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- PDB-6pyd: Structure of 3E9 antibody Fab bound to marinobufagenin -

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Basic information

Entry
Database: PDB / ID: 6pyd
TitleStructure of 3E9 antibody Fab bound to marinobufagenin
Components
  • 3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IgG4 C region
  • 3E9 antibody Fab light chain
KeywordsIMMUNE SYSTEM / Marinobufagenin / antibody engineering / Bence-Jones dimer
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-P4S
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFranklin, M.C. / Macdonald, L.E. / McWhirter, J. / Murphy, A.J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Kappa-on-Heavy (KoH) bodies are a distinct class of fully-human antibody-like therapeutic agents with antigen-binding properties.
Authors: Macdonald, L.E. / Meagher, K.A. / Franklin, M.C. / Levenkova, N. / Hansen, J. / Badithe, A.T. / Zhong, M. / Krueger, P. / Rafique, A. / Tu, N. / Shevchuk, J. / Wadhwa, S. / Ehrlich, G. / ...Authors: Macdonald, L.E. / Meagher, K.A. / Franklin, M.C. / Levenkova, N. / Hansen, J. / Badithe, A.T. / Zhong, M. / Krueger, P. / Rafique, A. / Tu, N. / Shevchuk, J. / Wadhwa, S. / Ehrlich, G. / Bautista, J. / Grant, C. / Esau, L. / Poueymirou, W.T. / Auerbach, W. / Morton, L. / Babb, R. / Chen, G. / Huang, T. / MacDonald, D. / Graham, K. / Gurer, C. / Voronina, V.A. / McWhirter, J.R. / Guo, C. / Yancopoulos, G.D. / Murphy, A.J.
#1: Journal: J. Hypertens. / Year: 2008
Title: Monoclonal antibody to an endogenous bufadienolide, marinobufagenin, reverses preeclampsia-induced Na/K-ATPase inhibition and lowers blood pressure in NaCl-sensitive hypertension.
Authors: Fedorova, O.V. / Simbirtsev, A.S. / Kolodkin, N.I. / Kotov, A.Y. / Agalakova, N.I. / Kashkin, V.A. / Tapilskaya, N.I. / Bzhelyansky, A. / Reznik, V.A. / Frolova, E.V. / Nikitina, E.R. / ...Authors: Fedorova, O.V. / Simbirtsev, A.S. / Kolodkin, N.I. / Kotov, A.Y. / Agalakova, N.I. / Kashkin, V.A. / Tapilskaya, N.I. / Bzhelyansky, A. / Reznik, V.A. / Frolova, E.V. / Nikitina, E.R. / Budny, G.V. / Longo, D.L. / Lakatta, E.G. / Bagrov, A.Y.
History
DepositionJul 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IgG4 C region
L: 3E9 antibody Fab light chain
A: 3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IgG4 C region
B: 3E9 antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3296
Polymers96,5284
Non-polymers8012
Water8,017445
1
H: 3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IgG4 C region
L: 3E9 antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6643
Polymers48,2642
Non-polymers4011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-26 kcal/mol
Surface area19370 Å2
MethodPISA
2
A: 3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IgG4 C region
B: 3E9 antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6643
Polymers48,2642
Non-polymers4011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-29 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.920, 67.690, 71.986
Angle α, β, γ (deg.)97.37, 106.35, 107.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21A
12L
22B

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _ / Label seq-ID: 2 - 215

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-ID
11VALVALHA2 - 215
21VALVALAC2 - 215
12ASNASNLB2 - 214
22ASNASNBD2 - 214

NCS ensembles :
ID
1
2

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Components

#1: Antibody 3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IgG4 C region


Mass: 24185.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 3E9 antibody Fab light chain


Mass: 24077.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-P4S / (3beta,5beta,14alpha,15beta)-3,5-dihydroxy-14,15-epoxybufa-20,22-dienolide


