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- PDB-2pa2: Crystal structure of human Ribosomal protein L10 core domain -

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Basic information

Entry
Database: PDB / ID: 2pa2
TitleCrystal structure of human Ribosomal protein L10 core domain
Components60S ribosomal protein L10
KeywordsRIBOSOMAL PROTEIN / ribosomal protein L10 / QM protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


embryonic brain development / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit ...embryonic brain development / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / regulation of translation / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein-containing complex / RNA binding / nucleus / membrane / cytosol
Similarity search - Function
Ribosomal protein L16/L10 / Aldehyde Oxidoreductase; domain 3 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNishimura, M. / Kaminishi, T. / Takemoto, C. / Kawazoe, M. / Yoshida, T. / Tanaka, A. / Sugano, S. / Shirouzu, M. / Ohkubo, T. / Yokoyama, S. ...Nishimura, M. / Kaminishi, T. / Takemoto, C. / Kawazoe, M. / Yoshida, T. / Tanaka, A. / Sugano, S. / Shirouzu, M. / Ohkubo, T. / Yokoyama, S. / Kobayashi, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of Human Ribosomal Protein L10 Core Domain Reveals Eukaryote-Specific Motifs in Addition to the Conserved Fold
Authors: Nishimura, M. / Kaminishi, T. / Takemoto, C. / Kawazoe, M. / Yoshida, T. / Tanaka, A. / Sugano, S. / Shirouzu, M. / Ohkubo, T. / Yokoyama, S. / Kobayashi, Y.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Structure summary
Category: struct_keywords / struct_ref_seq_dif / Item: _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 60S ribosomal protein L10
B: 60S ribosomal protein L10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4684
Polymers34,3902
Non-polymers782
Water63135
1
A: 60S ribosomal protein L10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2342
Polymers17,1951
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 60S ribosomal protein L10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2342
Polymers17,1951
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.724, 52.724, 185.489
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 60S ribosomal protein L10 / QM protein / Tumor suppressor QM / Laminin receptor homolog


Mass: 17195.111 Da / Num. of mol.: 2 / Fragment: core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32b-L10CD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27635
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 1.0M di-sodium hydroxyl phosphate, 1.0M potassium dihydroxyl phosphate, pH 4.5 100mM sodium acetate , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2006 / Details: rhodium-coated mirrors
RadiationMonochromator: Rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10870 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 60 Å2 / Rsym value: 0.05 / Net I/σ(I): 36.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.62 / Num. unique all: 1019 / Rsym value: 0.438 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S72 chain H

1s72


Resolution: 2.5→45.66 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 890089.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 567 5.2 %RANDOM
Rwork0.24 ---
obs0.24 10814 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1449 Å2 / ksol: 0.380904 e/Å3
Displacement parametersBiso mean: 56.4 Å2
Baniso -1Baniso -2Baniso -3
1-11.58 Å27.78 Å20 Å2
2--11.58 Å20 Å2
3----23.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 2 35 1787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
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
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 103 6.1 %
Rwork0.348 1593 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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