTEIN CASC3 / BARENTSZ / CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN / METASTATIC LYMPH NODE GENE 51 PROTEIN / ...BARENTSZ / CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN / METASTATIC LYMPH NODE GENE 51 PROTEIN / MLN 51 / BTZ


Mass: 17713.482 Da / Num. of mol.: 2 / Fragment: SELOR DOMAIN, RESIDUES 137-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15234

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RNA chain / Protein/peptide , 2 types, 3 molecules ERF

#4: RNA chain RNA POLY-U-RIBONUCLEOTIDE


Mass: 4547.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 15 POLY-U SYNTHETIC CONSTRUCT / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: Protein/peptide PUTATIVE REGULATOR OF NONSENSE TRANSCRIPTS 3B


Mass: 375.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BZI7*PLUS

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Non-polymers , 2 types, 4 molecules

#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 2.65 Å3/Da / Density % sol: 53.5 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M NA-CACODYLATE PH 6.5, 0.2M MG-ACETATE 4H2O, 10 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→60 Å / Num. obs: 29550 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 59.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 10 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J0S

2j0s


Resolution: 3.4→60 Å / Rfactor Rfree error: 0.0068 / Data cutoff high absF: 2650687.04 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 1460 4.9 %RANDOM
Rwork0.2204 ---
obs0.2204 29550 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3777 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 75.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.457 Å20 Å20 Å2
2--4.457 Å20 Å2
3----8.914 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.4→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11352 294 64 0 11710
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.58
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.4→3.44 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rfree0.3905 52 3.5 %
Rwork0.2925 945 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ANP.PARAM
X-RAY DIFFRACTION3DNA-RNA_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5WATER_REP.PARAM

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