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- PDB-4o4y: Crystal structure of the anti-hinge rabbit antibody 2095-2 in com... -

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Basic information

Entry
Database: PDB / ID: 4o4y
TitleCrystal structure of the anti-hinge rabbit antibody 2095-2 in complex with IDES hinge peptide
Components
  • 2095-2 heavy chain
  • 2095-2 light chain
  • IDES hinge peptide
KeywordsIMMUNE SYSTEM / immunoglobulin fold / antibody / hinge
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMalia, T.J. / Teplyakov, A. / Luo, J. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2014
Title: Structure and specificity of an antibody targeting a proteolytically cleaved IgG hinge.
Authors: Malia, T.J. / Teplyakov, A. / Brezski, R.J. / Luo, J. / Kinder, M. / Sweet, R.W. / Almagro, J.C. / Jordan, R.E. / Gilliland, G.L.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 2095-2 light chain
H: 2095-2 heavy chain
A: IDES hinge peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1558
Polymers48,6943
Non-polymers4605
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-27 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.410, 89.370, 83.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11L-726-

HOH

21H-590-

HOH

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Components

#1: Antibody 2095-2 light chain


Mass: 23724.293 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus, Homo sapiens / Production host: Homo sapiens (human)
#2: Antibody 2095-2 heavy chain


Mass: 23565.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus, Homo sapiens / Production host: Homo sapiens (human)
#3: Protein/peptide IDES hinge peptide


Mass: 1404.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01857*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE L CYS 300 IS A CYSTEINYLATION OF RESIDUE L CYS 81.

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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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 18.33% PEG3350, 0.2 M lithium sulfate, 5% isopropanol, cryoprotection: mother liquor + 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 16, 2009 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 37290 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 6.1 / % possible all: 51.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
d*TREK9.6Ldata reduction
d*TREK9.6Ldata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MA3

4ma3


Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.21 / SU B: 6.217 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 1875 5 %RANDOM
Rwork0.1919 35290 --
obs0.1942 35290 88.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.79 Å2 / Biso mean: 33.146 Å2 / Biso min: 5.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 30 492 3813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223544
X-RAY DIFFRACTIONr_bond_other_d0.0010.022362
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9644869
X-RAY DIFFRACTIONr_angle_other_deg0.8423.0035814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41224.32125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91415552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.561513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
X-RAY DIFFRACTIONr_mcbond_it0.6661.52279
X-RAY DIFFRACTIONr_mcbond_other0.1831.5927
X-RAY DIFFRACTIONr_mcangle_it1.16223729
X-RAY DIFFRACTIONr_scbond_it1.70131265
X-RAY DIFFRACTIONr_scangle_it2.6894.51119
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.594 91 -
Rwork0.464 1408 -
all-1499 -
obs--49.47 %
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)
11.7081-0.4092-0.49111.38480.16021.9781-0.0091-0.01380.31740.0865-0.011-0.076-0.2744-0.1060.02010.04970.0076-0.02170.06210.00150.0743-10.009832.5809-33.3543
21.1048-0.36910.68941.3269-0.4582.22640.07010.071-0.05150.0373-0.0686-0.02180.17140.1054-0.00140.0246-0.0129-0.00660.07020.0060.0232-0.147414.1693-33.8205
32.8047-2.6597-0.38425.20620.02692.5043-0.4587-0.4796-0.12750.70740.43170.20250.1855-0.05170.02690.25780.1250.11780.18560.03970.0639-15.364122.20742.7959
42.4439-3.2688-0.80195.31920.88772.0413-0.2822-0.0467-0.64970.65010.12411.28120.1089-0.31020.15810.2292-0.02090.15740.08050.04480.3644-15.89048.9105-6.134
514.25335.31-13.816310.155-4.410124.30970.11740.84410.246-0.71460.2043-0.3897-0.60730.06-0.32170.1131-0.00150.04070.18450.04270.05271.164925.8654-50.1496
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 110
2X-RAY DIFFRACTION2H1 - 113
3X-RAY DIFFRACTION3L111 - 300
4X-RAY DIFFRACTION4H114 - 214
5X-RAY DIFFRACTION5A230 - 236

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