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- PDB-4bkl: Crystal structure of the arthritogenic antibody M2139 (Fab fragme... -

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Basic information

Entry
Database: PDB / ID: 4bkl
TitleCrystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the triple-helical J1 peptide
Components
  • J1 EPITOPE
  • M2139 FAB FRAGMENT HEAVY CHAIN
  • M2139 FAB FRAGMENT LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ANTIBODY / RHEUMATOID ARTHRITIS / COLLAGEN TYPE II
Function / homology
Function and homology information


Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / MET activates PTK2 signaling / anterior head development ...Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / MET activates PTK2 signaling / anterior head development / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / embryonic skeletal joint morphogenesis / otic vesicle development / ECM proteoglycans / proteoglycan metabolic process / platelet-derived growth factor binding / Integrin cell surface interactions / notochord development / limb bud formation / extracellular matrix structural constituent conferring tensile strength / cartilage development involved in endochondral bone morphogenesis / limb morphogenesis / tissue homeostasis / MHC class II protein binding / cellular response to BMP stimulus / endochondral ossification / collagen trimer / collagen fibril organization / cartilage development / skeletal system morphogenesis / proteoglycan binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cartilage condensation / inner ear morphogenesis / roof of mouth development / inner ear development / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / ossification / extracellular matrix / skeletal system development / central nervous system development / sensory perception of sound / bone development / regulation of gene expression / collagen-containing extracellular matrix / protein homodimerization activity / extracellular space / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(II) chain
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsRaposo, B. / Dobritzsch, D. / Ge, C. / Ekman, D. / Lindh, I. / Foerster, M. / Uysal, H. / Schneider, G. / Holmdahl, R.
CitationJournal: J.Exp.Med. / Year: 2014
Title: Epitope-Specific Antibody Response is Controlled by Immunoglobulin Vh Polymorphisms.
Authors: Raposo, B. / Dobritzsch, D. / Ge, C. / Ekman, D. / Xu, B. / Lindh, I. / Forster, M. / Uysal, H. / Nandakumar, K.S. / Schneider, G. / Holmdahl, R.
History
DepositionApr 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: M2139 FAB FRAGMENT HEAVY CHAIN
B: M2139 FAB FRAGMENT LIGHT CHAIN
E: J1 EPITOPE
F: J1 EPITOPE
G: J1 EPITOPE


Theoretical massNumber of molelcules
Total (without water)58,5975
Polymers58,5975
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-50.5 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.180, 95.180, 190.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21F
12E
22G
13F
23G

NCS domain segments:

Component-ID: _ / End auth comp-ID: HYP / End label comp-ID: HYP / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROEC11 - 3311 - 33
21PROPROFD11 - 3311 - 33
12PROPROEC11 - 3311 - 33
22PROPROGE11 - 3311 - 33
13GLYGLYFD10 - 3310 - 33
23GLYGLYGE10 - 3310 - 33

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody M2139 FAB FRAGMENT HEAVY CHAIN


Mass: 24689.611 Da / Num. of mol.: 1 / Fragment: VH AND CH1 / Source method: isolated from a natural source
Details: HEAVY CHAIN CLEAVED BY PAPAIN, EXACT TERMINI UNCLEAR
Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA (NS0) / Strain: DBA/1
#2: Antibody M2139 FAB FRAGMENT LIGHT CHAIN


Mass: 23963.469 Da / Num. of mol.: 1 / Fragment: VL AND CL / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA (NS0) / Strain: DBA/1
#3: Protein/peptide J1 EPITOPE


Mass: 3314.599 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: TRIPLE-HELICAL SYNTHETIC PEPTIDE, CHAINS CROSSLINKED AT C-TERMINUS, CONTAINS J1-EPITOPE OF COLLAGEN TYPE II FROM MOUSE FLANKED BY GPO REPEATS
Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P28481*PLUS
Sequence detailsTHE ANTIBODY UNDERWENT SOMATIC MUTATION SEQUENCE IS LARGELY IDENTICAL WITH THAT OF IGHV1-4 THE ...THE ANTIBODY UNDERWENT SOMATIC MUTATION SEQUENCE IS LARGELY IDENTICAL WITH THAT OF IGHV1-4 THE ANTIBODY UNDERWENT SOMATIC MUTATION SEQUENCE IS LARGELY IDENTICAL WITH THAT OF IGKV3-1 ONE OF THE THREE PEPTIDE CHAINS HAS ADDITIONAL 4 RESIDUES (KKYG) AT THE C-TERMINUS, WHICH CROSSLINKS ALL THREE CHAINS WITH EACH OTHER WE HAVE NO WAY OF KNOWING WHICH OF THE 3 CHAINS E, F OR G IT IS, DUE TO LACK OF ELECTRON DENSITY FOR THE CROSSLINKED END

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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: 4.02 Å3/Da / Density % sol: 69.4 % / Description: NONE
Crystal growpH: 7
Details: 1.7 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.0, 10 % DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 3.25→82.5 Å / Num. obs: 16327 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y5T

2y5t


Resolution: 3.25→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 21.877 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R: 2.289 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY ONE OF THE TWO ALTERNATIVE CONFORMATION OF LOOP A158-164 WAS MODELED SEVERAL RESIDUES AT THE C-TERMINUS OF FAB HEAVY AND LIGHT CHAIN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY ONE OF THE TWO ALTERNATIVE CONFORMATION OF LOOP A158-164 WAS MODELED SEVERAL RESIDUES AT THE C-TERMINUS OF FAB HEAVY AND LIGHT CHAIN AND AT N- AND C-TERMINI OF THE PEPTIDE CHAINS ARE NOT MODELED DUE TO LACK OF ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 823 5.1 %RANDOM
Rwork0.22175 ---
obs0.22378 15468 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.469 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å22.42 Å20 Å2
2--2.42 Å20 Å2
3----7.86 Å2
Refinement stepCycle: LAST / Resolution: 3.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 0 0 3770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023879
X-RAY DIFFRACTIONr_bond_other_d0.0020.023497
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9935294
X-RAY DIFFRACTIONr_angle_other_deg1.7453.0028147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77724.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31715576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2071514
X-RAY DIFFRACTIONr_chiral_restr0.160.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02812
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_it7.07611.6892027
X-RAY DIFFRACTIONr_mcbond_other7.06411.6882026
X-RAY DIFFRACTIONr_mcangle_it10.88617.5032525
X-RAY DIFFRACTIONr_mcangle_other10.88517.5062526
X-RAY DIFFRACTIONr_scbond_it6.79512.1021852
X-RAY DIFFRACTIONr_scbond_other6.79312.1041853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.8217.9782770
X-RAY DIFFRACTIONr_long_range_B_refined16.78414850
X-RAY DIFFRACTIONr_long_range_B_other16.78314848
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)
11E5900.22
12F5900.22
21E6050.23
22G6050.23
31F6130.2
32G6130.2
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 62 -
Rwork0.378 1097 -
obs--98.64 %

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