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- PDB-4kuc: Crystal structure of ricin-A chain in complex with the antibody 6C2 -

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Basic information

Entry
Database: PDB / ID: 4kuc
TitleCrystal structure of ricin-A chain in complex with the antibody 6C2
Components
  • Ricin
  • mAb6c2 fab-Heavy chain
  • mAb6c2 fab-Light chain
KeywordsHYDROLASE/IMMUNE SYSTEM / RNA-N-glycosidase / 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 / 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 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 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 / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.787 Å
AuthorsZhu, Y. / Li, X. / Teng, M.
CitationJournal: To be Published
Title: Structural insights into the neutralization mechanism of mAb 6C2 against ricin
Authors: Zhu, Y. / Li, X. / Teng, M.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Ricin
D: mAb6c2 fab-Heavy chain
H: mAb6c2 fab-Light chain
I: Ricin
E: mAb6c2 fab-Heavy chain
F: mAb6c2 fab-Light chain


Theoretical massNumber of molelcules
Total (without water)161,1916
Polymers161,1916
Non-polymers00
Water00
1
A: Ricin
D: mAb6c2 fab-Heavy chain
H: mAb6c2 fab-Light chain


Theoretical massNumber of molelcules
Total (without water)80,5953
Polymers80,5953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Ricin
E: mAb6c2 fab-Heavy chain
F: mAb6c2 fab-Light chain


Theoretical massNumber of molelcules
Total (without water)80,5953
Polymers80,5953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.516, 151.803, 208.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ricin / Ricin A chain / rRNA N-glycosidase


Mass: 29936.758 Da / Num. of mol.: 2
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 mAb6c2 fab-Heavy chain


Mass: 25401.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: Hybridoma
#3: Antibody mAb6c2 fab-Light chain


Mass: 25257.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: Hybridoma
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Nacitrate,ph 5.0, 8% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9792 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.787→50 Å / Num. obs: 40594

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.787→36.436 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 34.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2889 1996 4.93 %
Rwork0.2384 --
obs0.2409 40513 93.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.787→36.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8287 0 0 0 8287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098489
X-RAY DIFFRACTIONf_angle_d1.21711624
X-RAY DIFFRACTIONf_dihedral_angle_d13.9192801
X-RAY DIFFRACTIONf_chiral_restr0.0491329
X-RAY DIFFRACTIONf_plane_restr0.0071526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7872-2.85680.3779880.2896169358
2.8568-2.93410.4131110.2892213374
2.9341-3.02040.43641280.2868247085
3.0204-3.11780.33441420.2833275095
3.1178-3.22920.35411490.279288399
3.2292-3.35840.34081510.26112896100
3.3584-3.51110.30781520.24662934100
3.5111-3.6960.31681510.23082897100
3.696-3.92740.26491500.21972929100
3.9274-4.23020.27261530.21082948100
4.2302-4.65510.25011510.18842930100
4.6551-5.32690.24691540.20072963100
5.3269-6.70450.2811550.26572999100
6.7045-36.43890.25091610.25153092100

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