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- PDB-7kbi: Ricin bound to VHH antibody V5E1 -

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Basic information

Entry
Database: PDB / ID: 7kbi
TitleRicin bound to VHH antibody V5E1
Components
  • Ricin chain A
  • Ricin chain B
  • VHH antibody V5E1
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
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: 3.049 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 2, 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 1.2Nov 6, 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 V5E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,98410
Polymers73,4063
Non-polymers1,5777
Water59433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-31 kcal/mol
Surface area26470 Å2
Unit cell
Length a, b, c (Å)161.418, 161.418, 67.031
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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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: Catalytic subunit, 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 V5E1


Mass: 14480.018 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)

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Sugars , 2 types, 3 molecules

#4: 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
#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.: 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 , 2 types, 37 molecules

#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 340 mM ammonium fluoride and 22% PEG 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.049→50 Å / Num. obs: 19234 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 49.64 Å2 / Rmerge(I) obs: 0.377 / Rpim(I) all: 0.126 / Rrim(I) all: 0.398 / Χ2: 1.015 / Net I/σ(I): 2.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.05-3.18.22.3779420.5860.882.540.937100
3.1-3.169.11.6749450.710.5851.7750.899100
3.16-3.229.41.4829510.7050.5071.5680.946100
3.22-3.299.61.2939500.7790.4391.3660.937100
3.29-3.369.81.0139650.7820.3391.0690.95100
3.36-3.439.90.9729550.8080.3231.0250.969100
3.43-3.5210.10.7579620.8440.250.7970.971100
3.52-3.6210.20.4959340.9240.1630.5220.946100
3.62-3.7210.20.369710.9340.1190.3791.198100
3.72-3.8410.30.3969450.9480.130.4171.041100
3.84-3.9810.20.5199650.9610.170.5461.012100
3.98-4.1410.20.4259620.9680.1390.4471.025100
4.14-4.3310.30.289480.9810.0920.2941.109100
4.33-4.5610.20.2349730.9750.0770.2471.284100
4.56-4.8410.20.2869660.9820.0940.3011.08100
4.84-5.2110.20.2589740.9820.0850.2720.988100
5.21-5.7410.30.2689550.9820.0870.2820.939100
5.74-6.5710.20.2899790.9740.0950.3050.987100
6.57-8.2710.10.1779900.9910.0580.1870.974100
8.27-509.50.07210020.9980.0240.0761.05898.7

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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: 2AA1

