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- PDB-4lhq: Ricin A chain bound to camelid nanobody (VHH8) -

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Open data


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Basic information

Entry
Database: PDB / ID: 4lhq
TitleRicin A chain bound to camelid nanobody (VHH8)
Components
  • Camelid nanobody
  • Ricin
KeywordsHYDROLASE/IMMUNE SYSTEM / Ribosome inhibiting protein / 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 / 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 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 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 / 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)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRudolph, M.J. / Cheung, J. / Franklin, M. / Burshteyn, F. / Cassidy, M. / Gary, E. / Mantis, N.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Crystal Structures of Ricin Toxin's Enzymatic Subunit (RTA) in Complex with Neutralizing and Non-Neutralizing Single-Chain Antibodies.
Authors: Rudolph, M.J. / Vance, D.J. / Cheung, J. / Franklin, M.C. / Burshteyn, F. / Cassidy, M.S. / Gary, E.N. / Herrera, C. / Shoemaker, C.B. / Mantis, N.J.
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Aug 20, 2014Group: Database references
Revision 1.4Mar 15, 2017Group: Source and taxonomy
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Camelid nanobody
C: Ricin
D: Camelid nanobody


Theoretical massNumber of molelcules
Total (without water)85,9644
Polymers85,9644
Non-polymers00
Water1,47782
1
A: Ricin
B: Camelid nanobody


Theoretical massNumber of molelcules
Total (without water)42,9822
Polymers42,9822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ricin
D: Camelid nanobody


Theoretical massNumber of molelcules
Total (without water)42,9822
Polymers42,9822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.048, 49.048, 339.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESSEQ 5:264 )
21CHAIN C AND (RESSEQ 5:264 )
12CHAIN B AND (RESSEQ 2:129 )
22CHAIN D AND (RESSEQ 2:129 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 5:264 )A5 - 264
211CHAIN C AND (RESSEQ 5:264 )C5 - 264
112CHAIN B AND (RESSEQ 2:129 )B2 - 129
212CHAIN D AND (RESSEQ 2:129 )D2 - 129

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.007869, 0.999908, 0.011026), (0.999961, -0.007912, 0.003869), (0.003956, 0.010995, -0.999932)23.9209, -24.8248, 22.843599
2given(0.007538, 0.999907, 0.01138), (0.999963, -0.007586, 0.00417), (0.004256, 0.011348, -0.999927)23.9032, -24.838301, 22.8437

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Components

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


Mass: 29129.852 Da / Num. of mol.: 2 / Fragment: UNP residues 39-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: pUTA / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody Camelid nanobody


