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- PDB-8bbh: The crystal structure of a mouse Fab fragment TL1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 8bbh
TitleThe crystal structure of a mouse Fab fragment TL1 in complex with a human Glucose-6-phosphate isomerase peptide 293-307
Components
  • Glucose-6-phosphate isomerase
  • Heavy Chain of TL1 Fab fragment
  • Light Chain of TL1 Fab fragment
KeywordsIMMUNE SYSTEM / Antibody Fab fragment
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane ...glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / hemostasis / glucose 6-phosphate metabolic process / carbohydrate derivative binding / Gluconeogenesis / monosaccharide binding / Glycolysis / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / response to testosterone / humoral immune response / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / positive regulation of endothelial cell migration / gluconeogenesis / cytokine activity / response to progesterone / glycolytic process / TP53 Regulates Metabolic Genes / growth factor activity / response to estradiol / glucose homeostasis / secretory granule lumen / in utero embryonic development / negative regulation of neuron apoptotic process / ficolin-1-rich granule lumen / carbohydrate metabolic process / learning or memory / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily
Similarity search - Domain/homology
Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.619 Å
AuthorsGe, C. / Holmdahl, R. / Li, T.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2019.0059 Sweden
Swedish Research Council2019-01209 Sweden
CitationJournal: Ann Rheum Dis / Year: 2023
Title: Pathogenic antibody response to glucose-6-phosphate isomerase targets a modified epitope uniquely exposed on joint cartilage.
Authors: Li, T. / Ge, C. / Kramer, A. / Sareila, O. / Leu Agelii, M. / Johansson, L. / Forslind, K. / Lonnblom, E. / Yang, M. / Xu, B. / Li, Q. / Cheng, L. / Bergstrom, G. / Fernandez, G. / Kastbom, ...Authors: Li, T. / Ge, C. / Kramer, A. / Sareila, O. / Leu Agelii, M. / Johansson, L. / Forslind, K. / Lonnblom, E. / Yang, M. / Xu, B. / Li, Q. / Cheng, L. / Bergstrom, G. / Fernandez, G. / Kastbom, A. / Rantapaa-Dahlqvist, S. / Gjertsson, I. / Holmdahl, R.
History
DepositionOct 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: Glucose-6-phosphate isomerase
H: Heavy Chain of TL1 Fab fragment
L: Light Chain of TL1 Fab fragment


Theoretical massNumber of molelcules
Total (without water)48,7453
Polymers48,7453
Non-polymers00
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-30 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.660, 75.545, 96.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein/peptide Glucose-6-phosphate isomerase / GPI / Autocrine motility factor / AMF / Neuroleukin / NLK / Phosphoglucose isomerase / PGI / ...GPI / Autocrine motility factor / AMF / Neuroleukin / NLK / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI / Sperm antigen 36 / SA-36


Mass: 2238.565 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Biotynylated (BTN) peptide containing region of Glucose-6-phosphate isomerase (GPI) 293-307
Source: (synth.) Homo sapiens (human) / References: UniProt: P06744, glucose-6-phosphate isomerase
#2: Antibody Heavy Chain of TL1 Fab fragment


Mass: 22698.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Light Chain of TL1 Fab fragment


Mass: 23807.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 300 K / Method: evaporation
Details: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.619→55.408 Å / Num. obs: 63532 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 12.4
Reflection shellResolution: 1.62→8.87 Å / Num. unique obs: 3127 / CC1/2: 0.666

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model structure

Resolution: 1.619→55.408 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.676 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2291 3038 4.782 %
Rwork0.1976 60494 -
all0.199 --
obs-63532 99.994 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.727 Å2
Baniso -1Baniso -2Baniso -3
1--0.017 Å20 Å2-0 Å2
2--0.028 Å20 Å2
3----0.011 Å2
Refinement stepCycle: LAST / Resolution: 1.619→55.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 0 336 3681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0113433
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163045
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.6424676
X-RAY DIFFRACTIONr_angle_other_deg0.5551.5527137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2855435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.298109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46510544
X-RAY DIFFRACTIONr_dihedral_angle_6_deg1810129
X-RAY DIFFRACTIONr_chiral_restr0.0760.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
X-RAY DIFFRACTIONr_nbd_refined0.30.2549
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.22836
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21638
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4760.223
X-RAY DIFFRACTIONr_nbd_other0.3230.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2910.213
X-RAY DIFFRACTIONr_mcbond_it2.32.6211752
X-RAY DIFFRACTIONr_mcbond_other2.32.6211752
X-RAY DIFFRACTIONr_mcangle_it3.33.9172183
X-RAY DIFFRACTIONr_mcangle_other3.2993.9182184
X-RAY DIFFRACTIONr_scbond_it3.9152.951681
X-RAY DIFFRACTIONr_scbond_other3.9142.9491680
X-RAY DIFFRACTIONr_scangle_it5.8384.2742493
X-RAY DIFFRACTIONr_scangle_other5.8374.2752494
X-RAY DIFFRACTIONr_lrange_it7.37137.8773734
X-RAY DIFFRACTIONr_lrange_other7.31336.4673676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.619-1.6610.3762170.3644540.36146710.8860.8921000.361
1.661-1.7060.3682360.34642720.34845080.8940.9081000.347
1.706-1.7560.3022150.31441830.31443980.9330.931000.315
1.756-1.810.2862200.27440540.27442740.9450.951000.271
1.81-1.8690.2582110.24139130.24241240.9560.961000.235
1.869-1.9350.2462000.20638430.20840430.9580.9711000.193
1.935-2.0080.2491770.19836830.238600.9580.9741000.182
2.008-2.0890.211830.19235410.19237240.9720.9771000.172
2.089-2.1820.221680.18134580.18336260.970.981000.162
2.182-2.2880.2361500.18632700.18834200.9660.9781000.162
2.288-2.4120.2371570.18931330.19132900.9650.9771000.164
2.412-2.5580.2481600.18229300.18630900.9640.9781000.158
2.558-2.7340.2471230.18828120.1929350.9590.9781000.164
2.734-2.9530.2281110.18226120.18327230.9640.9791000.163
2.953-3.2340.1761130.17624130.17625260.9790.9811000.16
3.234-3.6140.2241170.19121930.19323100.9680.9781000.179
3.614-4.170.19960.17119440.17220400.9780.9821000.166
4.17-5.10.173670.15816900.15817570.9840.9851000.159
5.1-7.1820.235780.22612990.22613770.9730.9761000.225
7.182-55.4080.264390.237970.2328380.9610.96399.76130.244

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