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- PDB-7kd2: Ricin bound to VHH antibody V11B2 -

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Basic information

Entry
Database: PDB / ID: 7kd2
TitleRicin bound to VHH antibody V11B2
Components
  • Ricin chain A
  • Ricin chain B
  • VHH antibody V11B2
KeywordsTOXIN / Ribosome inactivationg protein / VHH antibody
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
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 ...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
Similarity search - Domain/homology
Biological speciesVicugna pacos (alpaca)
Ricinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 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.Mol.Biol. / Year: 2021
Title: Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin's A-B Subunit Interface.
Authors: Rudolph, M.J. / Poon, A.Y. / Kavaliauskiene, S. / Myrann, A.G. / Reynolds-Peterson, C. / Davis, S.A. / Sandvig, K. / Vance, D.J. / Mantis, N.J.
History
DepositionOct 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin chain A
B: Ricin chain B
C: VHH antibody V11B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,68219
Polymers72,6933
Non-polymers1,98916
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-219 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.607, 99.559, 111.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ricin chain A


Mass: 29936.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Glycosidase / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase
#2: Protein Ricin chain B


Mass: 28989.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Lectin / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase

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Antibody , 1 types, 1 molecules C

#3: Antibody VHH antibody V11B2


Mass: 13766.271 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)

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Sugars , 3 types, 3 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 195 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 200 mM Zinc Acetate, 100 mM MES pH 6.0, 10% PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.546→50 Å / Num. obs: 28832 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 38.67 Å2 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.091 / Rrim(I) all: 0.23 / Χ2: 0.992 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.595.41.70914250.5590.8071.8950.8999.6
2.59-2.645.41.67313980.630.7861.8540.88299.9
2.64-2.695.41.38614180.6910.6531.5370.88499.6
2.69-2.755.51.33314170.7260.621.4740.91399.8
2.75-2.815.61.11714370.7850.5161.2340.925100
2.81-2.875.70.89214160.8040.4090.9840.93199.8
2.87-2.945.80.8514220.8460.3850.9350.98499.9
2.94-3.025.90.74214180.8760.3340.8160.925100
3.02-3.1160.54814450.9180.2430.6020.94599.8
3.11-3.216.20.41514200.9420.1820.4550.93599.9
3.21-3.336.30.32614300.9470.1410.3570.97899.7
3.33-3.466.40.26314090.9650.1120.2870.96999.9
3.46-3.626.50.18914490.9730.080.2061.00199.7
3.62-3.816.70.14514310.9780.0610.1571.06799.7
3.81-4.056.90.16414500.9950.0670.1781.076100
4.05-4.3670.12214580.9920.0490.1311.097100
4.36-4.87.10.10714600.9940.0430.1161.139100
4.8-5.497.10.12214820.9940.0490.1320.986100
5.49-6.9270.1414900.990.0570.1521.037100
6.92-506.40.06115570.9980.0260.0661.10597.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AAI, 3EZJ

