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- PDB-5j57: V5E1-RTA complex -

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Basic information

Entry
Database: PDB / ID: 5j57
TitleV5E1-RTA complex
Components
  • Ricin
  • VHH single chain antibody V5E1
KeywordsHYDROLASE/IMMUNE SYSTEM / Ricin / RTA / single chain antibodies (VHH) / HYDROLASE-IMMUNE SYSTEM 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 (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. / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...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. / Ricin-type beta-trefoil lectin domain / 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 / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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: 2017
Title: Structural Analysis of Single Domain Antibodies Bound to a Second Neutralizing Hot Spot on Ricin Toxin's Enzymatic Subunit.
Authors: Rudolph, M.J. / Vance, D.J. / Cassidy, M.S. / Rong, Y. / Mantis, N.J.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Apr 12, 2017Group: Source and taxonomy / Structure summary
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin
B: VHH single chain antibody V5E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,13010
Polymers43,7662
Non-polymers3638
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.692, 68.216, 71.570
Angle α, β, γ (deg.)90.000, 92.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ricin


Mass: 30067.953 Da / Num. of mol.: 1 / Fragment: UNP residues 39-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody VHH single chain antibody V5E1


Mass: 13698.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM Tris pH 7.0 and 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→33.631 Å / Num. obs: 39982 / % possible obs: 97.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Χ2: 1.081 / Net I/av σ(I): 24.621 / Net I/σ(I): 10.2 / Num. measured all: 127807
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.732.60.37118650.65493.5
1.73-1.762.80.31519530.64894.2
1.76-1.792.90.27520090.64498.7
1.79-1.833.10.2519940.7497.9
1.83-1.873.40.219870.68497.9
1.87-1.913.30.1720170.77298.9
1.91-1.963.30.14519870.78497.4
1.96-2.023.30.12120220.78599.2
2.02-2.073.30.10419930.86297.8
2.07-2.143.30.09420390.97398.7
2.14-2.223.30.08419801.00498.5
2.22-2.313.30.07820371.16898.4
2.31-2.413.30.0720361.08799.1
2.41-2.543.30.06620001.15298.8
2.54-2.73.30.0620261.24199
2.7-2.913.30.05620321.35798.5
2.91-3.23.20.05220311.59698.3
3.2-3.663.10.04820001.84697.6
3.66-4.613.10.04320091.92896.9
4.61-503.20.04219651.53492.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å33.58 Å
Translation2 Å33.58 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.2data extraction
HKL-2000v1.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.631 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.63
RfactorNum. reflection% reflection
Rfree0.1897 2042 5.11 %
Rwork0.163 --
obs0.1644 39956 97.43 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 44.288 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 83.05 Å2 / Biso mean: 25.31 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.206 Å20 Å2-1.0847 Å2
2---4.0618 Å20 Å2
3---5.2678 Å2
Refinement stepCycle: final / Resolution: 1.7→33.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 17 358 3402
Biso mean--33.8 36.52 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043150
X-RAY DIFFRACTIONf_angle_d0.8164276
X-RAY DIFFRACTIONf_chiral_restr0.058468
X-RAY DIFFRACTIONf_plane_restr0.004566
X-RAY DIFFRACTIONf_dihedral_angle_d11.8551152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6995-1.7390.29891200.25172367248791
1.739-1.78250.26991170.22872503262097
1.7825-1.83070.24361190.19672541266098
1.8307-1.88450.21231090.17772548265798
1.8845-1.94530.19341250.16592575270098
1.9453-2.01490.18091130.15912558267199
