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- PDB-3zhe: Structure of the C. elegans SMG5-SMG7 complex -

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Basic information

Entry
Database: PDB / ID: 3zhe
TitleStructure of the C. elegans SMG5-SMG7 complex
Components
  • NONSENSE-MEDIATED MRNA DECAY PROTEIN
  • PROTEIN SMG-7
KeywordsMRNA-BINDING PROTEIN / NMD / PHOSPHO-PEPTIDE BINDING DOMAINS
Function / homology
Function and homology information


embryonic genitalia morphogenesis / DEAD/H-box RNA helicase binding / protein phosphatase regulator activity / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / telomerase holoenzyme complex / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / RNA nuclease activity ...embryonic genitalia morphogenesis / DEAD/H-box RNA helicase binding / protein phosphatase regulator activity / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / telomerase holoenzyme complex / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / RNA nuclease activity / protein phosphatase 2A binding / nucleus / cytoplasm
Similarity search - Function
Delta-Endotoxin; domain 1 - #60 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #760 / : / EST1-like DNA-binding domain / DNA/RNA-binding domain, Est1-type / Est1/Ebs1-like / Est1 DNA/RNA binding domain / Large family of predicted nucleotide-binding domains / PIN domain / Delta-Endotoxin; domain 1 ...Delta-Endotoxin; domain 1 - #60 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #760 / : / EST1-like DNA-binding domain / DNA/RNA-binding domain, Est1-type / Est1/Ebs1-like / Est1 DNA/RNA binding domain / Large family of predicted nucleotide-binding domains / PIN domain / Delta-Endotoxin; domain 1 / Tetratricopeptide repeat domain / TPR repeat profile. / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nonsense-mediated mRNA decay protein / DNA/RNA-binding domain-containing protein
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3 Å
AuthorsJonas, S. / Weichenrieder, O. / Izaurralde, E.
CitationJournal: Genes Dev. / Year: 2013
Title: An Unusual Arrangement of Two 14-3-3-Like Domains in the Smg5-Smg7 Heterodimer is Required for Efficient Nonsense-Mediated Mrna Decay.
Authors: Jonas, S. / Weichenrieder, O. / Izaurralde, E.
History
DepositionDec 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NONSENSE-MEDIATED MRNA DECAY PROTEIN
B: PROTEIN SMG-7
C: NONSENSE-MEDIATED MRNA DECAY PROTEIN
D: PROTEIN SMG-7


Theoretical massNumber of molelcules
Total (without water)189,7464
Polymers189,7464
Non-polymers00
Water00
1
A: NONSENSE-MEDIATED MRNA DECAY PROTEIN
B: PROTEIN SMG-7


Theoretical massNumber of molelcules
Total (without water)94,8732
Polymers94,8732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-18 kcal/mol
Surface area35110 Å2
MethodPISA
2
C: NONSENSE-MEDIATED MRNA DECAY PROTEIN
D: PROTEIN SMG-7


Theoretical massNumber of molelcules
Total (without water)94,8732
Polymers94,8732
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-18.9 kcal/mol
Surface area34590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.160, 82.000, 154.510
Angle α, β, γ (deg.)90.00, 116.88, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0784, -0.129, 0.9885), (-0.1738, 0.9782, 0.1139), (-0.9816, -0.1629, -0.0991)35.9786, -35.3481, 168.2611
2given(0.0107, -0.0196, 0.9998), (-0.1792, 0.9836, 0.0212), (-0.9838, -0.1793, 0.007)25.964, -30.6423, 163.7186

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Components

#1: Protein NONSENSE-MEDIATED MRNA DECAY PROTEIN / PROTEIN SMG-5


Mass: 49004.523 Da / Num. of mol.: 2 / Fragment: 14-3-3 AND ALPHA-HELICAL DOMAINS, RESIDUES 1-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G5ECF1
#2: Protein PROTEIN SMG-7


Mass: 45868.605 Da / Num. of mol.: 2 / Fragment: 14-3-3 AND ALPHA-HELICAL DOMAINS, RESIDUES 1-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: G5EF47