2aa1


Resolution: 3.049→34.573 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2741 897 4.67 %
Rwork0.237 18316 -
obs0.2388 19213 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.81 Å2 / Biso mean: 53.1336 Å2 / Biso min: 17.29 Å2
Refinement stepCycle: final / Resolution: 3.049→34.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 99 33 5120
Biso mean--68.01 26.33 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025204
X-RAY DIFFRACTIONf_angle_d0.5437095
X-RAY DIFFRACTIONf_chiral_restr0.043805
X-RAY DIFFRACTIONf_plane_restr0.005916
X-RAY DIFFRACTIONf_dihedral_angle_d3.1683078
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.0495-3.24040.3871550.34242997
3.2404-3.49040.34491490.30463030
3.4904-3.84120.30051300.24213047
3.8412-4.39610.26471370.23473062
4.3961-5.53490.25511630.20633052
5.5349-34.5730.21011630.18793128
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)
17.43290.41184.56476.27580.03046.27471.32220.48-1.4501-0.16910.2991-0.10171.0517-0.4572-1.59350.3954-0.0924-0.15210.535-0.06270.851-36.397639.52395.5493
24.93774.49492.7145.54260.68765.41660.6614-0.0646-1.6065-0.07170.1116-0.71310.4304-0.2176-0.73580.5195-0.1024-0.06490.3597-0.03480.7054-29.294532.64196.8434
33.95693.39973.63033.39521.89734.97310.4528-0.211-0.0915-0.2715-0.20290.12050.1194-0.2672-0.21580.40080.11160.08060.4359-0.05490.6411-33.382940.43210.9693
40.00960.29090.09722.05428.31625.955-0.06110.4478-0.1735-0.73370.24270.2493-0.11610.29160.03910.8907-0.02540.08160.66690.01320.439-28.753738.3516-4.774
52.04920.884-0.42879.94754.90477.0268-0.4062-0.1776-0.18921.1341-0.27961.30990.6051-0.23050.71670.47770.03750.23870.37940.05440.6029-21.381862.835717.4832
65.6774-5.26261.5965.6999-0.7641.4251-0.6935-0.77170.01411.35180.73090.1068-0.306-0.38390.01790.54880.02440.09610.5107-0.02320.3077-16.822672.41719.867
75.5835-1.05880.23986.28411.71435.1121-0.1642-0.40450.11240.6465-0.0416-0.93530.01770.29440.19870.2672-0.0038-0.0460.37540.01840.4771-3.477666.698118.4483
86.70020.3902-0.1581.68531.17080.8785-0.2616-0.3443-0.90210.26780.17860.07340.2064-0.11310.030.43-0.04380.12190.3440.10380.3-11.499162.58578.5297
93.8404-1.71720.75512.821-2.31861.8805-0.06970.2890.0184-0.1468-0.2427-0.2563-0.09790.24740.32760.2618-0.08490.06440.3387-0.04240.3473-16.772278.41380.9173
101.43080.1295-0.52043.4058-1.31814.2429-0.34850.62220.35790.04250.13680.33450.18630.47170.35060.2461-0.0813-0.07820.4018-0.00040.5959-25.787593.5465-9.4968
116.6992-3.0408-2.55156.69054.28686.38980.0420.69870.6752-0.5611-0.2985-0.1073-0.64310.06290.27730.4055-0.0979-0.11890.47560.11380.5578-29.273198.3318-20.6076
121.7157-1.8313-0.68072.8112-0.21241.089-0.28210.45960.7015-0.00580.0737-0.3755-0.34350.06510.2340.3917-0.1098-0.10290.41710.06170.7677-31.1664102.5781-10.2781
132.0531-5.73880.48463.4535-1.82747.3913-0.1516-0.14610.29450.1467-0.124-0.4765-0.7904-0.23760.26950.3694-0.0982-0.03070.3572-0.00460.6484-36.189597.0067-1.8572
142.2441-1.3518-1.29913.136-0.49381.498-0.03430.10810.0066-0.36310.14390.8221-0.03820.1643-0.11360.3005-0.1176-0.1060.5061-0.03560.5743-36.437588.738-11.8999
158.7177-2.04180.90378.8243-8.55692.150.76640.8861-1.3746-0.5525-0.40280.71550.19320.181-0.4010.43840.02540.03390.5268-0.19490.5585-30.624961.7552-9.9352
162.624-0.75074.48682.8615-2.32378.0443-0.053-0.0578-0.2372-0.3029-0.17340.68560.3317-0.25270.18850.28570.00290.06130.3891-0.12550.8306-37.062173.5666-10.7914
172.54-2.1821.71587.08111.25363.548-0.3915-0.1036-0.9713-0.14740.33230.91190.221-0.1380.07970.3058-0.0810.10820.3878-0.02340.6752-38.240566.0033-0.562
183.5518-2.66792.71283.59991.20078.6661-0.67560.6972-1.7066-0.1976-0.2109-0.16370.88050.14720.80020.58090.03150.33450.508-0.08261.129-18.937838.7018-1.7149
196.5964-5.3098-0.014.3530.87332.0113-0.47310.1247-0.8943-0.2190.7652-1.89441.423-0.3443-0.27741.1348-0.141-0.08120.5073-0.18921.1749-33.804923.0781-6.3929
206.05388.18442.76132.02334.29847.29580.3110.2311-2.40791.07420.5366-0.63971.11150.9509-0.85560.64580.1362-0.08630.39030.03841.1431-19.371736.86925.1196
216.37881.26695.03063.5904-0.61132.1099-0.79070.6169-0.0756-0.53490.10360.3422-0.99990.73960.59610.5889-0.05210.20990.5474-0.10510.4748-29.472941.9763-0.8929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 46 through 64 )C46 - 64
2X-RAY DIFFRACTION2chain 'C' and (resid 65 through 83 )C65 - 83
3X-RAY DIFFRACTION3chain 'C' and (resid 84 through 109 )C84 - 109
4X-RAY DIFFRACTION4chain 'C' and (resid 110 through 126 )C110 - 126
5X-RAY DIFFRACTION5chain 'A' and (resid 5 through 32 )A5 - 32
6X-RAY DIFFRACTION6chain 'A' and (resid 33 through 75 )A33 - 75
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 155 )A76 - 155
8X-RAY DIFFRACTION8chain 'A' and (resid 156 through 194 )A156 - 194
9X-RAY DIFFRACTION9chain 'A' and (resid 195 through 263 )A195 - 263
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 26 )B2 - 26
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 42 )B27 - 42
12X-RAY DIFFRACTION12chain 'B' and (resid 43 through 83 )B43 - 83
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 103 )B84 - 103
14X-RAY DIFFRACTION14chain 'B' and (resid 104 through 139 )B104 - 139
15X-RAY DIFFRACTION15chain 'B' and (resid 140 through 171 )B140 - 171
16X-RAY DIFFRACTION16chain 'B' and (resid 172 through 223 )B172 - 223
17X-RAY DIFFRACTION17chain 'B' and (resid 224 through 262 )B224 - 262
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 8 )C1 - 8
19X-RAY DIFFRACTION19chain 'C' and (resid 9 through 18 )C9 - 18
20X-RAY DIFFRACTION20chain 'C' and (resid 19 through 28 )C19 - 28
21X-RAY DIFFRACTION21chain 'C' and (resid 29 through 45 )C29 - 45

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