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- PDB-7kdu: Ricin bound to VHH antibody V5E4 -

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Basic information

Entry
Database: PDB / ID: 7kdu
TitleRicin bound to VHH antibody V5E4
Components
  • Ricin chain A
  • Ricin chain B
  • VHH antibody V5E4
KeywordsTOXIN / Ribosome inactivating protein
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesVicugna pacos (alpaca)
Ricinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.809 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 9, 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 16, 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 V5E4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5969
Polymers73,1873
Non-polymers1,4096
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-46 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.281, 76.494, 101.440
Angle α, β, γ (deg.)90.000, 90.920, 90.000
Int Tables number4
Space group name H-MP1211

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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 V5E4


Mass: 14260.862 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 , 2 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.: 2
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

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Non-polymers , 3 types, 211 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 290 mM zinc Aaetate and 17% PEG 3,350

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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: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16859 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.077 / Rrim(I) all: 0.147 / Χ2: 1.136 / Net I/σ(I): 5.5 / Num. measured all: 58988
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.853.31.1088220.5560.7121.320.937100
2.85-2.93.30.9478240.7360.5961.1210.935100
2.9-2.963.40.9158290.6990.5771.0840.96799.9
2.96-3.023.40.7588670.7560.4780.8990.98199.9
3.02-3.083.40.5598090.8390.3510.6620.96999.8
3.08-3.153.50.4618590.8590.2880.5451.00799.9
3.15-3.233.50.388440.8920.2350.4480.981100
3.23-3.323.50.318170.9170.1930.3660.966100
3.32-3.423.50.2618580.9380.1610.3081.042100
3.42-3.533.50.2038410.9480.1250.2391.023100
3.53-3.653.60.1578300.9640.0970.1851.077100
3.65-3.83.60.1388520.9810.0860.1631.208100
3.8-3.973.60.1318370.9820.0810.1541.246100
3.97-4.183.60.1218550.9870.0740.1421.32399.9
4.18-4.443.60.0858460.990.0520.11.394100
4.44-4.793.50.0848340.9910.0520.0991.3100
4.79-5.273.60.0828480.9920.050.0961.138100
5.27-6.033.60.0818480.9910.050.0951.123100
6.03-7.593.50.0668740.9950.0410.0781.21100
7.59-503.40.0448650.9940.0280.0521.83797.7