2aai

3ezj


Resolution: 2.55→26.189 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2802 1454 5.06 %
Rwork0.2265 27281 -
obs0.2292 28735 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.62 Å2 / Biso mean: 52.5897 Å2 / Biso min: 16.93 Å2
Refinement stepCycle: final / Resolution: 2.55→26.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4952 0 104 182 5238
Biso mean--71.91 42.66 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015188
X-RAY DIFFRACTIONf_angle_d1.0817077
X-RAY DIFFRACTIONf_chiral_restr0.059805
X-RAY DIFFRACTIONf_plane_restr0.006914
X-RAY DIFFRACTIONf_dihedral_angle_d5.5654014
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.63720.35581370.2991264598
2.6372-2.74270.34941470.29582680100
2.7427-2.86740.36891360.28292723100
2.8674-3.01840.34731280.28852704100
3.0184-3.20720.34841640.27072679100
3.2072-3.45430.32061480.24782707100
3.4543-3.8010.29371640.21622712100
3.801-4.34880.2371490.1991273099
4.3488-5.47080.22621260.1819278999
5.4708-26.1890.21611550.19452912100
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)
17.54092.8644-5.89064.4033-1.07865.4483-0.50490.1097-0.4807-0.08190.2289-0.21990.6710.08450.2940.31470.0529-0.01880.4435-0.07930.2164-5.747317.7146-20.1162
26.3664-1.9272-2.57982.7147-0.17163.0548-0.056-0.3866-0.6574-0.1494-0.2032-0.29810.11820.24650.1790.35310.02190.00070.2969-0.0290.3209-1.546718.0944-16.3053
36.33711.59530.40032.008-0.0853.7505-0.1499-0.83290.42620.65130.4207-0.4529-0.18960.388-0.26150.29660.01890.05120.6096-0.13590.3479-5.788826.3253-10.1897
47.10860.51930.42972.4626-0.57263.0614-0.21850.01060.57030.13640.19740.01560.04480.04460.0240.23370.0109-0.0110.2779-0.05360.2281-6.334830.0287-18.7507
55.14021.278-0.01174.9350.29545.9085-0.0780.74210.8179-0.17390.7799-0.216-0.59680.7275-0.70360.3703-0.0610.13370.5250.06920.805515.913645.6056-25.4107
62.07-1.35193.5045.9774-3.27912.0833-0.1942-0.32471.4990.1619-0.2028-0.6285-0.11890.70840.51470.38720.0013-0.02271.0221-0.14140.711813.512239.3218-16.9322
79.0183-0.5296-2.68168.94842.56637.94820.1844-0.16912.47510.41560.079-0.57050.0524-0.1187-0.38670.27420.02270.07670.62660.04940.78655.276646.2269-19.2622
86.0391-0.1841-5.78893.5002-0.30665.59840.84070.39361.0184-1.15091.78990.4793-1.191-0.9206-2.44310.8941-0.31410.20340.73310.18141.333910.663149.8192-29.806
92.9384-1.1828-1.23463.50950.01140.492-0.03850.72780.5663-0.05350.4896-1.0791-0.26590.505-0.6290.3572-0.02970.0350.7958-0.10740.762313.189140.2055-21.8332
107.60776.32276.16668.28476.77617.6159-0.50520.70151.06490.09480.3512-0.6112-0.23261.04090.050.31230.0498-0.07380.69270.01581.067320.448941.7774-22.5837
112.0249-4.19822.69562.198-1.75621.65990.0231.05350.8963-0.333-0.4047-0.43060.21340.60110.34620.4908-0.23790.05110.99330.1480.4557-5.681428.2143-50.8064
127.7294-2.7596-0.32751.9105-0.32456.9344-0.10750.67820.41880.0530.16920.1552-0.4036-0.284-0.01380.2984-0.06170.00140.4690.03320.3277-18.366428.5529-42.1313
130.9108-1.1868-0.6053.45990.46274.4067-0.06511.11850.0903-0.09330.3035-0.11610.39850.1138-0.24490.3614-0.03130.00571.0632-0.03420.3088-12.22820.5811-55.8214
141.1005-1.1878-0.00532.302-1.7974.5037-0.03671.5162-0.4702-0.1096-0.17190.0932-0.049-0.17120.14650.588-0.0049-0.02541.5872-0.17760.3257-20.053318.558-61.7923
156.63040.59861.48869.9991-0.23078.2433-0.08090.4908-1.0488-0.59260.9225-0.21360.83920.9875-0.83670.58380.07060.01130.6774-0.20930.3865-9.80834.8324-46.915
162.9853-0.3021-1.48751.0651.04073.5067-0.13010.3898-0.2677-0.11460.0958-0.16680.19450.74990.02380.4198-0.00830.04290.789-0.05730.3085-4.919115.0089-47.8639
177.4396-3.5427-4.41773.28031.07027.9239-0.18010.3514-0.22280.0407-0.0597-0.00580.36060.2230.2640.3384-0.0318-0.02470.4567-0.02850.2127-13.720912.7468-36.2188
186.1342-2.0783-0.90725.57-0.56996.7412-0.44450.2039-0.410.09280.38380.19020.3015-0.53710.08430.2818-0.09590.03310.4407-0.10420.2966-20.877312.6329-26.0471
194.11142.65211.65334.1020.58676.9110.26151.03230.34880.2615-0.04050.0873-0.072-1.1294-0.44550.2877-0.03920.05250.66220.02880.3117-24.778723.2257-35.1005
204.07880.2689-1.11372.62210.04723.0293-0.12420.3201-0.43510.009-0.08750.23330.3582-0.49540.22870.2512-0.03050.04360.3786-0.03960.2236-34.815317.5014-9.096
215.2301-0.4504-1.0384.1368-1.60452.59660.0026-0.02790.1214-0.01280.02950.00750.0881-0.3822-0.0220.2336-0.0455-0.00830.2137-0.06360.2258-28.096527.1237-9.5585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 135 through 155 )B135 - 155
2X-RAY DIFFRACTION2chain 'B' and (resid 156 through 180 )B156 - 180
3X-RAY DIFFRACTION3chain 'B' and (resid 181 through 202 )B181 - 202
4X-RAY DIFFRACTION4chain 'B' and (resid 203 through 262 )B203 - 262
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 39 )C1 - 39
6X-RAY DIFFRACTION6chain 'C' and (resid 40 through 52 )C40 - 52
7X-RAY DIFFRACTION7chain 'C' and (resid 53 through 71 )C53 - 71
8X-RAY DIFFRACTION8chain 'C' and (resid 72 through 82 )C72 - 82
9X-RAY DIFFRACTION9chain 'C' and (resid 83 through 105 )C83 - 105
10X-RAY DIFFRACTION10chain 'C' and (resid 106 through 116 )C106 - 116
11X-RAY DIFFRACTION11chain 'A' and (resid 5 through 17 )A5 - 17
12X-RAY DIFFRACTION12chain 'A' and (resid 18 through 56 )A18 - 56
13X-RAY DIFFRACTION13chain 'A' and (resid 57 through 97 )A57 - 97
14X-RAY DIFFRACTION14chain 'A' and (resid 98 through 122 )A98 - 122
15X-RAY DIFFRACTION15chain 'A' and (resid 123 through 140 )A123 - 140
16X-RAY DIFFRACTION16chain 'A' and (resid 141 through 194 )A141 - 194
17X-RAY DIFFRACTION17chain 'A' and (resid 195 through 219 )A195 - 219
18X-RAY DIFFRACTION18chain 'A' and (resid 220 through 248 )A220 - 248
19X-RAY DIFFRACTION19chain 'A' and (resid 249 through 262 )A249 - 262
20X-RAY DIFFRACTION20chain 'B' and (resid 2 through 84 )B2 - 84
21X-RAY DIFFRACTION21chain 'B' and (resid 85 through 134 )B85 - 134

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