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- PDB-4u6v: Mechanisms of Neutralization of a Human Anti-Alpha Toxin Antibody -

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Basic information

Entry
Database: PDB / ID: 4u6v
TitleMechanisms of Neutralization of a Human Anti-Alpha Toxin Antibody
Components
  • Alpha-hemolysin
  • Fab, antigen binding fragment, heavy chain
  • Fab, antigen binding fragment, light chain
KeywordsIMMUNE SYSTEM / alpha toxin / Fab / Staphylococcus aureus / mutagenesis
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / extracellular region
Similarity search - Function
Leukocidin/porin MspA / Leukocidin-like / Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Immunoglobulins ...Leukocidin/porin MspA / Leukocidin-like / Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Staphylococcus aureus subsp. aureus TCH60 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsOganesyan, V.Y. / Peng, L. / Damschroder, M.M. / Cheng, L. / Sadowska, A. / Tkaczyk, C. / Sellman, B. / Wu, H. / Dall'Acqua, W.F.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mechanisms of Neutralization of a Human Anti-alpha-toxin Antibody.
Authors: Oganesyan, V. / Peng, L. / Damschroder, M.M. / Cheng, L. / Sadowska, A. / Tkaczyk, C. / Sellman, B.R. / Wu, H. / Dall'Acqua, W.F.
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 5, 2014Group: Database references
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: atom_site_anisotrop / chem_comp_atom ...atom_site_anisotrop / chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_ncs_dom_lim
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab, antigen binding fragment, heavy chain
L: Fab, antigen binding fragment, light chain
A: Alpha-hemolysin
K: Fab, antigen binding fragment, heavy chain
M: Fab, antigen binding fragment, light chain
B: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,57812
Polymers161,0016
Non-polymers5766
Water1,58588
1
H: Fab, antigen binding fragment, heavy chain
L: Fab, antigen binding fragment, light chain
A: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9818
Polymers80,5013
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-117 kcal/mol
Surface area31060 Å2
MethodPISA
2
K: Fab, antigen binding fragment, heavy chain
M: Fab, antigen binding fragment, light chain
B: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5974
Polymers80,5013
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-49 kcal/mol
Surface area31110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.524, 148.505, 93.824
Angle α, β, γ (deg.)90.00, 99.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21K
12L
22M
13A
23B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROHA1 - 2221 - 222
21GLUGLUPROPROKD1 - 2221 - 222
12ASPASPCYSCYSLB1 - 2131 - 213
22ASPASPCYSCYSME1 - 2131 - 213
13THRTHRASNASNAC12 - 29312 - 293
23THRTHRASNASNBF12 - 29312 - 293

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Fab, antigen binding fragment, heavy chain


Mass: 23794.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalian expression vector pBGSA (others)
#2: Antibody Fab, antigen binding fragment, light chain


Mass: 23404.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalian expression vector pBGSA (others)
#3: Protein Alpha-hemolysin / Alpha-HL / Alpha-toxin


Mass: 33302.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus TCH60 (bacteria)
Production host: Staphylococcus aureus (bacteria) / References: UniProt: Q2G1X0
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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: 3.5 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Diffraction quality crystals grew in about a week in hanging drops where 3 ul of the MEDI4893 Fab/AT complex at a concentration of 15 mg/ml in 50 mM Tris-HCl, pH 7.5, 100 mM NaCl was mixed ...Details: Diffraction quality crystals grew in about a week in hanging drops where 3 ul of the MEDI4893 Fab/AT complex at a concentration of 15 mg/ml in 50 mM Tris-HCl, pH 7.5, 100 mM NaCl was mixed with 2 ul of 10% (w/v) PEG 6000, 100 mM HEPES, pH 7.0 and let to equilibrate against 300 ul of 10% (w/v) PEG 6000, 100 mM HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→92.45 Å / Num. obs: 74008 / % possible obs: 97.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.5
Reflection shellResolution: 2.56→2.75 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1.3 / % possible all: 98.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AHL

7ahl


Resolution: 2.56→92.45 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 25.384 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23488 3716 5 %RANDOM
Rwork0.1978 ---
obs0.19966 69982 99.35 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.455 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0.57 Å2
2--2.5 Å20 Å2
3----1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.56→92.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10934 0 30 88 11052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211258
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210272
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.94215286
X-RAY DIFFRACTIONr_angle_other_deg0.848323734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06851402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46924.508488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.478151848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2391548
X-RAY DIFFRACTIONr_chiral_restr0.090.21670
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112812
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022600
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_it2.0224.2345638
X-RAY DIFFRACTIONr_mcbond_other2.0224.2345637
X-RAY DIFFRACTIONr_mcangle_it3.2216.3467030
X-RAY DIFFRACTIONr_mcangle_other3.2216.3467031
X-RAY DIFFRACTIONr_scbond_it2.5864.4725620
X-RAY DIFFRACTIONr_scbond_other2.4324.445596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8936.558220
X-RAY DIFFRACTIONr_long_range_B_refined6.06133.1911831
X-RAY DIFFRACTIONr_long_range_B_other6.04833.13811806
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11H114940.06
12K114940.06
21L118380.09
22M118380.09
31A167220.05
32B167220.05
LS refinement shellResolution: 2.56→2.628 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 253 -
Rwork0.385 5086 -
obs--97.64 %
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)
11.343-0.21830.50220.30580.4115.12660.0005-0.09360.00010.034-0.0595-0.0848-0.08380.76470.0590.0385-0.0069-0.03360.61220.05350.045822.8376.23443.676
21.8525-0.220.41670.32560.13865.2741-0.0503-0.434-0.00010.0690.029-0.0379-0.2140.03190.02140.060.027-0.02210.37030.00760.01015.6867.30650.318
31.1841.23680.57183.81012.1552.3697-0.08420.071-0.07390.0789-0.18030.40260.2928-0.13370.26450.15060.10330.03450.4523-0.05410.0962-7.634-10.797-6.859
42.3673-0.2734-0.83510.61330.34923.9030.07830.21220.1893-0.09590.017-0.1259-0.38150.8985-0.09520.1271-0.1985-0.01410.76820.01480.054527.752-57.50512.834
52.36330.0362-1.25910.4444-0.06495.1319-0.00520.47760.0216-0.18070.0472-0.0233-0.0780.4734-0.0420.1944-0.1088-0.03190.5223-0.00150.019214.089-58.9730.631
61.6963-2.109-0.78453.751.78041.66460.0418-0.0295-0.0442-0.2141-0.19410.3252-0.3533-0.17780.15240.2542-0.079-0.03310.4343-0.06170.0728-17.687-41.2950.21
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 222
2X-RAY DIFFRACTION2L1 - 213
3X-RAY DIFFRACTION3A12 - 293
4X-RAY DIFFRACTION4K1 - 222
5X-RAY DIFFRACTION5M1 - 213
6X-RAY DIFFRACTION6B12 - 293

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