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- PDB-2jdl: Structure of C-terminal region of acidic P2 ribosomal protein com... -

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Basic information

Entry
Database: PDB / ID: 2jdl
TitleStructure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin
Components
  • ACIDIC RIBOSOMAL PROTEIN P2
  • RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
KeywordsHYDROLASE / RIBOSOME INACTIVIATING PROTEIN / RIBOSOMAL PROTEIN / PROTEIN SYNTHESIS INHIBITOR / TOXIN / PLANT DEFENSE / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


cytoplasmic translational elongation / regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / 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 ...cytoplasmic translational elongation / regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / 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) / defense response / Regulation of expression of SLITs and ROBOs / toxin activity / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / structural constituent of ribosome / translation / focal adhesion / extracellular exosome / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 ...Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / 60s Acidic ribosomal protein / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein P2 / Ribosome-inactivating protein alpha-trichosanthin
Similarity search - Component
Biological speciesTRICHOSANTHES KIRILOWII (Chinese cucumber)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsToo, P.H. / Mak, A.N. / Zhu, G. / Au, S.W. / Wong, K.B. / Shaw, P.C.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The C-Terminal Fragment of the Ribosomal P Protein Complexed to Trichosanthin Reveals the Interaction between the Ribosome-Inactivating Protein and the Ribosome.
Authors: Too, P.H. / Ma, M.K. / Mak, A.N. / Wong, Y.T. / Tung, C.K. / Zhu, G. / Au, S.W. / Wong, K.B. / Shaw, P.C.
History
DepositionJan 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
B: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
C: ACIDIC RIBOSOMAL PROTEIN P2
D: ACIDIC RIBOSOMAL PROTEIN P2


Theoretical massNumber of molelcules
Total (without water)56,8024
Polymers56,8024
Non-polymers00
Water4,810267
1
A: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
C: ACIDIC RIBOSOMAL PROTEIN P2


Theoretical massNumber of molelcules
Total (without water)28,4012
Polymers28,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-6.7 kcal/mol
Surface area14100 Å2
MethodPQS
2
B: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
D: ACIDIC RIBOSOMAL PROTEIN P2


Theoretical massNumber of molelcules
Total (without water)28,4012
Polymers28,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-8.3 kcal/mol
Surface area13600 Å2
MethodPQS
Unit cell
Length a, b, c (Å)62.589, 43.964, 92.235
Angle α, β, γ (deg.)90.00, 92.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPASPASP2CC4 - 114 - 11
211ASPASPASPASP2DD4 - 114 - 11
112TYRTYRASNASN2AA141 - 143141 - 143
212TYRTYRASNASN2BB141 - 143141 - 143
122LEULEUPROPRO2AA41 - 4241 - 42
222LEULEUPROPRO2BB41 - 4241 - 42
132ASNASNASNASN4AA124124
232ASNASNASNASN4BB124124
142VALVALVALVAL4AA1616
242VALVALVALVAL4BB1616
152METMETMETMET4AA246246
252METMETMETMET4BB246246

NCS ensembles :
ID
1
2

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Components

#1: Protein RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN / RRNA N-GLYCOSIDASE / ALPHA-TCS / TRICHOSANTHIN


Mass: 27182.877 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHOSANTHES KIRILOWII (Chinese cucumber)
Plasmid: PET3D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P09989, rRNA N-glycosylase
#2: Protein/peptide ACIDIC RIBOSOMAL PROTEIN P2


Mass: 1218.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05387*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.2 Å3/Da / Density % sol: 44.6 % / Description: NONE
Crystal growDetails: 7% PEG 20000, 0.1M MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: VARIMAX HR
RadiationMonochromator: VARIMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→92 Å / Num. obs: 24055 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.2 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TCS

1tcs


Resolution: 2.2→25.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.878 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1283 5.1 %RANDOM
Rwork0.163 ---
obs0.167 24055 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å21.79 Å2
2---0.46 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 0 267 4245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224044
X-RAY DIFFRACTIONr_bond_other_d0.0010.023706
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9625487
X-RAY DIFFRACTIONr_angle_other_deg1.03338590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1615509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12924.19179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78915681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7721526
X-RAY DIFFRACTIONr_chiral_restr0.1310.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02825
X-RAY DIFFRACTIONr_nbd_refined0.1980.2837
X-RAY DIFFRACTIONr_nbd_other0.1930.23763
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21984
X-RAY DIFFRACTIONr_nbtor_other0.0940.22439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4941.53221
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80524114
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.91731736
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1164.51373
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C46tight positional0.130.05
2A29tight positional0.070.05
1C69medium positional0.610.5
2A101medium positional0.480.5
1C46tight thermal0.30.5
2A29tight thermal0.090.5
1C69medium thermal0.532
2A101medium thermal0.672
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 98
Rwork0.186 1775

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