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- PDB-9axq: Crystal Structure of HY11-7E1_Hu3 Fab in the Apo Conformation -

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Basic information

Entry
Database: PDB / ID: 9axq
TitleCrystal Structure of HY11-7E1_Hu3 Fab in the Apo Conformation
Components
  • HY11-7E1_Hu3 Fab Heavy Chain
  • HY11-7E1_Hu3 Fab Light Chain
KeywordsIMMUNE SYSTEM / opioids / mAb / apo / cross-reactive
Function / homologyACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRodarte, J.V. / Pancera, M. / Hannon, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)UG3 DA047711 United States
CitationJournal: Acs Omega / Year: 2024
Title: Structure-Based Engineering of Monoclonal Antibodies for Improved Binding to Counteract the Effects of Fentanyl and Carfentanil.
Authors: Rodarte, J. / Baehr, C. / Hicks, D. / McGovern, M. / Zhang, Y. / Silva-Ortiz, P. / Hannon, B. / Duddu, S. / Pancera, M. / Pravetoni, M.
History
DepositionMar 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 12, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: HY11-7E1_Hu3 Fab Heavy Chain
L: HY11-7E1_Hu3 Fab Light Chain
A: HY11-7E1_Hu3 Fab Heavy Chain
C: HY11-7E1_Hu3 Fab Heavy Chain
E: HY11-7E1_Hu3 Fab Heavy Chain
B: HY11-7E1_Hu3 Fab Light Chain
D: HY11-7E1_Hu3 Fab Light Chain
F: HY11-7E1_Hu3 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,35423
Polymers194,3218
Non-polymers1,03415
Water7,080393
1
H: HY11-7E1_Hu3 Fab Heavy Chain
L: HY11-7E1_Hu3 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9497
Polymers48,5802
Non-polymers3695
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-33 kcal/mol
Surface area19680 Å2
MethodPISA
2
A: HY11-7E1_Hu3 Fab Heavy Chain
B: HY11-7E1_Hu3 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7575
Polymers48,5802
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-34 kcal/mol
Surface area19810 Å2
MethodPISA
3
C: HY11-7E1_Hu3 Fab Heavy Chain
D: HY11-7E1_Hu3 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7575
Polymers48,5802
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-37 kcal/mol
Surface area19470 Å2
MethodPISA
4
E: HY11-7E1_Hu3 Fab Heavy Chain
F: HY11-7E1_Hu3 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8906
Polymers48,5802
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-30 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.581, 151.103, 104.604
Angle α, β, γ (deg.)90.00, 91.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
HY11-7E1_Hu3 Fab Heavy Chain


Mass: 25201.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
HY11-7E1_Hu3 Fab Light Chain


Mass: 23378.889 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 3 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium sulfate, 0.1M sodium acetate pH 4.6, 25% PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 111677 / % possible obs: 95.7 % / Redundancy: 2.5 % / CC1/2: 0.978 / CC star: 0.995 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.091 / Rrim(I) all: 0.161 / Χ2: 4.489 / Net I/σ(I): 7.4 / Num. measured all: 284536
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.241.90.87644050.4170.7670.7111.1340.57976.1
2.24-2.282.30.80555150.3750.7390.631.0280.65293.7
2.28-2.322.30.7954570.5440.840.6111.0040.61494.9
2.32-2.372.30.71155570.5790.8570.5480.9030.67595.6
2.37-2.422.40.62756090.6490.8870.4760.7920.73495.9
2.42-2.482.40.52555410.7180.9140.3950.660.77995.8
2.48-2.542.40.43655730.7930.940.3260.5470.8695.3
2.54-2.612.30.36555250.6120.8720.2810.4631.06394.6
2.61-2.692.60.31556700.8650.9630.2280.391.21297.7
2.69-2.772.60.27756840.8750.9660.1970.3411.51297.7
2.77-2.872.60.23556670.9080.9760.1680.291.79697.7
2.87-2.992.60.19856740.9340.9830.1420.2442.397.3
2.99-3.122.50.17556160.9380.9840.1280.2183.1896.5
3.12-3.292.60.16256420.9420.9850.1140.1994.69196.8
3.29-3.492.80.14557560.960.990.10.1775.92998
3.49-3.762.80.13357060.9620.990.0910.1627.09597.8
3.76-4.142.70.12456900.9660.9910.0870.1528.4697.3
4.14-4.742.90.11657540.9730.9930.0780.1419.86698.6
4.74-5.972.90.10857800.9730.9930.0730.1319.88798.2
5.97-5030.10158560.980.9950.0680.12215.17698.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.83 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 5437 4.96 %
Rwork0.2077 --
obs0.2091 109545 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13013 0 64 393 13470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313387
X-RAY DIFFRACTIONf_angle_d0.58318213
X-RAY DIFFRACTIONf_dihedral_angle_d12.7554776
X-RAY DIFFRACTIONf_chiral_restr0.0442045
X-RAY DIFFRACTIONf_plane_restr0.0052327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.37911560.35533090X-RAY DIFFRACTION85
2.23-2.250.38261770.36183304X-RAY DIFFRACTION92
2.25-2.280.41891830.34543353X-RAY DIFFRACTION93
2.28-2.310.35451580.33413400X-RAY DIFFRACTION94
2.31-2.340.37262070.32973407X-RAY DIFFRACTION95
2.34-2.370.33491720.31043424X-RAY DIFFRACTION96
2.37-2.40.36741710.29813469X-RAY DIFFRACTION96
2.4-2.440.36151830.29973413X-RAY DIFFRACTION95
2.44-2.480.32541910.28273437X-RAY DIFFRACTION95
2.48-2.520.32981840.27083433X-RAY DIFFRACTION95
2.52-2.560.29631580.25933388X-RAY DIFFRACTION94
2.56-2.610.31621850.25683472X-RAY DIFFRACTION96
2.61-2.660.27461850.25063518X-RAY DIFFRACTION97
2.66-2.710.27491760.25813482X-RAY DIFFRACTION98
2.71-2.770.29622080.25393522X-RAY DIFFRACTION98
2.77-2.840.29321570.25983545X-RAY DIFFRACTION97
2.84-2.910.29171950.26873513X-RAY DIFFRACTION97
2.91-2.990.32881830.24833479X-RAY DIFFRACTION97
2.99-3.070.31391870.25153491X-RAY DIFFRACTION96
3.07-3.170.28921740.24193421X-RAY DIFFRACTION95
3.17-3.290.29151650.23163598X-RAY DIFFRACTION98
3.29-3.420.25371740.22273537X-RAY DIFFRACTION98
3.42-3.570.25491790.20913527X-RAY DIFFRACTION98
3.57-3.760.20982030.19853523X-RAY DIFFRACTION98
3.76-40.19332120.18423525X-RAY DIFFRACTION98
4-4.310.1781570.15973539X-RAY DIFFRACTION97
4.31-4.740.17771910.14313572X-RAY DIFFRACTION99
4.74-5.420.15292170.14173548X-RAY DIFFRACTION98
5.42-6.830.20531850.17653572X-RAY DIFFRACTION98
6.83-42.830.1881640.17473606X-RAY DIFFRACTION97

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