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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: 2.809→30.536 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2937 879 5.22 %
Rwork0.2367 15948 -
obs0.2396 16827 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.47 Å2 / Biso mean: 79.984 Å2 / Biso min: 18.15 Å2
Refinement stepCycle: final / Resolution: 2.809→30.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 86 208 5086
Biso mean--86.13 57.2 -
Num. residues----611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044980
X-RAY DIFFRACTIONf_angle_d0.6896770
X-RAY DIFFRACTIONf_chiral_restr0.045771
X-RAY DIFFRACTIONf_plane_restr0.005864
X-RAY DIFFRACTIONf_dihedral_angle_d13.4422955
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8091-2.98490.36931440.3025250094
2.9849-3.21520.36461410.28922671100
3.2152-3.53830.34011650.26832657100
3.5383-4.04930.27531580.23172662100
4.0493-5.09780.26441340.20282710100
5.0978-30.5360.26511370.22562748100
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)
16.3395-2.11640.28175.57830.85326.44850.43170.1427-0.1310.9547-0.58682.39490.5186-1.24990.2460.8918-0.3010.50150.8887-0.43331.496535.6383-16.6038128.2136
23.17090.89823.45180.98720.06044.73040.2612-0.4816-0.48390.5678-0.42230.4222-0.15440.2599-0.09042.4375-0.17470.40970.0065-0.76171.972436.5508-22.6988136.7007
34.9343-0.6903-0.16173.388-0.53560.09510.0058-0.10910.1721-0.2347-0.1750.6577-0.302-0.13230.09250.6988-0.2387-0.04770.9908-0.77182.609829.1342-29.249122.6569
42.01255.14553.68692.01625.6992.0155-0.1432-0.7016-1.38520.9408-0.46431.19920.2917-0.03080.82851.30970.0790.63991.4622-0.29711.046445.4081-25.5618128.343
58.95522.08873.25162.5513-2.48086.2955-0.6158-0.32810.46080.5038-0.2423-0.0112-1.13010.14810.76430.7302-0.08280.02210.6031-0.24110.976258.9956-21.8226129.4592
69.82081.98722.07910.40560.47610.4558-0.9047-0.1175-2.33040.38170.07830.43910.60640.03120.61581.13740.05920.17730.595-0.12591.177646.7728-29.6892128.806
74.3058-2.57281.0325.18641.26513.52310.2172-0.0921-0.2339-0.1096-0.32160.27590.2509-0.22070.08810.4215-0.07180.0150.24670.00780.336761.41182.9863145.0157
810.0342-4.44020.71227.94661.01645.632-0.2001-0.46521.0091.03890.2915-1.3076-0.51710.0777-0.12880.6017-0.06520.03590.3174-0.06220.628372.53359.3763155.9474
95.0999-2.0962.40375.6781-0.10455.66740.05830.79410.0101-0.5047-0.3222-0.3862-0.25070.43880.23910.3878-0.06570.04580.34640.00830.325770.97932.535134.5111
101.5297-0.53381.21950.9299-1.32432.0408-0.17390.61110.9853-0.37190.05940.1946-0.59750.81550.3371.3284-0.0931-0.33011.08380.46190.639459.839523.0824118.341
111.1306-0.1093-0.55332.76781.88171.82230.57311.08130.4895-1.22490.57080.1088-0.73750.2163-0.57671.43370.434-0.13132.21030.65610.360953.628321.469799.3537
123.5791-0.33370.95172.582-1.0562.6076-0.93131.22441.16350.30440.3276-0.5604-0.49440.6420.52481.3351-0.2618-0.30541.24510.43180.815857.399225.6292108.2387
134.1244-0.05381.29363.15130.8474.6321-0.83010.74451.1772-0.0917-0.2480.1595-1.08610.32491.02241.11230.0121-0.41020.99740.24210.749844.816526.2419111.1015
142.26770.27721.69712.3592-1.52642.3335-0.02531.9390.1022-0.71340.28350.40010.4704-0.2788-0.24081.0258-0.0737-0.19691.37730.19210.50948.027913.8405108.0344
151.2062-0.20660.3923.525-1.50923.36770.38991.5206-0.2706-0.68430.1153-0.70090.6050.0022-0.37940.74780.1257-0.1191.168-0.42340.575457.6805-8.656118.1484
163.0007-0.25520.59245.2984-0.27681.80890.07351.1473-0.4912-1.3056-0.0856-0.1947-0.2981-0.37730.06340.81460.068-0.06071.0452-0.25830.556555.5187-5.6822110.3325
171.9178-0.30580.20572.8436-0.86976.99820.12911.2778-0.0978-1.2184-0.54421.0911-0.208-1.63140.31840.85120.1587-0.2421.3111-0.1680.734544.145-1.1769114.6858
181.1591-1.8413-1.41544.59670.45654.14240.09161.1575-0.4442-0.2019-0.16970.88780.31740.03590.10420.587-0.0734-0.18450.8286-0.22380.600547.1563-6.4751122.8145
198.02042.0430.49891.65640.94527.26190.3626-0.8082-0.63412.3668-0.31931.68840.99140.0814-0.21831.6274-0.24050.5550.7515-0.32161.734243.3587-30.0859135.3332
203.02481.7969-0.7817.259-4.63254.5237-0.5426-0.51040.45430.4984-0.16020.67650.62750.12960.40981.7527-0.53391.10891.9736-0.94091.02748.8183-20.3054137.6155
215.7573-3.3013-0.07268.30760.49575.18111.21520.7770.0585-0.0349-1.33951.22660.05330.20410.26310.7008-0.17060.13961.3068-0.69131.555239.1726-26.7467121.614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 51 through 73 )C51 - 73
2X-RAY DIFFRACTION2chain 'C' and (resid 74 through 83 )C74 - 83
3X-RAY DIFFRACTION3chain 'C' and (resid 84 through 94 )C84 - 94
4X-RAY DIFFRACTION4chain 'C' and (resid 95 through 100 )C95 - 100
5X-RAY DIFFRACTION5chain 'C' and (resid 101 through 109 )C101 - 109
6X-RAY DIFFRACTION6chain 'C' and (resid 110 through 117 )C110 - 117
7X-RAY DIFFRACTION7chain 'A' and (resid 6 through 86 )A6 - 86
8X-RAY DIFFRACTION8chain 'A' and (resid 87 through 113 )A87 - 113
9X-RAY DIFFRACTION9chain 'A' and (resid 114 through 261 )A114 - 261
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 15 )B3 - 15
11X-RAY DIFFRACTION11chain 'B' and (resid 16 through 37 )B16 - 37
12X-RAY DIFFRACTION12chain 'B' and (resid 38 through 66 )B38 - 66
13X-RAY DIFFRACTION13chain 'B' and (resid 67 through 102 )B67 - 102
14X-RAY DIFFRACTION14chain 'B' and (resid 103 through 139 )B103 - 139
15X-RAY DIFFRACTION15chain 'B' and (resid 140 through 155 )B140 - 155
16X-RAY DIFFRACTION16chain 'B' and (resid 156 through 192 )B156 - 192
17X-RAY DIFFRACTION17chain 'B' and (resid 193 through 221 )B193 - 221
18X-RAY DIFFRACTION18chain 'B' and (resid 222 through 262 )B222 - 262
19X-RAY DIFFRACTION19chain 'C' and (resid -1 through 23 )C-1 - 23
20X-RAY DIFFRACTION20chain 'C' and (resid 24 through 33 )C24 - 33
21X-RAY DIFFRACTION21chain 'C' and (resid 34 through 49 )C34 - 49

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