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- PDB-9gxh: Nanobody bound to TBA G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 9gxh
TitleNanobody bound to TBA G-quadruplex
Components
  • Nanobody
  • Thrombin-binding aptamer (TBA)
KeywordsIMMUNE SYSTEM / G-quadruplex / DNA / thrombin / nanobody / thrombin-binding aptamer / TBA
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesLama glama (llama)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHadzi, S. / Pevec, M.
Funding support Slovenia, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0201 Slovenia
Slovenian Research AgencyJ1-50026 Slovenia
Slovenian Research AgencyP1-0242 Slovenia
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural basis of G-quadruplex recognition by a camelid antibody fragment.
Authors: Pevec, M. / Medved, T. / Kovacic, M. / Zerjav, N. / Imperl, J. / Plavec, J. / Lah, J. / Loris, R. / Hadzi, S.
History
DepositionSep 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 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: Nanobody
B: Nanobody
C: Thrombin-binding aptamer (TBA)
D: Thrombin-binding aptamer (TBA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5158
Polymers36,3364
Non-polymers1794
Water6,215345
1
A: Nanobody
hetero molecules

C: Thrombin-binding aptamer (TBA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3085
Polymers18,1682
Non-polymers1403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
2
B: Nanobody
D: Thrombin-binding aptamer (TBA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2073
Polymers18,1682
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.284, 59.331, 70.625
Angle α, β, γ (deg.)90.00, 95.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Nanobody


Mass: 13424.901 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#2: DNA chain Thrombin-binding aptamer (TBA)


Mass: 4743.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Sodium chloride, 0.1 M Phosphate/citrate, pH = 4.2, 20 % w/v PEG 8000 cryosoak: same solution with 30% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.39→70.26 Å / Num. obs: 43889 / % possible obs: 72.7 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.061 / Rrim(I) all: 0.152 / Χ2: 0.85 / Net I/σ(I): 6.8 / Num. measured all: 253447
Reflection shellResolution: 1.39→1.46 Å / Redundancy: 2.4 % / Rmerge(I) obs: 3.649 / Num. unique obs: 1022 / CC1/2: 0.109 / Rpim(I) all: 2.682 / Rrim(I) all: 4.567 / Χ2: 0.67

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
STARANISOanisotropy correctiondata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.332 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 2000 8.64 %
Rwork0.1542 --
obs0.1581 23145 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 630 7 345 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082567
X-RAY DIFFRACTIONf_angle_d0.9733615
X-RAY DIFFRACTIONf_dihedral_angle_d20.8231387
X-RAY DIFFRACTIONf_chiral_restr0.055392
X-RAY DIFFRACTIONf_plane_restr0.005350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.22381430.17321513X-RAY DIFFRACTION100
1.9475-2.00020.22051470.16741562X-RAY DIFFRACTION100
2.0002-2.05910.20161440.15931511X-RAY DIFFRACTION100
2.0591-2.12550.2381460.16731543X-RAY DIFFRACTION100
2.1255-2.20150.23561430.16191517X-RAY DIFFRACTION100
2.2015-2.28960.24981470.17131553X-RAY DIFFRACTION100
2.2896-2.39380.23371450.16391529X-RAY DIFFRACTION100
2.3938-2.520.25041440.17511534X-RAY DIFFRACTION100
2.52-2.67790.23951270.17461347X-RAY DIFFRACTION87
2.6779-2.88460.21551450.15961527X-RAY DIFFRACTION100
2.8846-3.17480.19391460.16491542X-RAY DIFFRACTION100
3.1748-3.63410.16191330.1311408X-RAY DIFFRACTION90
3.6341-4.57790.14651400.11911481X-RAY DIFFRACTION95
4.5779-45.3320.16241500.15021578X-RAY DIFFRACTION100
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)
11.74760.36370.03941.1082-0.00381.1019-0.05720.0881-0.0249-0.03150.0406-0.04250.0270.02310.01980.05110.00580.00110.06310.0020.048810.8192-3.715524.4925
21.4601-0.347-0.53531.8710.19922.2112-0.0708-0.00420.0348-0.05780.1047-0.15-0.1240.17830.00910.1136-0.041-0.00010.124-0.00330.071426.819518.460110.7345
31.04850.5908-0.11373.60141.75072.4986-0.02970.00060.0778-0.03280.07770.1173-0.07680.0536-0.04250.0740.0024-0.00220.0776-0.00050.046321.116119.280527.5851
40.7125-1.06710.01173.6621-0.55582.6454-0.0173-0.06240.07670.41890.0278-0.1416-0.10770.3179-0.00780.1574-0.0305-0.01460.1650.02010.079228.322125.4863-7.2336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 115)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 115)
3X-RAY DIFFRACTION3(chain 'D' and resid 1 through 15)
4X-RAY DIFFRACTION4(chain 'C' and resid 1 through 15)

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