Mass: 400.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H32O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, PEG 3350, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2→80 Å / Num. obs: 51985 / % possible obs: 89.7 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.031 / Rrim(I) all: 0.043 / Net I/σ(I): 17.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1404 / CC1/2: 0.827 / Rpim(I) all: 0.324 / Rrim(I) all: 0.458 / % possible all: 47.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PUB

4pub


Resolution: 2→67.23 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.17 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.357 / ESU R Free: 0.25 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 2269 5.1 %RANDOM
Rwork0.22851 ---
obs0.23098 41801 77.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0.47 Å20.03 Å2
2---0.13 Å2-0.23 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 2→67.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6455 0 58 445 6958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026682
X-RAY DIFFRACTIONr_bond_other_d0.0030.026138
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9699110
X-RAY DIFFRACTIONr_angle_other_deg1.009314223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9145830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11924.102256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.153151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8911525
X-RAY DIFFRACTIONr_chiral_restr0.0790.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217395
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021480
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_it0.3721.4323344
X-RAY DIFFRACTIONr_mcbond_other0.3721.4323343
X-RAY DIFFRACTIONr_mcangle_it0.6792.1444166
X-RAY DIFFRACTIONr_mcangle_other0.6792.1454167
X-RAY DIFFRACTIONr_scbond_it0.3161.4793338
X-RAY DIFFRACTIONr_scbond_other0.3161.4793339
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5762.2074939
X-RAY DIFFRACTIONr_long_range_B_refined5.21612.0587193
X-RAY DIFFRACTIONr_long_range_B_other5.13611.7617101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11H22830
12A22830
21L23056
22B23056
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 26 -
Rwork0.264 751 -
obs--18.44 %
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)
12.8693-0.716-1.17423.74161.17352.5149-0.1628-0.19530.01330.23260.37470.15050.06780.4791-0.21190.03020.05320.02890.21060.02240.063655.5482-42.0115-3.9635
26.9117-0.195-1.41893.33320.27212.16470.21780.5185-0.1377-0.4088-0.0203-0.08220.044-0.165-0.19750.19150.1091-0.040.1325-0.02290.0435.4227-71.497-6.0921
34.39290.71-0.66822.91080.78521.694-0.0244-0.13070.23190.16780.0121-0.02220.02860.19780.01240.06280.02950.01780.06430.04360.067538.0338-36.11168.4732
43.5582-1.0781-1.93363.82210.58631.50130.1612-0.3344-0.19610.158-0.097-0.1160.18510.2978-0.06420.18520.043-0.12240.0995-0.00950.08534.4712-70.357210.2428
52.9644-0.7808-1.81964.23980.82893.6985-0.237-0.366-0.04790.23080.4120.09310.05040.2327-0.1750.03220.02840.01340.19810.03790.024319.0329-52.1986-20.1317
62.2881-0.1361-0.53333.6323-0.44776.2881-0.03580.06670.28770.259-0.20860.3192-0.2217-0.62650.24450.1222-0.00460.0660.0891-0.07610.186926.6206-19.005-30.1012
72.32670.1835-1.91593.2128-1.24145.55730.0133-0.0143-0.129-0.30110.0633-0.06830.26460.1237-0.07650.0662-0.0349-0.02160.05350.0080.032129.9274-56.1513-38.9828
81.29610.61670.24534.03342.71165.19850.0072-0.18770.04280.3996-0.1147-0.25520.03550.45120.10750.1323-0.04030.03380.10830.05060.168941.9966-24.8803-32.7068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 120
2X-RAY DIFFRACTION2H121 - 219
3X-RAY DIFFRACTION3L2 - 108
4X-RAY DIFFRACTION4L109 - 212
5X-RAY DIFFRACTION5A2 - 120
6X-RAY DIFFRACTION6A121 - 216
7X-RAY DIFFRACTION7B1 - 108
8X-RAY DIFFRACTION8B109 - 212

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