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- PDB-7tgi: Single-domain VHH intrabodies neutralize ricin toxin -

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Basic information

Entry
Database: PDB / ID: 7tgi
TitleSingle-domain VHH intrabodies neutralize ricin toxin
Components
  • Ricin chain A
  • VHH antibody
KeywordsIMMUNE SYSTEM/TOXIN / ricin toxin / VHH antibody / IMMUNE SYSTEM / IMMUNE SYSTEM-TOXIN 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
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.104 Å
AuthorsRudolph, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins.
Authors: Czajka, T.F. / Vance, D.J. / Davis, S. / Rudolph, M.J. / Mantis, N.J.
History
DepositionJan 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin chain A
B: VHH antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8208
Polymers44,5812
Non-polymers2396
Water2,162120
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)44.129, 84.407, 109.945
Angle α, β, γ (deg.)90.000, 97.060, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

CL

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Components

#1: Protein Ricin chain A


Mass: 29936.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody VHH antibody


Mass: 14644.257 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VHH antibody / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG'
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM magnesium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 22929 / % possible obs: 98.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.85 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.059 / Rrim(I) all: 0.109 / Χ2: 1.243 / Net I/σ(I): 6.5 / Num. measured all: 74897
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.80.68210870.5860.480.8380.54797
2.14-2.182.90.58311630.6480.4060.7140.59897.7
2.18-2.223.30.51411170.7060.3350.6160.61399.4
2.22-2.263.30.47511620.780.3070.5670.62399.1
2.26-2.313.40.40911420.850.2610.4860.66199.6
2.31-2.373.40.35811480.8760.2260.4250.68499.2
2.37-2.423.30.3311400.8750.2120.3930.71299.5
2.42-2.493.30.29511690.9040.1890.3510.73498.9
2.49-2.563.20.24211380.9250.1570.290.81998.9
2.56-2.653.10.20611380.9330.1390.2490.98398.4
2.65-2.743.50.17211470.9650.1080.2040.99799.5
2.74-2.853.50.15111510.9710.0950.1791.05799.6
2.85-2.983.40.12911780.9740.0820.1541.24499.3
2.98-3.143.40.10711550.9750.0690.1281.48298.8
3.14-3.333.20.09111060.9820.0590.1091.63898
3.33-3.593.20.07411350.9880.0480.0881.86997.3
3.59-3.953.50.06311710.9920.040.0741.8398.4
3.95-4.523.30.05911300.990.0380.072.16198.1
4.52-5.73.20.06111590.9870.0410.0742.38598.6
5.7-503.20.06311930.9930.0420.0772.96398.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTC, 4LGR

