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- PDB-3mca: Structure of the Dom34-Hbs1 Complex and implications for its role... -

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Basic information

Entry
Database: PDB / ID: 3mca
TitleStructure of the Dom34-Hbs1 Complex and implications for its role in No-Go decay
Components
  • Elongation factor 1 alpha-like protein
  • Protein dom34
KeywordsTranslation regulation/HYDROLASE / protein protein complex / Translation regulation / No-Go Decay / Translation regulation-HYDROLASE complex
Function / homology
Function and homology information


Eukaryotic Translation Elongation / HSF1 activation / Protein methylation / Dom34-Hbs1 complex / Neutrophil degranulation / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / cytoplasmic translational termination / GTPase regulator activity / nuclear-transcribed mRNA catabolic process, non-stop decay ...Eukaryotic Translation Elongation / HSF1 activation / Protein methylation / Dom34-Hbs1 complex / Neutrophil degranulation / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / cytoplasmic translational termination / GTPase regulator activity / nuclear-transcribed mRNA catabolic process, non-stop decay / translation release factor activity / nonfunctional rRNA decay / ribosome disassembly / negative regulation of G0 to G1 transition / translational elongation / translation elongation factor activity / endoplasmic reticulum unfolded protein response / meiotic cell cycle / ribosome binding / endonuclease activity / Hydrolases; Acting on ester bonds / translation / cell division / GTPase activity / GTP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pelota, domain A / eRF1 domain 2 / HBS1-like protein, N-terminal / HBS1 N-terminus / Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like ...Pelota, domain A / eRF1 domain 2 / HBS1-like protein, N-terminal / HBS1 N-terminus / Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / 60s Ribosomal Protein L30; Chain: A; / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / 50S ribosomal protein L30e-like / SH3 type barrels. / Nucleotidyltransferase; domain 5 / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Elongation factor 1 alpha-like protein / Protein dom34
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 Å
AuthorsChen, L. / Song, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure of the Dom34-Hbs1 complex and implications for no-go decay
Authors: Chen, L. / Muhlrad, D. / Hauryliuk, V. / Cheng, Z. / Lim, M.K. / Shyp, V. / Parker, R. / Song, H.
History
DepositionMar 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 1 alpha-like protein
B: Protein dom34


Theoretical massNumber of molelcules
Total (without water)110,4962
Polymers110,4962
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-4 kcal/mol
Surface area35980 Å2
Unit cell
Length a, b, c (Å)76.741, 113.423, 124.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Elongation factor 1 alpha-like protein / Hbs1


Mass: 66100.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O74774
#2: Protein Protein dom34


Mass: 44395.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: PET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q9USL5, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.46 Å3/Da / Density % sol: 49.93 % / Mosaicity: 0.28 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 6% PEG 8000, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.6→83.919 Å / Num. all: 34234 / Num. obs: 34234 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.084 / Rsym value: 0.069 / Net I/av σ(I): 7.386 / Net I/σ(I): 18.7 / Num. measured all: 270895
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.6-2.648.11.0650.9330.81375317020.371.0650.9332.1100
2.64-2.698.10.9120.8010.91319116250.3160.9120.8012.5100
2.69-2.748.10.7860.6891.11303516110.2730.7860.6892.8100
2.74-2.798.10.6430.5621.31272415640.2230.6430.5623.5100
2.79-2.858.10.5080.4471.71289615910.1760.5080.4474.2100
2.85-2.918.10.4620.4041.91218515050.160.4620.4044.8100
2.91-2.978.10.3620.3182.41208414890.1250.3620.3186100
2.97-3.048.10.3010.2662.81202614850.1050.3010.2667.1100
3.04-3.118.10.2510.223.41144414180.0870.2510.228.5100
3.11-3.1880.1960.1724.41137214140.0680.1960.17210.299.9
3.18-3.278.10.1670.14551084313450.0580.1670.14511.9100
3.27-3.3680.1340.1186.31077813430.0470.1340.11814100
3.36-3.4580.110.0967.11040712950.0380.110.09616.5100
3.45-3.5680.0910.0789.21008612630.0320.0910.07818.7100
3.56-3.687.90.0820.0710.2978312320.0290.0820.0720.2100
3.68-3.8180.070.05911.9954111930.0240.070.05922.399.9
3.81-3.9580.0630.05312.8895211250.0220.0630.05323.9100
3.95-4.117.90.0560.04813.7875511050.020.0560.04825.8100
4.11-4.297.80.0550.04713.4850210860.0190.0550.04727.8100
4.29-4.57.80.060.05111.9791610120.0210.060.05130.5100
4.5-4.757.80.070.069.276179790.0250.070.0634.2100
4.75-5.037.70.080.0677.770609170.0290.080.06735.9100
5.03-5.387.60.0790.0658.165988710.0290.0790.06538100
5.38-5.817.40.0740.069.860618160.0270.0740.0641.399.7
5.81-6.377.30.0620.04612.854997580.0230.0620.04648.599.6
6.37-7.126.60.0530.0331845136790.020.0530.03352.999.2
7.12-8.227.80.0510.0331746926040.0180.0510.03361.9100
8.22-10.077.60.040.02819.140685350.0140.040.02864.3100
10.07-14.247.20.0430.02918.530594250.0160.0430.02960.999.3
14.24-113.4235.90.0420.02820.714552470.0160.0420.02849.295.6

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.74→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 1 / SU B: 31.08 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.802 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1460 5 %RANDOM
Rwork0.2467 27715 --
obs0.2486 29175 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 165.29 Å2 / Biso mean: 66.9494 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-0 Å2
2--0.87 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5685 0 0 168 5853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225785
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9637824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8925707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6724.091264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.287151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4781540
X-RAY DIFFRACTIONr_chiral_restr0.1040.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214292
X-RAY DIFFRACTIONr_mcbond_it0.4321.53567
X-RAY DIFFRACTIONr_mcangle_it0.81925783
X-RAY DIFFRACTIONr_scbond_it1.10632218
X-RAY DIFFRACTIONr_scangle_it1.9334.52041
LS refinement shellResolution: 2.74→2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 99 -
Rwork0.38 1996 -
all-2095 -
obs--100 %
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)
11.6033-1.0222-0.30531.53340.09020.58260.129-0.0360.194-0.1515-0.0554-0.332-0.00950.1645-0.07350.0556-0.00810.03950.08410.03670.145543.784-9.3664-5.7946
20.8261-0.20020.27092.46-1.10172.65820.01860.06160.24-0.03450.0530.3972-0.447-0.4485-0.07160.12310.06290.00160.1710.0280.20876.15146.0244-1.3181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A155 - 592
2X-RAY DIFFRACTION2B8 - 379

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