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- PDB-7kd0: Ricin bound to VHH antibody V2C11 -

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Basic information

Entry
Database: PDB / ID: 7kd0
TitleRicin bound to VHH antibody V2C11
Components
  • Anti-RON nanobody
  • Ricin chain A
  • Ricin chain B
KeywordsTOXIN / Ribosome inactivating 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
beta-D-galactopyranose / Ricin
Similarity search - Component
Biological speciesLama glama (llama)
Ricinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.768 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

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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: Anti-RON nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,28717
Polymers72,7813
Non-polymers2,50614
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-48 kcal/mol
Surface area26410 Å2
Unit cell
Length a, b, c (Å)76.223, 100.817, 129.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase

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Antibody , 1 types, 1 molecules C

#3: Antibody Anti-RON nanobody


Mass: 13854.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 5 molecules

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


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 2
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
#6: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 167 molecules

#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM Zinc Acetate, 14% PEG 8,000, 22% Glycerol, 80 mM NaCaco pH 6.5, 3% D+Galactose

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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: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.768→50 Å / Num. obs: 26051 / % possible obs: 99.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.081 / Rrim(I) all: 0.198 / Χ2: 1.231 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.77-2.822.90.81612420.6850.5410.9850.98795.3
2.82-2.873.70.82212560.720.4840.9590.93498.9
2.87-2.924.50.72712800.7970.3790.8230.98599.6
2.92-2.985.20.70712880.8540.3390.7870.97299.8
2.98-3.055.50.63112930.8750.2920.6970.994100
3.05-3.125.60.512680.90.2290.5520.96599.9
3.12-3.25.60.43713040.9230.20.4820.96899.8
3.2-3.285.60.35212850.9410.1610.3880.99999.6
3.28-3.385.60.33712800.9450.1540.3721.0699.8
3.38-3.495.60.25913060.9650.1170.2851.08199.6
3.49-3.615.60.21112880.9720.0940.2321.1799.8
3.61-3.765.70.19812870.970.0890.2171.6999.7
3.76-3.935.70.16113110.9860.0720.1761.29799.7
3.93-4.145.90.15312840.9860.0680.1681.3799.9
4.14-4.460.12813210.990.0560.141.73299.9
4.4-4.746.20.11313170.9940.0490.1241.658100
4.74-5.216.50.11213180.9940.0480.1221.215100
5.21-5.966.60.12713380.9910.0530.1381.11100
5.96-7.516.50.11913630.9930.050.1291.14799.9
7.51-5060.06814220.9960.030.0751.72298.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AAI, 3EZJ

