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- PDB-9ty2: Crystal structure of a Picomolar Nanobody in complex with Maltose... -

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Basic information

Entry
Database: PDB / ID: 9ty2
TitleCrystal structure of a Picomolar Nanobody in complex with Maltose Binding Protein, MBP, and maltose
Components
  • Maltose/maltodextrin-binding periplasmic protein
  • Nanobody, single fragment heavy chain antibody, NbCM1, sdAbCM1
KeywordsIMMUNE SYSTEM / Nanobody / Single Chain Antibody / Maltose Binding protein
Function / homology
Function and homology information


carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
beta-maltose / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChinellato, M. / Franzin, E. / Vascon, F. / Schmit, F. / Pontisso, P. / Cendron, L.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
Italian Ministry of Health Italy
CitationJournal: Acs Bio Med Chem Au / Year: 2026
Title: A Picomolar MBP-Binding Nanobody for Target Enrichment and Modular Complex Engineering
Authors: Chinellato, M. / Franzin, E. / Vascon, F. / Koenig, P.A. / Schmidt, F.I. / Pontisso, P. / Cendron, L.
History
DepositionJan 16, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein
B: Nanobody, single fragment heavy chain antibody, NbCM1, sdAbCM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8953
Polymers56,5532
Non-polymers3421
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint4 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.602, 52.158, 77.144
Angle α, β, γ (deg.)90, 92.075, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 42554.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the missing residues derive from the recombinant construct and are not visible in the electron density maps
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, Z5632, ECs5017 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEY0
#2: Antibody Nanobody, single fragment heavy chain antibody, NbCM1, sdAbCM1


Mass: 13997.679 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: missing residues are not visible in the electron density maps
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Komagataella pastoris (fungus)
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MIB (Sodium malonate dibasic monohydrate, Imidazole, Boric acid) pH 7.0, 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.75→52.23 Å / Num. obs: 54091 / % possible obs: 98 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.5
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 1.16 / Num. unique obs: 2962 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→52.177 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.807 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.026 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2362 2745 5.077 %
Rwork0.1775 51325 -
all0.181 --
obs-54070 97.868 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.013 Å2
Baniso -1Baniso -2Baniso -3
1-2.539 Å20 Å21.15 Å2
2---2.377 Å2-0 Å2
3----0.162 Å2
Refinement stepCycle: LAST / Resolution: 1.75→52.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 23 372 4162
LS refinement shellResolution: 1.75→1.795 Å
RfactorNum. reflection% reflection
Rfree0.358 199 -
Rwork0.248 3794 -
obs--98.4953 %
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)
10.03360.0459-0.0270.1001-0.07170.15080.00190.00110.00320.00120.0024-0.01230.0171-0.0123-0.00430.0035-0.0037-0.0020.0176-0.00040.011-14.4895-7.377322.5127
20.09940.16010.05960.3628-0.05060.2699-0.0180.0238-0.0041-0.00980.01740.0048-0.04560.06060.00050.0099-0.0157-0.00240.02910.00670.014315.40823.437413.9625
Refinement TLS groupSelection: ALL

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