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- PDB-7u62: Crystal structure of Anti-Heroin Antibody HY4-1F9 Fab Complexed w... -

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Basic information

Entry
Database: PDB / ID: 7u62
TitleCrystal structure of Anti-Heroin Antibody HY4-1F9 Fab Complexed with Morphine
Components
  • HY4-1F9 Fab Heavy Chain
  • HY4-1F9 Fab Light Chain
KeywordsIMMUNE SYSTEM / mAb / opioid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / Chem-MOI
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsRodarte, J.V. / Pancera, M.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)UG3 DA047711 United States
CitationJournal: Structure / Year: 2023
Title: Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding.
Authors: Rodarte, J.V. / Baehr, C. / Hicks, D. / Liban, T.L. / Weidle, C. / Rupert, P.B. / Jahan, R. / Wall, A. / McGuire, A.T. / Strong, R.K. / Runyon, S. / Pravetoni, M. / Pancera, M.
History
DepositionMar 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
H: HY4-1F9 Fab Heavy Chain
L: HY4-1F9 Fab Light Chain
I: HY4-1F9 Fab Heavy Chain
M: HY4-1F9 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,70617
Polymers94,4864
Non-polymers1,22013
Water7,206400
1
H: HY4-1F9 Fab Heavy Chain
L: HY4-1F9 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8238
Polymers47,2432
Non-polymers5816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-26 kcal/mol
Surface area19620 Å2
MethodPISA
2
I: HY4-1F9 Fab Heavy Chain
M: HY4-1F9 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8839
Polymers47,2432
Non-polymers6407
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-27 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.792, 97.179, 76.132
Angle α, β, γ (deg.)90.000, 91.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody HY4-1F9 Fab Heavy Chain


Mass: 24433.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody HY4-1F9 Fab Light Chain


Mass: 22809.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-MOI / (7R,7AS,12BS)-3-METHYL-2,3,4,4A,7,7A-HEXAHYDRO-1H-4,12-METHANO[1]BENZOFURO[3,2-E]ISOQUINOLINE-7,9-DIOL / MORPHINE / (5A,6A)-7,8-DIDEHYDRO-4,5-EPOXY-17-METHYLMORPHINIAN-3,6-DIOL / MORPHIUM / MORPHIA / DOLCONTIN / DUROMORPH / MORPHINA / NEPENTHE


Mass: 285.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 8000 0.1M Sodium Cacodylate 0.2M Magnesium Acetate 2.25% Xylitol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 76214 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.97 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.038 / Rrim(I) all: 0.072 / Χ2: 0.942 / Net I/σ(I): 13.3 / Num. measured all: 262956
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.81-1.843.10.27636890.9020.1820.3320.88197
1.84-1.873.30.23238270.9020.1510.2780.96599.1
1.87-1.913.30.20737930.9340.1340.2471.05999.5
1.91-1.953.30.17338780.8060.1120.2061.06899.6
1.95-1.993.40.14137610.9680.090.1680.97899.5
1.99-2.043.40.12537570.9750.0790.1480.97398.5
2.04-2.093.30.12837810.8430.0840.1531.24897.3
2.09-2.153.50.09737800.9810.0610.1150.94599
2.15-2.213.60.09138190.9840.0560.1080.94299.3
2.21-2.283.60.09438220.9840.0570.111.06799.4
2.28-2.363.50.07838340.9850.0490.0920.88199.4
2.36-2.463.50.07437960.9830.0460.0870.9199.4
2.46-2.573.30.06837900.9840.0430.0810.88297.8
2.57-2.73.60.06438140.990.0390.0750.83199.6
2.7-2.873.60.05738250.990.0350.0680.73599.5
2.87-3.093.60.05338530.9930.0330.0630.80599.7
3.09-3.413.40.05237810.9920.0330.0620.78397.9
3.41-3.93.70.04938690.9930.030.0580.83899.8
3.9-4.913.50.05138290.9910.0320.060.79198.8
4.91-503.60.06139160.9860.0380.0721.29199.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLB, 4WEB

1mlb

4web


Resolution: 1.82→47.01 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 3617 4.76 %
Rwork0.1698 72303 -
obs0.1716 75920 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.56 Å2 / Biso mean: 22.5428 Å2 / Biso min: 5.54 Å2
Refinement stepCycle: final / Resolution: 1.82→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6610 0 157 1200 7967
Biso mean--29.95 29.26 -
Num. residues----865
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.840.27051320.22762479261188
1.84-1.870.22631550.19732716287198
1.87-1.890.23271460.18742754290098
1.89-1.920.28231240.18922742286699
1.92-1.950.24781470.18562825297299
1.95-1.980.2111430.18122787293099
1.98-2.020.2581560.17942787294399
2.02-2.050.24951570.16932749290698
2.05-2.090.24941030.17312782288598
2.09-2.130.19661290.17172739286898
2.13-2.180.22391450.17452816296199
2.18-2.230.21761160.17792823293999
2.23-2.290.23581370.17182803294099
2.29-2.350.231550.17552792294799
2.35-2.420.21061510.176727942945100
2.42-2.50.20771180.17712795291399
2.5-2.590.20291190.17452776289598
2.59-2.690.20481560.175628192975100
2.69-2.810.24391430.17872812295599
2.81-2.960.20051360.178627972933100
2.96-3.150.20161320.179928372969100
3.15-3.390.2161310.17542749288097
3.39-3.730.23421580.175328332991100
3.73-4.270.18421150.14822846296199
4.27-5.380.13111570.12882802295999
5.38-47.010.19271560.16372849300599

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