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- PDB-4eow: Crystal structure of a disease-associated anti-human GM-CSF autoa... -

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Basic information

Entry
Database: PDB / ID: 4eow
TitleCrystal structure of a disease-associated anti-human GM-CSF autoantibody MB007
Components
  • MB007 IgG1 Fab fragment light chain
  • MB007 human IgG1 Fab fragment heavy chain
KeywordsIMMUNE SYSTEM / Immunsystem / alpha-helical stretch in CDR3-H / protein-docking / Immunoglobulin IgG1 (lambda) / autoantibody causing PAP / GM-CSF
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin lambda constant 2 / Immunoglobulin lambda constant 3 / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBlech, M.
CitationJournal: Biochem.J. / Year: 2012
Title: Molecular structure of human GM-CSF in complex with a disease-associated anti-human GM-CSF autoantibody and its potential biological implications.
Authors: Blech, M. / Seeliger, D. / Kistler, B. / Bauer, M.M. / Hafner, M. / Horer, S. / Zeeb, M. / Nar, H. / Park, J.E.
History
DepositionApr 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.src_method / _struct_ref.db_code ..._entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: MB007 human IgG1 Fab fragment heavy chain
L: MB007 IgG1 Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)47,5422
Polymers47,5422
Non-polymers00
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-17 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.289, 47.786, 159.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMB007 Fab biological assembly consists of one monomer of light chain and heavy chain covalently linked by disulphide bonds

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Components

#1: Antibody MB007 human IgG1 Fab fragment heavy chain


Mass: 24574.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: S6B291, UniProt: P01857*PLUS
#2: Antibody MB007 IgG1 Fab fragment light chain / Ig lambda chain C region Kern / Ig lambda chain C region NIG-64 / Ig lambda chain C region SH / Ig ...Ig lambda chain C region Kern / Ig lambda chain C region NIG-64 / Ig lambda chain C region SH / Ig lambda chain C region X / Ig lambda-2 chain C region


Mass: 22967.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLC2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOY2, UniProt: P0DOY3*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: 19% PEG 4000, 0.1M ammonium sulphate, 0.1M sodium acetate, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 37111 / % possible obs: 83.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 31.11 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.057 / Net I/σ(I): 21
Reflection shellResolution: 1.9→2.1 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2869 / Rsym value: 0.518 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.2refinement
autoPROCdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→40 Å / Cor.coef. Fo:Fc: 0.9303 / Cor.coef. Fo:Fc free: 0.9147 / SU R Cruickshank DPI: 0.186 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 1771 4.99 %RANDOM
Rwork0.2239 ---
obs0.2256 35513 95.47 %-
all-37111 --
Displacement parametersBiso mean: 42.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.2649 Å20 Å20 Å2
2--0.459 Å20 Å2
3----2.7238 Å2
Refine analyzeLuzzati coordinate error obs: 0.382 Å
Refinement stepCycle: LAST / Resolution: 1.97→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 0 316 3626
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1098SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes501HARMONIC5
X-RAY DIFFRACTIONt_it3402HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion449SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3859SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3402HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4642HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion19.51
LS refinement shellResolution: 1.97→2.03 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.284 128 4.46 %
Rwork0.2465 2741 -
all0.2481 2869 -
obs-35513 95.47 %
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)
10.31810.25710.27382.22961.01610.86490.0111-0.1976-0.03550.2765-0.18510.13830.0273-0.15080.174-0.20260.01060.00470.085-0.0485-0.0536-11.7798-20.901419.2674
20.41390.0682-0.18721.21220.78482.2997-0.0373-0.09280.05810.0870.1349-0.0951-0.24070.2043-0.0976-0.2115-0.0101-0.02390.0548-0.0427-0.03694.5091-17.111512.533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|* }H1 - 228
2X-RAY DIFFRACTION2{ L|* }L2 - 212

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