2aai

3ezj


Resolution: 2.768→32.428 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 1339 5.15 %
Rwork0.2071 24637 -
obs0.2095 25976 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.62 Å2 / Biso mean: 43.3933 Å2 / Biso min: 9.61 Å2
Refinement stepCycle: final / Resolution: 2.768→32.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 155 158 5290
Biso mean--67.98 36.83 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035245
X-RAY DIFFRACTIONf_angle_d0.5997150
X-RAY DIFFRACTIONf_chiral_restr0.046823
X-RAY DIFFRACTIONf_plane_restr0.004916
X-RAY DIFFRACTIONf_dihedral_angle_d14.4863137
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.768-2.86690.33241450.269232696
2.8669-2.98160.36131340.26442427100
2.9816-3.11720.33571320.24942435100
3.1172-3.28140.31311310.25052452100
3.2814-3.48680.28951280.22392452100
3.4868-3.75560.24641220.19482457100
3.7556-4.13290.21951350.18582456100
4.1329-4.72930.1971410.15882480100
4.7293-5.95240.22221350.18772510100
5.9524-32.4280.24121360.21542642100
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)
18.5776-3.84423.3624.464-4.68754.97690.5511-0.4164-0.6082-0.3519-0.11690.84710.1314-0.451-0.37390.508-0.0648-0.07740.5164-0.03410.6134-25.1467118.793729.7776
23.5084.9154-0.18267.1831-1.26892.5195-0.0920.25170.59-0.341-0.05320.513-0.1895-0.13660.19470.25110.0818-0.03640.2658-0.01630.28952.6624122.335954.7456
35.1138-0.5191-4.01430.84080.44313.01550.16540.1020.432-0.00670.0719-0.17480.0163-0.1832-0.16890.1826-0.0166-0.03030.2585-0.02380.206913.1703122.693857.3705
46.3633.9972-0.20425.240.18896.87520.1404-0.3824-0.07320.3653-0.0362-0.2286-0.27670.4433-0.08290.2085-0.0089-0.02720.27440.01910.207914.4834123.457171.6243
55.3143-0.6036-1.11235.64770.51645.3586-0.0256-0.4133-0.02720.07630.0655-0.17570.2936-0.1365-0.06620.1494-0.00320.00360.23180.03760.20262.9229111.294570.8074
67.31750.87-0.66911.88090.91160.59130.11990.5993-0.4196-0.0049-0.1177-0.01-0.05990.0959-0.09660.2234-0.0230.01750.2357-0.08650.28023.706110.007453.5838
73.2891-0.2908-3.50193.3603-0.14644.4931-0.31270.1345-0.2158-0.03050.2220.08520.52680.10950.12910.29570.0048-0.04360.2987-0.04250.205214.1674101.704552.277
88.47874.20136.07368.52954.03714.5167-0.65990.1739-0.0386-0.79610.4262-0.8005-0.41210.35180.13970.3309-0.0320.02240.3012-0.03670.257121.6601112.859448.5871
92.47170.1096-0.52121.7104-0.24442.9796-0.0269-0.06130.0626-0.07550.1849-0.2719-0.07790.3314-0.14420.2603-0.00690.02580.3016-0.09910.277129.945796.636829.9585
104.394-2.4426-0.73142.9170.45392.05870.0220.2044-0.3972-0.1748-0.00790.38560.2216-0.2077-0.01910.2673-0.0531-0.03470.2686-0.07090.25592.2844102.41633.5768
114.8967-0.4572-1.93853.69220.11092.0186-0.16220.101-0.1604-0.4551-1.07130.19760.51530.65881.34060.69840.04310.04390.36550.01040.7581-24.5365125.017428.4918
128.6487-0.17222.73555.11110.42342.23750.16480.1029-0.6602-0.05270.42370.7570.1706-0.2566-0.55390.39860.04870.02320.36810.08570.4988-18.5807119.991832.0612
138.1891-3.4906-0.85447.1335-1.10643.90740.52650.59030.7511-0.7191-0.1652-0.25530.0347-0.3775-0.30990.32930.03560.0220.34170.14780.471-11.2404123.213627.7413
141.6932-1.9081.69743.5194-4.39128.60390.22240.6691-0.7119-0.5455-0.35240.4773-0.00180.23960.14550.51390.1098-0.1720.69620.04760.7065-21.4213119.666721.2879
153.8175-3.54061.07524.8911.0472.8984-0.1825-0.8715-1.41020.85-0.26610.22520.2789-0.35530.38770.3580.02490.04940.3730.0371.0297-16.4991110.035141.9077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 106 through 116 )C106 - 116
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 32 )A5 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 75 )A33 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 122 )A76 - 122
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 174 )A123 - 174
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 193 )A175 - 193
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 247 )A194 - 247
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 263 )A248 - 263
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 134 )B1 - 134
10X-RAY DIFFRACTION10chain 'B' and (resid 135 through 262 )B135 - 262
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 17 )C0 - 17
12X-RAY DIFFRACTION12chain 'C' and (resid 18 through 45 )C18 - 45
13X-RAY DIFFRACTION13chain 'C' and (resid 46 through 83 )C46 - 83
14X-RAY DIFFRACTION14chain 'C' and (resid 84 through 97 )C84 - 97
15X-RAY DIFFRACTION15chain 'C' and (resid 98 through 105 )C98 - 105

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