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- PDB-7v5n: Crystal structure of Fab fragment of bevacizumab bound to DNA aptamer -

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Basic information

Entry
Database: PDB / ID: 7v5n
TitleCrystal structure of Fab fragment of bevacizumab bound to DNA aptamer
Components
  • (bevacizumab fab ...) x 2
  • DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
KeywordsIMMUNE SYSTEM/DNA / antibody / DNA complex / DNA BINDING PROTEIN / IMMUNE SYSTEM-DNA complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IMIDAZOLE / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHishiki, A. / Tong, J. / Todoroki, K. / Hashimoto, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H03360 Japan
CitationJournal: Biosens.Bioelectron. / Year: 2022
Title: Development of a DNA aptamer that binds to the complementarity-determining region of therapeutic monoclonal antibody and affinity improvement induced by pH-change for sensitive detection.
Authors: Saito, T. / Shimizu, Y. / Tsukakoshi, K. / Abe, K. / Lee, J. / Ueno, K. / Asano, R. / Jones, B.V. / Yamada, T. / Nakano, T. / Tong, J. / Hishiki, A. / Hara, K. / Hashimoto, H. / Sode, K. / ...Authors: Saito, T. / Shimizu, Y. / Tsukakoshi, K. / Abe, K. / Lee, J. / Ueno, K. / Asano, R. / Jones, B.V. / Yamada, T. / Nakano, T. / Tong, J. / Hishiki, A. / Hara, K. / Hashimoto, H. / Sode, K. / Toyo'oka, T. / Todoroki, K. / Ikebukuro, K.
History
DepositionAug 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bevacizumab fab light chain
B: bevacizumab fab heavy chain
D: DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
E: bevacizumab fab light chain
F: bevacizumab fab heavy chain
G: DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,35531
Polymers111,6536
Non-polymers1,70225
Water11,728651
1
E: bevacizumab fab light chain
F: bevacizumab fab heavy chain
G: DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,64615
Polymers55,8263
Non-polymers82012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-36 kcal/mol
Surface area21770 Å2
MethodPISA
2
A: bevacizumab fab light chain
B: bevacizumab fab heavy chain
D: DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,70816
Polymers55,8263
Non-polymers88213
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-54 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.543, 130.599, 90.244
Angle α, β, γ (deg.)90.00, 103.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 1 types, 2 molecules DG

#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*TP*TP*GP*GP*TP*GP*GP*TP*AP*GP*TP*TP*AP*CP*GP*TP*TP*CP*GP*C)-3')


Mass: 7463.784 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA aptamer / Source: (synth.) synthetic construct (others)

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Antibody , 2 types, 4 molecules AEBF

#1: Antibody bevacizumab fab light chain


Mass: 23471.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody bevacizumab fab heavy chain


Mass: 24890.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 676 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 104111 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.6
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.511 / Num. unique obs: 15208

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bj1

1bj1


Resolution: 1.7→19.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.389 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21002 5050 4.9 %RANDOM
Rwork0.178 ---
obs0.17952 99026 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.467 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 990 106 651 8357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0127984
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.56811049
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03423.31290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.354151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3131520
X-RAY DIFFRACTIONr_chiral_restr0.0790.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025690
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2723.013447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0774.5094300
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6643.0494537
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.89439.37512370
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 398 -
Rwork0.27 7235 -
obs--99.86 %

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