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- PDB-1p27: Crystal Structure of the Human Y14/Magoh complex -

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Basic information

Entry
Database: PDB / ID: 1p27
TitleCrystal Structure of the Human Y14/Magoh complex
Components
  • Mago nashi protein homolog
  • RNA-binding protein 8A
KeywordsRNA BINDING PROTEIN / RNA-binding / Nuclear protein / mRNA splicing
Function / homology
Function and homology information


exon-exon junction subcomplex mago-y14 / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exon-exon junction complex / regulation of mRNA processing / mRNA 3'-end processing / 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 / regulation of alternative mRNA splicing, via spliceosome ...exon-exon junction subcomplex mago-y14 / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exon-exon junction complex / regulation of mRNA processing / mRNA 3'-end processing / 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 / regulation of alternative mRNA splicing, via spliceosome / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / regulation of translation / nuclear speck / mRNA binding / neuronal cell body / dendrite / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Mago nashi protein / Mago nashi / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...Mago nashi protein / Mago nashi / Mago nashi protein / RNA-binding motif protein 8 / RBM8, RNA recognition motif / Mago nashi superfamily / Mago nashi protein / 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
Protein mago nashi homolog / RNA-binding protein 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLau, C.K. / Diem, M.D. / Dreyfuss, G. / Van Duyne, G.D.
CitationJournal: Curr.Biol. / Year: 2003
Title: Structure of the y14-magoh core of the exon junction complex.
Authors: Lau, C.K. / Diem, M.D. / Dreyfuss, G. / Van Duyne, G.D.
History
DepositionApr 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mago nashi protein homolog
B: RNA-binding protein 8A
C: Mago nashi protein homolog
D: RNA-binding protein 8A


Theoretical massNumber of molelcules
Total (without water)58,1674
Polymers58,1674
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Mago nashi protein homolog
B: RNA-binding protein 8A


Theoretical massNumber of molelcules
Total (without water)29,0842
Polymers29,0842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-17 kcal/mol
Surface area11930 Å2
MethodPISA
3
C: Mago nashi protein homolog
D: RNA-binding protein 8A


Theoretical massNumber of molelcules
Total (without water)29,0842
Polymers29,0842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-14 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.150, 108.455, 50.942
Angle α, β, γ (deg.)90.00, 90.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mago nashi protein homolog


Mass: 16945.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAGOH / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61326
#2: Protein RNA-binding protein 8A / RNA binding motif protein 8A / Ribonucleoprotein RBM8A / RNA-binding protein Y14 / Binder of OVCA1- 1 / BOV-1


Mass: 12138.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM8A OR RBM8 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9Y5S9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.35 Å3/Da / Density % sol: 47.1 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoirpH6.2
325 %MPD1reservoir
420 mM1reservoirCaCl2

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.7114, 1.7113, 1.6755
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.71141
21.71131
31.67551
ReflectionResolution: 2→46.11 Å / Num. all: 33810 / Num. obs: 33810 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rsym value: 0.07
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 54 Å / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 83 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.225

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→46.11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.42 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26828 1701 5 %RANDOM
Rwork0.21985 ---
obs0.22232 32107 97.78 %-
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: 21.407 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.08 Å2
2--0.08 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 0 100 3966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213962
X-RAY DIFFRACTIONr_bond_other_d0.0030.023502
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9535346
X-RAY DIFFRACTIONr_angle_other_deg0.93138182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024396
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02830
X-RAY DIFFRACTIONr_nbd_refined0.2210.2780
X-RAY DIFFRACTIONr_nbd_other0.2450.24037
X-RAY DIFFRACTIONr_nbtor_other0.0920.22323
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.360.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.52340
X-RAY DIFFRACTIONr_mcangle_it1.75923778
X-RAY DIFFRACTIONr_scbond_it2.41431622
X-RAY DIFFRACTIONr_scangle_it3.8954.51568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 103
Rwork0.268 2150
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)
13.83020.7878-1.06682.3477-0.18562.04010.14510.1969-0.2751-0.0002-0.05160.17290.0573-0.1961-0.09350.17610.0399-0.10520.2223-0.04470.21160.3824-30.600918.6055
21.7937-0.0288-1.45782.9338-0.16463.3361-0.26370.06480.006-0.04960.06880.11680.02480.00420.1950.19920.0297-0.0760.2439-0.02720.157514.2365-37.4592-0.5268
33.87550.269-1.66923.62180.78073.45530.536-0.14420.81610.3074-0.0950.0608-0.50060.0947-0.4410.255-0.04220.1610.0787-0.07070.28767.024-9.912525.9099
43.83350.9201-2.45513.1231-0.43873.3633-0.5343-0.2782-0.64350.04070.1139-0.2060.53980.23610.42040.38710.13180.23710.07630.05140.246418.3839-60.21431.2065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1452 - 144
2X-RAY DIFFRACTION2CC3 - 1452 - 144
3X-RAY DIFFRACTION3BB64 - 15515 - 106
4X-RAY DIFFRACTION4DD64 - 15515 - 106
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 54 Å / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.65
LS refinement shell
*PLUS
Rfactor Rfree: 0.323 / Rfactor Rwork: 0.272

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