2.0149-2.09550.21251520.15782514266698
2.0955-2.19090.20771790.15852519269898
2.1909-2.30640.17681560.15192534269098
2.3064-2.45080.20231580.15742555271399
2.4508-2.640.17741340.1592544267899
2.64-2.90550.17221060.15892602270899
2.9055-3.32560.1942030.1622498270198
3.3256-4.18870.14211520.14662523267597
4.1887-33.6380.2125990.1662533263294
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)
11.599-0.37930.4762.731.11481.3075-0.05730.0020.1891-0.09560.0362-0.1044-0.18630.09380.03440.1083-0.01370.0180.1276-0.00070.09952.474242.84853.4587
23.60680.1568-0.13344.3206-0.3951-0.07440.06750.0987-0.0295-0.2644-0.04880.0418-0.102-0.02930.00110.09390.0064-0.01840.10860.0010.0608-11.4539.995351.3212
33.43490.6124-0.74113.7249-2.21233.5361-0.02060.0440.3506-0.16860.10840.3658-0.1574-0.1939-0.02340.14310.0169-0.04640.1128-0.01170.1785-17.567247.77552.8191
44.712-1.07230.84951.92630.36982.2447-0.0162-0.0757-0.26820.00710.02210.08590.0923-0.0614-0.01330.0822-0.03320.01050.07390.01720.1015-15.358929.04558.1858
53.17023.13021.76783.20491.16971.8348-0.0423-0.0820.0852-0.05870.04210.01790.0758-0.05020.02520.1220.0110.00330.14040.00750.1094-10.41632.306459.1671
62.5855-0.985-0.89282.90284.11916.3731-0.1347-0.1719-0.1705-0.01390.1115-0.03060.19760.1789-0.02390.08270.0317-0.00880.14420.04490.12931.662724.47360.4481
72.08590.75380.63965.5750.14093.3047-0.0127-0.47130.3550.398-0.0270.0876-0.2530.12370.02550.14650.01540.01050.2596-0.06250.11853.192941.670773.7463
84.46776.1472-1.38298.4029-2.36743.68640.3949-0.5433-0.31580.7129-0.4683-0.4465-0.09640.4668-0.05940.21430.0545-0.05680.28640.01140.18745.302432.232776.8935
93.4541-0.32470.59130.0185-0.18391.139-0.0431-0.29790.50280.0418-0.0890.0875-0.33510.25580.08310.2003-0.0329-0.0090.2674-0.06890.20369.980650.583767.6643
101.9637-0.936-0.45891.3157-0.07920.219-0.3569-0.3008-0.61910.46720.15410.79140.33750.12940.19650.42390.02660.12940.17990.04140.46667.6349-3.703943.2944
114.8639-2.42190.80677.2245-0.20492.5645-0.2627-0.1583-0.61210.2090.11480.81770.3771-0.16950.13020.24450.01280.0710.1445-0.02150.20914.13418.677843.7496
123.3391-0.89660.75764.8202-4.52344.2597-0.3658-1.0207-0.25321.03570.5022-0.2726-0.01810.0953-0.10980.42540.1715-0.060.33690.00510.212716.31856.972247.6962
135.3179-1.38530.94462.9469-0.222.6536-0.01480.0755-0.07560.0204-0.07270.07920.29540.05880.06190.20750.02060.040.1031-0.02440.116410.70317.765537.1424
140.8406-1.82130.15266.14191.70561.8087-0.3062-0.1532-0.16350.29060.2370.01850.55010.51690.0280.43730.09970.11460.22430.02810.195914.9257-1.575444.3585
157.4865-2.3966-5.8632.54152.7574.99740.2650.47650.1216-0.41790.0078-0.4603-0.22530.1245-0.37370.20290.03060.01870.2127-0.01670.235112.688319.881645.6066
161.253-2.49-0.72566.06793.01781.8508-0.3947-0.295-0.53370.7551-0.01980.88140.69640.23580.25740.4350.09620.16690.11880.04380.43810.44560.142948.1318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:56)A4 - 56
2X-RAY DIFFRACTION2chain 'A' and (resseq 57:97)A57 - 97
3X-RAY DIFFRACTION3chain 'A' and (resseq 98:122)A98 - 122
4X-RAY DIFFRACTION4chain 'A' and (resseq 123:160)A123 - 160
5X-RAY DIFFRACTION5chain 'A' and (resseq 161:180)A161 - 180
6X-RAY DIFFRACTION6chain 'A' and (resseq 181:201)A181 - 201
7X-RAY DIFFRACTION7chain 'A' and (resseq 202:229)A202 - 229
8X-RAY DIFFRACTION8chain 'A' and (resseq 230:248)A230 - 248
9X-RAY DIFFRACTION9chain 'A' and (resseq 249:267)A249 - 267
10X-RAY DIFFRACTION10chain 'B' and (resseq 2:17)B2 - 17
11X-RAY DIFFRACTION11chain 'B' and (resseq 18:39)B18 - 39
12X-RAY DIFFRACTION12chain 'B' and (resseq 40:51)B40 - 51
13X-RAY DIFFRACTION13chain 'B' and (resseq 52:83)B52 - 83
14X-RAY DIFFRACTION14chain 'B' and (resseq 84:98)B84 - 98
15X-RAY DIFFRACTION15chain 'B' and (resseq 99:109)B99 - 109
16X-RAY DIFFRACTION16chain 'B' and (resseq 110:128)B110 - 128

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