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- PDB-9e40: RTA-RUNT-202 complex -

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Basic information

Entry
Database: PDB / ID: 9.0E+40
TitleRTA-RUNT-202 complex
ComponentsRicin A chain
KeywordsTOXIN / HYDROLASE/INHIBITOR / N-linked Glycosidase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function
Ricin-type beta-trefoil lectin domain / 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 / Ricin-type beta-trefoil ...Ricin-type beta-trefoil lectin domain / 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 / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins
Similarity search - Domain/homology
: / IMIDAZOLE / NICKEL (II) ION / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRudolph, M.J. / Tumer, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072425 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Binding of small molecules at the P-stalk site of ricin A subunit trigger conformational changes that extend into the active site.
Authors: McLaughlin, J.E. / Rudolph, M.J. / Dutta, A. / Li, X.P. / Tsymbal, A.M. / Chen, Y. / Bhattacharya, S. / Algava, B. / Goger, M. / Roberge, J.Y. / Tumer, N.E.
History
DepositionOct 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,41314
Polymers30,3401
Non-polymers1,07213
Water6,125340
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.544, 81.654, 89.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ricin A chain


Mass: 30340.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ricin catalytic subunit, N-linked glycosidase / Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli B (bacteria) / References: UniProt: P02879, rRNA N-glycosylase

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Non-polymers , 6 types, 353 molecules

#2: Chemical ChemComp-A1BH3 / 5-(4-fluoro-2,6-dimethylphenyl)thiophene-2-carboxylic acid


Mass: 250.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11FO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: Tris pH 7.0, 40% PEG 300, and 5% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 25633 / % possible obs: 99.8 % / Redundancy: 9 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.037 / Rrim(I) all: 0.115 / Χ2: 1.311 / Net I/σ(I): 9.5 / Num. measured all: 230090
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.836.40.26312730.9520.9880.1120.2870.62599.7
1.83-1.866.60.26612620.9490.9870.1130.290.67899.7
1.86-1.96.10.2512280.9110.9760.1120.2760.69899.4
1.9-1.946.10.22312600.9660.9910.0980.2450.77599.5
1.94-1.988.10.21612510.9780.9950.0830.2320.847100
1.98-2.038.70.20912820.9860.9960.0770.2230.916100
2.03-2.088.80.18612380.9880.9970.0670.1980.992100
2.08-2.139.10.17712740.9890.9970.0630.1881.05399.9
2.13-2.29.20.16112540.990.9980.0560.1711.12399.9
2.2-2.2790.16412770.9940.9980.0580.1751.15599.7
2.27-2.358.90.1612490.9920.9980.0570.1711.18699.8
2.35-2.449.20.15313060.9940.9980.0540.1621.253100
2.44-2.559.30.14612640.9890.9970.0510.1551.33899.8
2.55-2.698.60.13412780.9780.9940.0490.1441.413100
2.69-2.869.30.12512770.9940.9990.0430.1331.51899.6
2.86-3.0811.50.11712980.9970.9990.0360.1221.639100
3.08-3.3911.90.09612970.99810.0290.11.756100
3.39-3.8810.70.08413090.99810.0260.0891.772100
3.88-4.8810.80.06513310.9980.9990.0210.0691.86899.8
4.88-5010.70.0614250.99810.0190.0631.90799.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.31 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 16.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1801 1322 5.17 %
Rwork0.158 --
obs0.1592 25582 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 52 340 2493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052192
X-RAY DIFFRACTIONf_angle_d0.6962978
X-RAY DIFFRACTIONf_dihedral_angle_d14.347798
X-RAY DIFFRACTIONf_chiral_restr0.047326
X-RAY DIFFRACTIONf_plane_restr0.007392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.22871410.17692616X-RAY DIFFRACTION99
1.87-1.960.22221450.16842651X-RAY DIFFRACTION100
1.96-2.060.19921330.1572663X-RAY DIFFRACTION100
2.06-2.190.19171600.15272651X-RAY DIFFRACTION100
2.19-2.360.19221420.15382691X-RAY DIFFRACTION100
2.36-2.60.18891490.16472665X-RAY DIFFRACTION100
2.6-2.970.18171380.16252715X-RAY DIFFRACTION100
2.97-3.740.16261510.15452742X-RAY DIFFRACTION100
3.74-39.310.15121630.15162866X-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)
11.92031.3038-1.37841.2731-0.82281.0089-0.0096-0.0389-0.0301-0.1283-0.0120.02710.0534-0.0814-0.01980.04610.0084-0.03160.09140.01410.07420.8493-8.5532-18.8239
20.9155-0.0709-0.25931.3103-0.23041.11610.05530.03640.09710.0631-0.06490.1354-0.0906-0.2510.0640.04090.01490.00360.06910.01670.07894.8987-7.027-10.8167
32.1737-0.6826-0.71451.5902-0.78431.4021-0.0011-0.0677-0.11990.0078-0.01440.07110.1348-0.06930.02150.0411-0.0285-0.00270.0480.00810.053513.5892-18.1849-8.9826
41.950.46740.30721.84290.21912.06760.010.14680.07-0.0642-0.0291-0.12740.04360.13830.00840.01710.01220.02060.0572-0.00150.056123.2965-10.3387-20.7475
50.8024-0.3136-0.30721.16330.29051.3878-0.02760.01060.07350.06660.0385-0.0268-0.1270.0257-0.03030.0394-0.0098-0.00620.0415-0.00010.064516.5033.1982-14.1585
62.15210.8229-0.84122.1286-0.61851.26860.0612-0.14840.2530.0785-0.06610.064-0.29070.13530.00010.1917-0.0171-0.01450.0724-0.010.097714.598111.1014-5.9162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 122 )
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 160 )
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 262 )

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