Mass: 13852.220 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) Rosetta
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 100 mM NaAcetate, 2 M NaFormate, pH 4.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.496
ReflectionResolution: 2.3→50 Å / Num. all: 35498 / Num. obs: 34433 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.076 / Χ2: 1.391 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.343.30.3814270.42178.9
2.34-2.383.40.34515040.424185.6
2.38-2.433.40.3216480.422194.5
2.43-2.483.60.27117340.458197.8
2.48-2.533.70.25217380.47199.7
2.53-2.593.80.20618030.517199.8
2.59-2.663.80.18817230.5731100
2.66-2.733.80.15718330.602199.9
2.73-2.813.80.12817280.7451100
2.81-2.93.80.12318040.8031100
2.9-33.80.09817190.938199.9
3-3.123.80.09417921.1521100
3.12-3.265.20.11917901.271199.9
3.26-3.447.50.10817631.36199.8
3.44-3.657.40.09617561.561199.5
3.65-3.937.30.08817461.844199.5
3.93-4.336.50.07417482.134197.7
4.33-4.956.10.06617152.364195.3
4.95-6.246.90.06417382.339198.1
6.24-506.30.04917242.511194.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.39 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.02 Å47.15 Å
Translation3.02 Å47.15 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.544 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7453 / σ(F): 0 / Phase error: 32.1 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2483 1752 5.1 %
Rwork0.1918 --
obs0.1929 34330 97.01 %
all-35388 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.322 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 253.69 Å2 / Biso mean: 86.0425 Å2 / Biso min: 29.76 Å2
Baniso -1Baniso -2Baniso -3
1-9.3588 Å20 Å2-0 Å2
2--9.3588 Å2-0 Å2
3----18.7175 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 0 0 82 6140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046214
X-RAY DIFFRACTIONf_angle_d0.8798446
X-RAY DIFFRACTIONf_chiral_restr0.062928
X-RAY DIFFRACTIONf_plane_restr0.0031108
X-RAY DIFFRACTIONf_dihedral_angle_d13.0192246
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2066X-RAY DIFFRACTIONPOSITIONAL0.006
12C2066X-RAY DIFFRACTIONPOSITIONAL0.006
21B974X-RAY DIFFRACTIONPOSITIONAL0.006
22D974X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.36840.3381340.35622260239477
2.3684-2.44480.36541330.32722650278389
2.4448-2.53210.35311320.30672733286594
2.5321-2.63340.33161400.31342792293295
2.6334-2.7530.3311340.29562832296695
2.753-2.8980.35821580.29082795295395
2.898-3.07920.28861500.26022761291195
3.0792-3.31640.28861540.24062781293595
3.3164-3.64910.2831390.19492794293395
3.6491-4.17490.21981400.15912762290294
4.1749-5.25110.17751570.11742668282591
5.2511-24.27350.2161560.14222713286991
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)
14.3169-0.2924-0.13481.75570.03240.06-0.1972-0.15090.48250.14570.2434-0.3719-0.08690.6764-0.05070.1378-0.0292-0.16250.7308-0.35610.490111.54847.1098-6.0994
23.1884-0.2535-0.15442.08090.83211.6844-0.0396-0.05140.16320.14690.2409-0.22380.20510.16320.6966-0.0754-0.0018-0.40330.3843-0.45260.26362.66943.1439-11.0627
35.8827-0.29573.1315.9573-0.2114.23640.46170.3398-0.1704-0.3562-0.38560.13630.39670.0532-0.1340.69620.1863-0.24920.2818-0.15470.37972.6671-5.9023-21.5965
44.63870.7298-0.49612.58211.55923.0832-0.2932-1.0554-0.97771.1530.4199-0.49391.04810.6758-0.1140.70320.2646-0.08020.44180.06170.48739.7788-13.3849-7.7111
52.3248-0.5880.10082.29420.61343.6907-0.3018-1.44770.15370.85550.5707-0.64120.53620.6454-0.22350.530.2599-0.16810.891-0.15660.40559.0367-4.53082.4693
64.9504-3.7285-1.33726.23610.11365.1202-0.5967-0.3053-0.60261.0658-0.27670.64660.9715-0.37890.60840.5759-0.06780.19890.6146-0.29840.4477-9.6849-1.60887.7805
71.92570.74870.70742.02981.35554.4541-0.10470.18870.18840.0701-0.17720.3792-0.2057-0.96020.37280.4416-0.0757-0.1060.7075-0.31560.5128-10.64956.5872-1.7488
83.12191.1717-0.55334.0175-0.53820.78970.07690.3226-0.59410.4108-0.01160.46891.2718-0.5025-0.0070.6275-0.2443-0.09560.317-0.1310.7544-3.9672-35.6544-36.5505
92.3942-0.2476-2.71940.15810.12253.2803-0.33290.6193-0.07740.3135-0.02250.31940.2087-0.56520.40180.781-0.33430.01070.5556-0.24450.7019-6.8691-31.5212-31.4568
106.5536-1.1934-0.84817.46362.74456.1075-0.4763-0.5249-0.16381.02080.46680.25070.73740.28090.11960.28450.2341-0.10580.4951-0.14480.37680.4263-26.108-26.6132
116.6717-5.6817-2.53244.86172.34522.168-0.42520.0769-0.31390.29080.29190.17730.60170.6230.22280.26320.08620.05570.4755-0.26780.80979.3182-30.2331-36.6183
