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- PDB-3cxd: Crystal structure of anti-osteopontin antibody 23C3 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3cxd
TitleCrystal structure of anti-osteopontin antibody 23C3 in complex with its epitope peptide
Components
  • Fab fragment of anti-osteopontin antibody 23C3, Heavy chain
  • Fab fragment of anti-osteopontin antibody 23C3, Light chain
  • a peptide from osteopontin
KeywordsIMMUNE SYSTEM / Fab / osteopontin / OPN / antibody-antigen complex
Function / homology
Function and homology information


negative regulation of collateral sprouting of intact axon in response to injury / positive regulation of estradiol secretion / androgen catabolic process / biomineral tissue development / response to macrophage colony-stimulating factor / response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to testosterone stimulus / Signaling by PDGF / RUNX3 Regulates Immune Response and Cell Migration / positive regulation of bone resorption ...negative regulation of collateral sprouting of intact axon in response to injury / positive regulation of estradiol secretion / androgen catabolic process / biomineral tissue development / response to macrophage colony-stimulating factor / response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to testosterone stimulus / Signaling by PDGF / RUNX3 Regulates Immune Response and Cell Migration / positive regulation of bone resorption / extracellular matrix binding / response to steroid hormone / response to vitamin D / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / small molecule binding / decidualization / Integrin cell surface interactions / Degradation of the extracellular matrix / embryo implantation / cytokine activity / cell projection / Post-translational protein phosphorylation / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / osteoblast differentiation / cell adhesion / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Osteopontin / Osteopontin, conserved site / Osteopontin / Osteopontin signature. / Osteopontin / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsDu, J. / Yang, H. / Zhong, C. / Ding, J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Molecular basis of recognition of human osteopontin by 23C3, a potential therapeutic antibody for treatment of rheumatoid arthritis
Authors: Du, J. / Hou, S. / Zhong, C. / Lai, Z. / Yang, H. / Dai, J. / Zhang, D. / Wang, H. / Guo, Y. / Ding, J.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab fragment of anti-osteopontin antibody 23C3, Light chain
H: Fab fragment of anti-osteopontin antibody 23C3, Heavy chain
P: a peptide from osteopontin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3084
Polymers47,5593
Non-polymers7491
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-20 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.318, 92.020, 122.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab fragment of anti-osteopontin antibody 23C3, Light chain


Mass: 23070.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: ascites
#2: Antibody Fab fragment of anti-osteopontin antibody 23C3, Heavy chain


Mass: 23131.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: ascites
#3: Protein/peptide a peptide from osteopontin


Mass: 1356.502 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the osteopontin peptide is synthesized at Shanghai HD Bioscience Company
References: UniProt: P10451
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
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: 2.51 Å3/Da / Density % sol: 50.94 % / Mosaicity: 1.19 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2M di-sodium tartrate, 20% PEG3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 12125 / % possible obs: 98.4 % / Redundancy: 6.65 % / Rmerge(I) obs: 0.135 / Χ2: 1.07 / Net I/σ(I): 5 / Scaling rejects: 2282
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.8-2.97.040.2932.1841511940.53100
2.9-3.0270.272.3851112130.62100
3.02-3.156.960.2462.6840312050.82100
3.15-3.326.890.2223846912241.07100
3.32-3.526.790.1863.7833512141.2599.6
3.52-3.86.690.1524.6811111881.498.8
3.8-4.176.570.1325.6832012291.4498.6
4.17-4.776.190.0938.1778411971.4197.2
4.77-5.986.260.0868.8807412321.2397.6
5.98-206.160.06410.685451229192.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JHK

1jhk


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.858 / SU B: 40.348 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.292 613 5.1 %RANDOM
Rwork0.248 ---
obs0.251 12083 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.378 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å20 Å20 Å2
2---1.43 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 50 0 3373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223464
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.9574733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9255435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1124.453137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79815515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5441512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022614
X-RAY DIFFRACTIONr_nbd_refined0.1880.21335
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22310
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0580.22
X-RAY DIFFRACTIONr_mcbond_it0.6971.52222
X-RAY DIFFRACTIONr_mcangle_it1.24423519
X-RAY DIFFRACTIONr_scbond_it1.3231438
X-RAY DIFFRACTIONr_scangle_it1.6524.51214
X-RAY DIFFRACTIONr_rigid_bond_restr1.5133660
X-RAY DIFFRACTIONr_sphericity_bonded0.55533373
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 32 -
Rwork0.373 836 -
all-868 -
obs--100 %

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