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- PDB-9riu: Co-crystal of broadly neutralizing VHH in complex with short neur... -

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Basic information

Entry
Database: PDB / ID: 9riu
TitleCo-crystal of broadly neutralizing VHH in complex with short neurotoxin 1 (P01426) Naja pallida
Components
  • Short neurotoxin 1
  • Variable Domain of Heavy-Chain only Antibody (VHH)
KeywordsTOXIN / nanobody / VHH / antibody / snake toxin / snake venom / neutralizing
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Short neurotoxin 1
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Naja pallida (red spitting cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Ahmadhi, 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. / Nguyen, G.T.T. / ...Authors: Ahmadhi, 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. / Nguyen, G.T.T. / O'Brien, C. / Wouters, Y. / Kalogeropoulos, K. / Thumtecho, S. / Ebersole, T.W. / Dahl, C.H. / Glegg-Sorensen, E.U. / Jansen, T. / Boddum, K. / Manousaki, E. / Rivera-de-Torre, E. / Morth, J.P. / Alagon, A. / Jenkins, T.P. / Mackessy, S.P. / Ainsworth, S. / Casewell, 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: Short neurotoxin 1
C: Variable Domain of Heavy-Chain only Antibody (VHH)
D: Short neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,35120
Polymers41,4124
Non-polymers93916
Water63135
1
A: Variable Domain of Heavy-Chain only Antibody (VHH)
B: Short neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,23411
Polymers20,7062
Non-polymers5289
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Variable Domain of Heavy-Chain only Antibody (VHH)
D: Short neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1179
Polymers20,7062
Non-polymers4117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.150, 104.090, 79.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11C-203-

NI

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2chain "B"
d_2ens_2chain "D"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLNGLNTYRTYRAA1 - 1271 - 127
d_2ens_1GLNGLNTYRTYRCC1 - 1271 - 127
d_1ens_2LEULEUASNASNBB1 - 611 - 61
d_2ens_2LEULEUASNASNDD1 - 611 - 61

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.000103012567131, -0.999996011809, -0.00282236667785), (0.999992512252, -0.000113929542274, 0.0038681338568), (-0.00386843998089, -0.00282194707828, 0.999988535828)52.1367866457, -0.157350529292, -19.791661517
2given(0.0123824017265, -0.999919316165, -0.00283501091477), (0.999920177204, 0.0123751872772, 0.00254832491773), (-0.0025130355181, -0.00286633899913, 0.99999273435)51.9867943054, -0.296526867547, -19.7305510052

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Components

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


Mass: 13900.173 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 Short neurotoxin 1 / Neurotoxin alpha / Toxin alpha


Mass: 6805.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: short neurotoxin 1 / Source: (natural) Naja pallida (red spitting cobra) / References: UniProt: P01426
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M sodium chloride, 0.1M sodium acetate, pH 4.6, 30% v/v MPD. 25% (v/v) glycerol as crypreservative

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.72931 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72931 Å / Relative weight: 1
ReflectionResolution: 2.5→23.29 Å / Num. obs: 28844 / % possible obs: 99.9 % / Redundancy: 7.15 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Net I/σ(I): 19.86
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 7.22 % / Rmerge(I) obs: 0.498 / Num. unique obs: 4687 / CC1/2: 0.929 / Rpim(I) all: 0.2 / Rrim(I) all: 0.537 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→23.29 Å / SU ML: 0.5963 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 47.2762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.361 760 4.99 %
Rwork0.3238 14465 -
obs0.3258 15225 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 16 35 2903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522902
X-RAY DIFFRACTIONf_angle_d0.8913932
X-RAY DIFFRACTIONf_chiral_restr0.0599430
X-RAY DIFFRACTIONf_plane_restr0.0063524
X-RAY DIFFRACTIONf_dihedral_angle_d5.6132406
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.59658569777
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.825749911019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.49551500.44062841X-RAY DIFFRACTION99.93
2.69-2.960.38781500.41062868X-RAY DIFFRACTION99.8
2.96-3.390.41571510.39252861X-RAY DIFFRACTION99.93
3.39-4.270.35871520.31592898X-RAY DIFFRACTION99.97
4.27-23.290.32431570.27712997X-RAY DIFFRACTION99.53

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