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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: 3.82 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 5
Details: 0.1 M SODIUM CITRATE (PH 5.0), 8% (W/V) PEG 8000, 10% GLYCEROL, 500 MM NACL, 60 MM (NH4)2SO4, 4 MM DTT AND 2 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 55840 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 94.31 Å2 / Rsym value: 0.08 / Net I/σ(I): 14.5
Reflection shellResolution: 3→3.2 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.37 / Rsym value: 0.73 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 3→49.337 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 32.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 2826 5.1 %
Rwork0.2218 --
obs0.2232 55765 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105 Å2
Refinement stepCycle: LAST / Resolution: 3→49.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12141 0 0 0 12141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312414
X-RAY DIFFRACTIONf_angle_d0.68516889
X-RAY DIFFRACTIONf_dihedral_angle_d13.4044396
X-RAY DIFFRACTIONf_chiral_restr0.0471927
X-RAY DIFFRACTIONf_plane_restr0.0032161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.05170.42421440.36062643X-RAY DIFFRACTION100
3.0517-3.10720.42181190.3462615X-RAY DIFFRACTION100
3.1072-3.1670.36731440.32292641X-RAY DIFFRACTION100
3.167-3.23160.36371450.31062605X-RAY DIFFRACTION100
3.2316-3.30190.32751380.29192618X-RAY DIFFRACTION100
3.3019-3.37870.30321390.27142634X-RAY DIFFRACTION100
3.3787-3.46310.33561440.27222615X-RAY DIFFRACTION100
3.4631-3.55670.31751650.2522635X-RAY DIFFRACTION100
3.5567-3.66140.23771390.24592624X-RAY DIFFRACTION100
3.6614-3.77950.30691360.23922641X-RAY DIFFRACTION100
3.7795-3.91450.2731410.21782640X-RAY DIFFRACTION100
3.9145-4.07120.23041370.21882669X-RAY DIFFRACTION100
4.0712-4.25640.23421450.21872615X-RAY DIFFRACTION100
4.2564-4.48070.26441480.20942649X-RAY DIFFRACTION100
4.4807-4.76120.24091440.20342622X-RAY DIFFRACTION100
4.7612-5.12840.2251500.21142689X-RAY DIFFRACTION100
5.1284-5.64390.23441290.22882653X-RAY DIFFRACTION100
5.6439-6.4590.29841630.2362663X-RAY DIFFRACTION100
6.459-8.13180.21971250.20852704X-RAY DIFFRACTION100
8.1318-49.34360.16451310.17212764X-RAY DIFFRACTION100
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)
11.242-0.6968-0.18071.87-0.60091.07160.07170.20570.20870.2155-0.01360.0763-0.5007-0.30990.0411.10120.61490.0320.75950.0140.702769.611418.4454114.9369
24.0304-0.76721.38751.345-0.71675.64550.379-0.1904-0.3625-0.107-0.4075-0.06410.46050.0829-0.00530.95680.25890.01990.75080.12490.688778.2828-1.1049147.0945
33.17330.1031-0.48671.85660.92731.53640.01030.1325-0.1028-0.1389-0.0413-0.0864-0.02510.0771-0.03560.830.59050.03010.8384-0.05260.664677.83380.3469104.2104
43.0394-0.77630.03412.7022-0.66972.123-0.36840.26240.40560.09520.5247-0.3044-0.15830.28470.0090.7330.23910.04740.984-0.39611.0315111.13792.728789.993
52.80441.89850.97252.5573-0.37991.3284-0.27480.7750.6125-0.10420.16850.3523-0.11110.2211-0.01050.5599-0.1311-0.00210.95090.48581.030439.834556.705544.8415
62.9560.27520.38920.3385-0.75753.78390.2199-0.3653-0.20010.0898-0.2780.07580.8728-0.66060.020.9473-0.55290.00630.99160.17320.792311.739731.796247.6117
73.1846-0.40410.79392.5757-0.41283.33980.2010.7536-0.21830.0145-0.2981-0.29530.37070.8229-0.00390.73610.045-0.01311.09120.31950.865253.156339.924152.2863
81.82820.49180.61362.9269-1.52232.9598-0.29140.14220.18570.44210.4252-0.0124-0.44270.10580.01590.94290.4502-0.02170.83750.11150.84467.540544.375185.6355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:141)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 142:400)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 1:161)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 162:391)
5X-RAY DIFFRACTION5CHAIN C AND (RESSEQ 5:141)
6X-RAY DIFFRACTION6CHAIN C AND (RESSEQ 142:399)
7X-RAY DIFFRACTION7CHAIN D AND (RESSEQ 3:161)
8X-RAY DIFFRACTION8CHAIN D AND (RESSEQ 162:391)

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