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- PDB-3n3x: Crystal Structure of the complex formed between type I ribosome i... -

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Basic information

Entry
Database: PDB / ID: 3n3x
TitleCrystal Structure of the complex formed between type I ribosome inactivating protein and hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 1.7 A resolution
Components
  • Ribosome inactivating proteinRibosome-inactivating protein
  • SDDDMG peptide
KeywordsHYDROLASE / RIP / Plant protein / Ribosome inactivating protein / hexapeptide
Function / homology
Function and homology information


cytoplasmic translational elongation / fungal-type vacuole / rRNA N-glycosylase / rRNA N-glycosylase activity / molecular function inhibitor activity / protein kinase activator activity / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...cytoplasmic translational elongation / fungal-type vacuole / rRNA N-glycosylase / rRNA N-glycosylase activity / molecular function inhibitor activity / protein kinase activator activity / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / cytosolic large ribosomal subunit / cytoplasmic translation / toxin activity / negative regulation of translation / structural constituent of ribosome / nucleotide binding / cytosol
Similarity search - Function
Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / 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. ...Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / 60s Acidic ribosomal protein / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANINE / rRNA N-glycosylase / Large ribosomal subunit protein P2B
Similarity search - Component
Biological speciesMomordica balsamina (balsam apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKushwaha, G.S. / Vikram, G. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of the complex formed between type I ribosome inactivating protein and hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 1.7 A resolution
Authors: Kushwaha, G.S. / Vikram, G. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionMay 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Ribosome inactivating protein
B: SDDDMG peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3084
Polymers27,7322
Non-polymers5762
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.241, 130.241, 39.974
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Ribosome inactivating protein / Ribosome-inactivating protein


Mass: 27093.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica balsamina (balsam apple) / References: UniProt: D9J2T9*PLUS, rRNA N-glycosylase
#2: Protein/peptide SDDDMG peptide


Mass: 638.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P02400*PLUS
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE GIVEN FOR MOMORDICA BALSAMINA IS CORRECT, ITS GENBANK ACCESSION NO. IS HM367595.

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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: 47.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 14% PEG6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 20, 2009 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 27745 / Num. obs: 27745 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.038 / Net I/σ(I): 56.9
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 4.9 / Rsym value: 0.28 / % possible all: 92.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AHA

1aha


Resolution: 1.7→37.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.659 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22165 1384 5 %RANDOM
Rwork0.19772 ---
all0.2105 27745 --
obs0.20996 26128 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.068 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.53 Å20 Å2
2---1.06 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 39 258 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222031
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9912767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1845250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74724.13887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29815329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4741513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021520
X-RAY DIFFRACTIONr_nbd_refined0.2070.21047
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2204
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5260.232
X-RAY DIFFRACTIONr_mcbond_it0.5831.51286
X-RAY DIFFRACTIONr_mcangle_it1.02422032
X-RAY DIFFRACTIONr_scbond_it1.6693843
X-RAY DIFFRACTIONr_scangle_it2.654.5735
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 106 -
Rwork0.308 1756 -
obs--91.81 %

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