1rtc

4lgr


Resolution: 2.104→42.203 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1089 4.75 %
Rwork0.1763 21837 -
obs0.1784 22926 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.17 Å2 / Biso mean: 45.7338 Å2 / Biso min: 23 Å2
Refinement stepCycle: final / Resolution: 2.104→42.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 9 120 3068
Biso mean--50.94 46.81 -
Num. residues----371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083024
X-RAY DIFFRACTIONf_angle_d0.8714110
X-RAY DIFFRACTIONf_chiral_restr0.056454
X-RAY DIFFRACTIONf_plane_restr0.005537
X-RAY DIFFRACTIONf_dihedral_angle_d2.8492254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.104-2.19930.29381350.2423263096
2.1993-2.31530.23731350.2265274199
2.3153-2.46030.30311450.2136274899
2.4603-2.65030.25581200.2024272999
2.6503-2.91690.25621530.1874273599
2.9169-3.33890.22511450.1819271599
3.3389-4.2060.19681320.1582273798
4.206-42.2030.18711240.1536280298
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)
15.94350.1778-1.76984.0437-4.46867.2942-0.1315-0.17170.614-0.0431-0.5797-1.1849-0.18151.0640.71450.2688-0.0032-0.05660.45270.06930.520525.5128-8.89441.7104
28.70615.0803-0.79413.4263-2.14066.24380.3492-0.12180.5898-0.113-0.55130.52010.69330.12180.13150.3630.0004-0.02650.2284-0.0260.257915.2636-13.647137.3236
36.1671-0.92021.24879.52523.06064.2890.03370.2859-0.4108-0.728-0.15031.55180.33450.0758-0.10270.43120.0157-0.05580.29690.05060.407510.6086-16.607335.2032
44.65172.5871-3.55674.88611.09045.79370.93230.8832.9682-0.1358-1.0074-0.4747-2.38240.1396-0.46120.8173-0.04210.02030.35580.0820.772916.35741.963739.3245
57.8623.0019-2.33244.6045-5.21297.0530.32520.10290.63740.540.24281.2542-0.2273-0.6958-0.44490.37140.0370.00730.34040.01140.33467.3316-7.922642.1009
67.94820.3674-1.79895.12090.85176.1362-0.0282-0.4677-0.12040.32990.2043-0.6769-0.37070.5929-0.2840.338-0.0225-0.03810.423-0.00970.341417.966-9.235647.4339
73.81350.5917-1.82527.9055-1.75027.8801-0.1603-0.1325-0.02130.217-0.01710.23470.6118-0.60840.18020.3162-0.0496-0.01680.3535-0.020.254512.1048-18.8642.3975
86.6011-0.78561.01651.0652.71998.63310.39930.72010.1656-1.0037-0.6989-0.8907-0.19840.64070.22710.41090.05650.04070.31820.12710.475116.39-7.411729.5659
95.3622-2.50894.53652.9089-1.14054.40330.39251.4440.1982-0.5514-0.3773-0.6598-0.19290.8775-0.03090.37330.06860.05820.41870.04380.376621.6694-12.071730.1466
102.29831.65041.7482.18771.53812.1475-0.2125-0.9974-0.89160.1214-0.3807-0.30540.95450.99290.40660.58510.03920.06630.37590.10.365416.3132-24.63343.2893
112.8850.0151-1.69513.1649-0.69443.1069-0.2336-0.21370.13520.47480.05090.1732-0.2808-0.04070.10590.34950.0051-0.07220.2927-0.00960.27239.285312.478127.394
121.9898-0.66570.17983.8991-0.67735.1143-0.22490.0909-0.06070.13020.0301-0.1197-0.2782-0.0770.07780.27660.0263-0.01850.1795-0.00790.2537.611217.720914.586
133.2789-0.4246-0.28584.53350.96524.2013-0.0668-0.02320.0286-0.0820.07670.3238-0.2399-0.10440.04270.2443-0.0105-0.02540.31260.03570.2513.324812.40798.6963
143.9358-1.48883.07977.1684-6.14818.8418-0.17430.3329-0.1791-0.332-0.0437-0.56170.06050.64980.47490.2911-0.02080.01790.45910.02470.259418.253612.13027.0203
156.133-0.24950.9244.4209-1.18567.34350.1030.53440.1723-0.15150.0552-0.3757-0.06980.1821-0.11670.25670.03630.05250.32190.03650.343411.69599.02465.5568
169.4366-3.4595-2.48196.4902-0.83863.3861-0.1231-0.1671-0.65750.1988-0.1381-0.13480.15190.37920.36280.30810.0056-0.01210.26670.03270.340414.80221.420422.9256
172.54660.1261-0.68322.4610.27463.6988-0.2828-0.0014-0.5551-0.3411-0.03560.09380.28410.23740.35590.29930.02840.00590.28090.06310.31527.3833-2.864120.4904
187.3693-4.0651-4.56516.9244.31713.8860.0582-0.2119-0.7470.0343-0.21190.43580.5548-0.67370.12870.3694-0.0717-0.09190.47530.07490.37710.1046-9.878628.4909
195.8469-0.35651.04127.6085-1.50652.9105-0.353-0.5052-0.53310.47670.59770.74470.1361-0.3906-0.19740.253-0.03550.0950.34570.06250.32160.4826-3.194930.4056
202.5772-1.7016-3.47153.45732.41215.3117-0.071-1.1197-0.20611.12190.16870.11280.60340.90850.19950.8065-0.0832-0.0930.57940.11060.353515.7372-25.640848.3052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 17 through 31 )B17 - 31
2X-RAY DIFFRACTION2chain 'B' and (resid 32 through 38 )B32 - 38
3X-RAY DIFFRACTION3chain 'B' and (resid 39 through 50 )B39 - 50
4X-RAY DIFFRACTION4chain 'B' and (resid 51 through 56 )B51 - 56
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 63 )B57 - 63
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 82 )B64 - 82
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 98 )B83 - 98
8X-RAY DIFFRACTION8chain 'B' and (resid 99 through 108 )B99 - 108
9X-RAY DIFFRACTION9chain 'B' and (resid 109 through 113 )B109 - 113
10X-RAY DIFFRACTION10chain 'B' and (resid 114 through 122 )B114 - 122
11X-RAY DIFFRACTION11chain 'A' and (resid 6 through 52 )A6 - 52
12X-RAY DIFFRACTION12chain 'A' and (resid 53 through 97 )A53 - 97
13X-RAY DIFFRACTION13chain 'A' and (resid 98 through 140 )A98 - 140
14X-RAY DIFFRACTION14chain 'A' and (resid 141 through 154 )A141 - 154
15X-RAY DIFFRACTION15chain 'A' and (resid 155 through 174 )A155 - 174
16X-RAY DIFFRACTION16chain 'A' and (resid 175 through 193 )A175 - 193
17X-RAY DIFFRACTION17chain 'A' and (resid 194 through 219 )A194 - 219
18X-RAY DIFFRACTION18chain 'A' and (resid 220 through 238 )A220 - 238
19X-RAY DIFFRACTION19chain 'A' and (resid 239 through 259 )A239 - 259
20X-RAY DIFFRACTION20chain 'B' and (resid 4 through 16 )B4 - 16

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