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- PDB-4z9k: Ricin A chain bound to camelid nanobody (VHH2)(F5) -

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Basic information

Entry
Database: PDB / ID: 4z9k
TitleRicin A chain bound to camelid nanobody (VHH2)(F5)
Components
  • Ricin
  • VHH2(F5) antibody
KeywordsHydrolase/Immune system / Ricin toxin / nanobodies / 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 / 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 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 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 / 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: 1.5 Å
AuthorsRudolph, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Citation
Journal: Proteins / Year: 2016
Title: Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit.
Authors: Rudolph, M.J. / Vance, D.J. / Cassidy, M.S. / Rong, Y. / Shoemaker, C.B. / Mantis, N.J.
#1: Journal: To Be Published
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
DepositionApr 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references / Source and taxonomy / Structure summary
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin
B: VHH2(F5) antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6167
Polymers41,3562
Non-polymers2605
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-45 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.376, 107.085, 111.944
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-270-

HOH

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Ricin /


Mass: 28935.625 Da / Num. of mol.: 1 / Fragment: UNP residues 39-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody VHH2(F5) antibody


Mass: 12419.934 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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Non-polymers , 4 types, 335 molecules

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


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


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 15% PEG 3000, 2 mM Zinc acetate, 10 mM sulfobetaine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→111.94 Å / Num. obs: 75050 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Net I/σ(I): 12 / Num. measured all: 480384 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.5-1.536.61.4971.42379936300.5350.62499
8.22-111.945.90.04638.831205290.9960.02199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.72 Å55.09 Å
Translation1.72 Å55.09 Å

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Processing

Software
NameVersionClassification
Aimless0.3.3data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→55.065 Å / FOM work R set: 0.8581 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 3741 4.99 %
Rwork0.1777 137886 -
obs0.1786 75015 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.84 Å2 / Biso mean: 27.81 Å2 / Biso min: 11.24 Å2
Refinement stepCycle: final / Resolution: 1.5→55.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 11 330 3254
Biso mean--33.52 38.86 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193029
X-RAY DIFFRACTIONf_angle_d1.6824117
X-RAY DIFFRACTIONf_chiral_restr0.101455
X-RAY DIFFRACTIONf_plane_restr0.01543
X-RAY DIFFRACTIONf_dihedral_angle_d13.9331108
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5170.35342390.3294538477799
1.517-1.53490.32142320.31314585481798
1.5349-1.55360.30732210.2954596481799
1.5536-1.57330.29722640.29114555481999
1.5733-1.5940.32162450.28744530477599
1.594-1.61580.3072360.27944606484299
1.6158-1.63890.26192300.26914565479599
1.6389-1.66340.26592630.25534596485999
1.6634-1.68940.26542460.248945924838100
1.6894-1.71710.27062420.24254544478699
1.7171-1.74670.26052510.22554650490199
1.7467-1.77840.22782300.21845364766100
1.7784-1.81260.24142480.208745964844100
1.8126-1.84960.2242480.203746314879100
1.8496-1.88990.22372300.197745954825100
1.8899-1.93380.20432730.186745544827100
1.9338-1.98220.18092080.17746424850100
1.9822-2.03580.19452150.174646494864100
2.0358-2.09570.2042500.173445774827100
2.0957-2.16330.18412620.166346024864100
2.1633-2.24070.16031850.163246874872100
2.2407-2.33040.18752320.162345974829100
2.3304-2.43640.16682650.166646074872100
2.4364-2.56490.21412350.167545964831100
2.5649-2.72560.1992560.168345994855100
2.7256-2.9360.19762470.171146294876100
2.936-3.23150.18292770.174645764853100
3.2315-3.6990.16922540.154446394893100
3.699-4.65990.14522340.137545794813100
4.6599-55.10230.17032290.154846384867100
Refinement TLS params.Method: refined / Origin x: 32.9217 Å / Origin y: 37.2273 Å / Origin z: 2.2663 Å
111213212223313233
T0.1136 Å2-0.0089 Å2-0.0074 Å2-0.102 Å2-0.0026 Å2--0.1503 Å2
L1.4188 °20.1783 °20.021 °2-0.8142 °2-0.2075 °2--2.4481 °2
S0.0256 Å °-0.1115 Å °-0.0751 Å °0.0161 Å °0.0057 Å °0.0208 Å °0.1295 Å °-0.2324 Å °-0.0263 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 262
2X-RAY DIFFRACTION1allB2 - 117
3X-RAY DIFFRACTION1allZ1 - 5
4X-RAY DIFFRACTION1allS1 - 372

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