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- PDB-7te8: CA14-CBD-DB21 ternary complex -

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Basic information

Entry
Database: PDB / ID: 7te8
TitleCA14-CBD-DB21 ternary complex
Components
  • CA14
  • DB21
KeywordsBIOSYNTHETIC PROTEIN / Nanobody / Cannabidiol / Sensor / Molecular glue
Function / homologycannabidiol
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsCao, S. / Zheng, N.
Funding support United States, 4items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM128918 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R21DA051555 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R21DA051194 United States
CitationJournal: Nat Commun / Year: 2022
Title: Defining molecular glues with a dual-nanobody cannabidiol sensor.
Authors: Cao, S. / Kang, S. / Mao, H. / Yao, J. / Gu, L. / Zheng, N.
History
DepositionJan 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 6, 2022Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: CA14
A: DB21
D: CA14
B: DB21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5496
Polymers52,9204
Non-polymers6292
Water5,909328
1
C: CA14
A: DB21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7743
Polymers26,4602
Non-polymers3141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area10900 Å2
MethodPISA
2
D: CA14
B: DB21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7743
Polymers26,4602
Non-polymers3141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-5 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.672, 69.153, 109.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody CA14


Mass: 13144.321 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody DB21


Mass: 13315.685 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-P0T / cannabidiol / (1'R,2'R)-5'-methyl-4-pentyl-2'-(prop-1-en-2-yl)-1',2',3',4'-tetrahydro[1,1'-biphenyl]-2,6-diol


Mass: 314.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium citrate tribasic, pH 7.0, 0.1 M imidazole, pH 7.0 and 20% polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.998→41.15 Å / Num. obs: 32845 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.996 / Net I/σ(I): 57.4
Reflection shellResolution: 1.998→2.07 Å / Num. unique obs: 3172 / CC1/2: 0.948

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Processing

Software
NameVersionClassification
PHENIXv1.14refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Predicted model of each nanobody by PHYRE2

Resolution: 1.998→41.149 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 1655 5.05 %
Rwork0.1803 --
obs0.1819 32798 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→41.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 46 329 4083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093844
X-RAY DIFFRACTIONf_angle_d1.0595196
X-RAY DIFFRACTIONf_dihedral_angle_d9.8882224
X-RAY DIFFRACTIONf_chiral_restr0.072524
X-RAY DIFFRACTIONf_plane_restr0.006682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9983-2.05710.24131260.20672515X-RAY DIFFRACTION98
2.0571-2.12350.25321510.19812534X-RAY DIFFRACTION100
2.1235-2.19930.23021280.19382573X-RAY DIFFRACTION100
2.1993-2.28740.2581330.1972564X-RAY DIFFRACTION100
2.2874-2.39150.29521310.20092594X-RAY DIFFRACTION100
2.3915-2.51760.23951380.20172565X-RAY DIFFRACTION100
2.5176-2.67530.26061380.19652569X-RAY DIFFRACTION100
2.6753-2.88180.23221450.20362593X-RAY DIFFRACTION100
2.8818-3.17170.22881250.18692606X-RAY DIFFRACTION100
3.1717-3.63040.18211380.17212618X-RAY DIFFRACTION100
3.6304-4.5730.18371490.15082639X-RAY DIFFRACTION100
4.573-41.1490.16661530.16662773X-RAY DIFFRACTION100

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