122.42452.10112.41381.8222.12833.49590.09560.03020.06020.08060.06690.48930.1413-0.8147-0.1260.44090.2322-0.06750.4206-0.1470.5382-2.9395-14.9969-27.7752
136.6705-0.0953-5.56794.48351.06888.5357-0.08540.88950.08830.23080.17680.11140.6216-0.2611-0.04460.33440.1849-0.10460.771-0.22850.4669-2.5402-23.5789-35.97
140.7485-0.42110.05951.41531.1961.43410.10190.3079-0.38380.17220.09030.18240.23220.1498-0.02860.68630.4177-0.16920.5043-0.28790.55745.1983-25.9036-33.4559
151.19370.99270.95272.81280.1921.81990.13830.2541-0.25160.5189-0.47260.26940.4979-0.2570.19720.69450.1184-0.10050.404-0.30290.60113.6966-33.5041-31.7643
164.4491-0.2723-0.33353.63730.31070.18940.12270.05960.5217-0.2121-0.4126-0.3805-0.4854-0.15130.15850.61730.06140.33840.6404-0.05050.568931.7218-12.94128.9276
172.655-0.48180.4552.71240.77021.13620.15980.30740.1408-0.014-0.0733-0.4593-0.2802-0.01610.04250.4509-0.12310.1430.674-0.13710.365627.6659-21.844133.7773
184.48361.09551.51415.4024-0.44860.96230.007-0.1074-0.37960.3150.03890.10190.0173-0.1872-0.130.7034-0.2090.30870.4529-0.27660.506218.5778-21.889844.277
193.20051.99290.31772.65350.06780.0437-0.13860.57260.3616-0.7974-0.21550.4944-0.1559-0.35090.07470.82970.32310.29780.6306-0.22790.281511.2074-14.567530.441
201.6718-0.0605-0.36433.1054-1.28691.40640.23261.36520.2875-0.8621-0.1472-0.0887-0.6512-0.2338-0.10560.85610.20470.1141.0273-0.19150.31620.0959-15.267620.2873
213.5846-1.57860.03472.04690.7651.04130.18210.3922-0.3457-0.6536-0.07680.1001-0.3822-0.1273-0.15040.5403-0.03630.29630.6664-0.27250.068322.8911-33.951814.7815
221.6841.34361.01012.56350.71216.19390.2275-0.3639-0.0990.015-0.0646-0.18260.19030.5448-0.03980.64180.09980.12980.667-0.26530.387731.0414-35.086524.3315
233.90030.8973-0.10812.97170.14010.0761-0.2289-0.03220.1724-0.10710.12890.00210.2759-0.63610.21641.02140.16380.21010.8021-0.53221.0735-11.2788-28.458759.0275
242.92681.63831.66543.3773-1.29066.56230.04260.2889-0.3048-0.1734-0.14310.34190.9227-0.46090.46170.3861-0.25610.13690.8285-0.26760.6575-3.5141-26.499550.7848
254.2476-5.1584-1.31836.25961.59830.40810.30510.05440.11340.0112-0.20240.0597-0.4989-0.4884-0.08370.68370.00210.42030.8541-0.30070.6491-5.7573-15.218559.269
262.4610.8101-0.86812.31230.86772.77910.0618-0.1764-0.01150.246-0.2808-0.12660.1631-0.29080.30270.4994-0.21910.21790.2708-0.22750.78092.2908-27.182557.1096
270.77830.1589-0.24630.03940.00520.9569-0.12550.06590.17620.07630.01850.2224-0.22260.09070.06630.6725-0.2140.23660.3794-0.19970.6691-1.4455-19.333456.078
281.64310.9219-0.43971.0724-0.89080.9894-0.35690.0302-0.1661-0.07260.0030.16260.1146-0.39280.23540.87220.09880.27560.6749-0.43460.89-9.051-20.757954.3386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 5:33)A5 - 33
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 34:87)A34 - 87
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 88:113)A88 - 113
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 114:161)A114 - 161
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 162:202)A162 - 202
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 203:249)A203 - 249
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 250:263)A250 - 264
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 2:17)B2 - 17
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 18:25)B18 - 25
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 26:39)B26 - 39
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 40:51)B40 - 51
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 52:57)B52 - 57
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 58:83)B58 - 83
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 84:112)B84 - 112
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 113:129)B113 - 129
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 5:33)C5 - 33
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 34:87)C34 - 87
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 88:113)C88 - 113
19X-RAY DIFFRACTION19CHAIN C AND (RESSEQ 114:161)C114 - 161
20X-RAY DIFFRACTION20CHAIN C AND (RESSEQ 162:202)C162 - 202
21X-RAY DIFFRACTION21CHAIN C AND (RESSEQ 203:249)C203 - 249
22X-RAY DIFFRACTION22CHAIN C AND (RESSEQ 250:263)C250 - 264
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 2:17)D2 - 17
24X-RAY DIFFRACTION24CHAIN D AND (RESSEQ 18:39)D18 - 39
25X-RAY DIFFRACTION25CHAIN D AND (RESSEQ 40:51)D40 - 51
26X-RAY DIFFRACTION26CHAIN D AND (RESSEQ 52:83)D52 - 83
27X-RAY DIFFRACTION27CHAIN D AND (RESSEQ 84:112)D84 - 112
28X-RAY DIFFRACTION28CHAIN D AND (RESSEQ 113:129)D113 - 129

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