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- PDB-9rit: Co-crystal of broadly neutralizing biparatopic VHH in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9rit
TitleCo-crystal of broadly neutralizing biparatopic VHH in complex with cardiotoxin (P01468) Naja pallida
Components
  • Cytotoxin 1
  • Variable Domain of Heavy-Chain only Antibody (VHH)
KeywordsTOXIN / nanobody / VHH / antibody / snake toxin / snake venom / neutralizing / cytotoxin / biparatopic
Function / homology
Function and homology information


other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
Similarity search - Domain/homology
ACETATE ION / Cytotoxin 1
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Naja pallida (red spitting cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBurlet, N.J. / Laustsen, A.H. / Morth, J.P.
Funding supportEuropean Union, United Kingdom, Denmark, 3items
OrganizationGrant numberCountry
European Research Council (ERC)850974European Union
Wellcome Trust221702/Z/20/Z United Kingdom
Novo Nordisk FoundationNNF24OC0088714 Denmark
CitationJournal: To Be Published / Year: 2025
Title: Nanobody-based recombinant antivenom for cobra, mamba, and rinkhals bites
Authors: Ahmadi, S. / Burlet, N.J. / Benard-Valle, M. / Guadarrama-Martinez, A. / Kerwin, S. / Menzies, S.K. / Cardoso, I.A. / Marriott, A. / Edge, R. / Crittenden, E. / Neri, E. / Fernandez- ...Authors: Ahmadi, S. / Burlet, N.J. / Benard-Valle, M. / Guadarrama-Martinez, A. / Kerwin, S. / Menzies, S.K. / Cardoso, I.A. / Marriott, A. / Edge, R. / Crittenden, E. / Neri, E. / Fernandez-Quintero, M. / Nguyen, G.T.T. / O'Brien, C. / Wouters, Y. / Kalogeropoulos, K. / Thumtecho, S. / Wainani Ebersole, T. / Holst Dahl, C. / Glegg-Sorensen, E.U. / Jansen, T. / Boddum, K. / Manousaki, E. / Rivera-de-Torre, E. / Ward, A. / Morth, J.P. / Alagon, A. / Jenkins, T.P. / Mackessy, S.P. / Ainsworth, S. / Caswell, N. / Ljungars, A. / Laustsen, A.H.
History
DepositionJun 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variable Domain of Heavy-Chain only Antibody (VHH)
B: Variable Domain of Heavy-Chain only Antibody (VHH)
C: Cytotoxin 1
D: Cytotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,69510
Polymers41,3414
Non-polymers3546
Water4,864270
1
A: Variable Domain of Heavy-Chain only Antibody (VHH)
C: Cytotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7894
Polymers20,6702
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Cytotoxin 1
hetero molecules

B: Variable Domain of Heavy-Chain only Antibody (VHH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9076
Polymers20,6702
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)41.943, 54.905, 143.014
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11D-232-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 6 or resid 8 through 44 or resid 46 through 118))
d_2ens_1(chain "B" and (resid 1 through 6 or resid 8 through 44 or resid 46 through 118))
d_1ens_2(chain "C" and (resid 1 through 12 or resid 14 through 60))
d_2ens_2(chain "D" and (resid 1 through 12 or resid 14 through 60))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNGLUGLUAA1 - 61 - 6
d_12ens_1GLYGLYGLUGLUAA8 - 448 - 44
d_13ens_1GLUGLUSERSERAA46 - 11846 - 118
d_21ens_1GLNGLNGLUGLUBB1 - 61 - 6
d_22ens_1GLYGLYGLUGLUBB8 - 448 - 44
d_23ens_1GLUGLUSERSERBB46 - 11846 - 118
d_11ens_2LEULEULYSLYSCC1 - 121 - 12
d_12ens_2CYSCYSASNASNCC14 - 6014 - 60
d_21ens_2LEULEULYSLYSDD1 - 121 - 12
d_22ens_2CYSCYSASNASNDD14 - 6014 - 60

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999983194091, 0.00333076201669, 0.00474526720404), (-0.00311096570675, 0.998955088239, -0.0455966399449), (-0.00489218037494, 0.0455811112884, 0.998948661776)21.0054196831, -27.721962682, -0.0593838494185
2given(0.999985901169, -0.00181443161809, -0.00499052104615), (0.00170720904824, 0.99976940281, -0.0214062290654), (0.00502821038486, 0.0213974073999, 0.999758404844)-21.1812876688, -27.0392375538, -0.0383283169662

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Components

#1: Antibody Variable Domain of Heavy-Chain only Antibody (VHH)


Mass: 13832.026 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein. Variable Domain of Heavy-Chain only Antibody (VHH)
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Cytotoxin 1 / CTX-1 / Cardiotoxin gamma


Mass: 6838.462 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cytotoxin 1 / Source: (natural) Naja pallida (red spitting cobra) / References: UniProt: P01468
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate, pH 4.6, 30% w/v PEG 4000. 25% (v/v) glycerol as cryoprotection.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.6→51.26 Å / Num. obs: 42821 / % possible obs: 95.87 % / Redundancy: 7.9 % / Biso Wilson estimate: 16.63 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.05 / Rrim(I) all: 0.14 / Net I/σ(I): 9.49
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 6553 / CC1/2: 0.81 / Rpim(I) all: 0.39 / Rrim(I) all: 0.98 / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→51.26 Å / SU ML: 0.2116 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 2138 4.99 %
Rwork0.222 40683 -
obs0.2238 42821 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.98 Å2
Refinement stepCycle: LAST / Resolution: 1.6→51.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 24 270 3052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782865
X-RAY DIFFRACTIONf_angle_d1.12823867
X-RAY DIFFRACTIONf_chiral_restr0.0604404
X-RAY DIFFRACTIONf_plane_restr0.0079499
X-RAY DIFFRACTIONf_dihedral_angle_d6.3484395
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.727805390131
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.544190076484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.33561270.31982439X-RAY DIFFRACTION87.7
1.64-1.680.36051380.30762605X-RAY DIFFRACTION93.3
1.68-1.720.35671410.28732693X-RAY DIFFRACTION96.86
1.72-1.770.31531430.27372711X-RAY DIFFRACTION96.88
1.77-1.830.30991400.26962665X-RAY DIFFRACTION95.31
1.83-1.90.30371420.25152702X-RAY DIFFRACTION96.97
1.9-1.970.29921440.24042726X-RAY DIFFRACTION97.85
1.97-2.060.28311430.22882722X-RAY DIFFRACTION97.25
2.06-2.170.27411440.22562722X-RAY DIFFRACTION96.76
2.17-2.310.28631330.21252519X-RAY DIFFRACTION88.93
2.31-2.480.26921450.22662756X-RAY DIFFRACTION97.58
2.48-2.730.23481480.22562816X-RAY DIFFRACTION98.77
2.73-3.130.22981470.21762827X-RAY DIFFRACTION98.71
3.13-3.940.22221490.19552850X-RAY DIFFRACTION98.59
3.94-51.260.21681540.18542930X-RAY DIFFRACTION95.72

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