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- PDB-8oxx: Transglutaminase 3 in complex with inhibitor Z-don and DH patient... -

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Basic information

Entry
Database: PDB / ID: 8oxx
TitleTransglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-B02
Components
  • (Antibody fab fragment ...) x 2
  • Protein-glutamine gamma-glutamyltransferase E 27 kDa non-catalytic chain
KeywordsTRANSFERASE / Transglutaminase / TGM3 / TG3 / Transglutaminase 3 / enzyme / antibody / dermatitis herpetiformis / inhibitor / Z-don / IGHV3-9 / IGLV6-57
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / extrinsic component of cytoplasmic side of plasma membrane / catalytic activity / keratinocyte differentiation / protein modification process ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / extrinsic component of cytoplasmic side of plasma membrane / catalytic activity / keratinocyte differentiation / protein modification process / calcium ion binding / structural molecule activity / protein-containing complex / extracellular exosome / cytoplasm
Similarity search - Function
: / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily ...: / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Transglutaminase-like superfamily / Papain-like cysteine peptidase superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
D-PROLINE / D-VALINE / METHYL L-LEUCINATE / 5-OXO-L-NORLEUCINE / benzyl hydrogen carbonate / Protein-glutamine gamma-glutamyltransferase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHeggelund, J.E. / Sollid, L.M.
Funding support Norway, 3items
OrganizationGrant numberCountry
Other government2020027 Norway
Other privateSKGJ-MED-017 Norway
Other governmentWL-IMMUNOLOGY Norway
CitationJournal: Nat Commun / Year: 2023
Title: Autoantibody binding and unique enzyme-substrate intermediate conformation of human transglutaminase 3.
Authors: Heggelund, J.E. / Das, S. / Stamnaes, J. / Iversen, R. / Sollid, L.M.
History
DepositionMay 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-glutamine gamma-glutamyltransferase E 27 kDa non-catalytic chain
B: Antibody fab fragment heavy chain
C: Antibody fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,26118
Polymers97,9983
Non-polymers1,26315
Water8,161453
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-55 kcal/mol
Surface area37170 Å2
Unit cell
Length a, b, c (Å)79.271, 65.005, 90.908
Angle α, β, γ (deg.)90.000, 96.854, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein-glutamine gamma-glutamyltransferase E 27 kDa non-catalytic chain


Mass: 50925.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGM3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08188

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Antibody , 2 types, 2 molecules BC

#2: Antibody Antibody fab fragment heavy chain


Mass: 23922.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IGHV3-9 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Antibody fab fragment light chain


Mass: 23149.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IGLV6-57 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 9 types, 468 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca
#7: Chemical ChemComp-P6S / benzyl hydrogen carbonate


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ONL / 5-OXO-L-NORLEUCINE


Type: L-peptide linking / Mass: 145.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-DVA / D-VALINE


Type: D-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-DPR / D-PROLINE


Type: D-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-MLL / METHYL L-LEUCINATE


Type: L-peptide linking / Mass: 145.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO2 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1M Hepes-mops pH 7.1, 22% ethylene glycol, 11% PEG8000, 8 mM CaCl2, 8 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 5, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→52.804 Å / Num. obs: 30234 / % possible obs: 94.6 % / Redundancy: 3.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.09 / Rrim(I) all: 0.135 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.01-52.753.50.0317240.9980.0280.041
2.5-2.63.90.57635360.790.5160.776

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
REFMAC5.8.0411refinement
Coot0.9.8.7model building
PHASER2.8.3phasing
XDS20220110data reduction
Aimless0.7.9data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→52.804 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.143 / SU B: 19.249 / SU ML: 0.221 / Average fsc free: 0.9615 / Average fsc work: 0.9808 / Cross valid method: FREE R-VALUE / ESU R Free: 0.293
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2221 1532 5.069 %
Rwork0.1544 28690 -
all0.158 --
obs-30222 94.299 %
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: 43.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.347 Å2-0 Å2-1.621 Å2
2---1.578 Å2-0 Å2
3---0.603 Å2
Refinement stepCycle: LAST / Resolution: 2.5→52.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6898 0 75 453 7426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127158
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166506
X-RAY DIFFRACTIONr_ext_dist_refined_b0.0140.149359
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.6449704
X-RAY DIFFRACTIONr_angle_other_deg0.571.56815001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1965898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.703545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.107101116
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg15.602101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.12910308
X-RAY DIFFRACTIONr_chiral_restr0.0730.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021687
X-RAY DIFFRACTIONr_nbd_refined0.2090.21249
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.26004
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23445
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.23860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2336
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.218
X-RAY DIFFRACTIONr_nbd_other0.1850.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2490.215
X-RAY DIFFRACTIONr_mcbond_it4.0763.4923603
X-RAY DIFFRACTIONr_mcbond_other4.0723.4933603
X-RAY DIFFRACTIONr_mcangle_it6.2446.2574494
X-RAY DIFFRACTIONr_mcangle_other6.2486.2594495
X-RAY DIFFRACTIONr_scbond_it4.8013.9013555
X-RAY DIFFRACTIONr_scbond_other4.8013.9023556
X-RAY DIFFRACTIONr_scangle_it7.4326.9525210
X-RAY DIFFRACTIONr_scangle_other7.4316.9535211
X-RAY DIFFRACTIONr_lrange_it9.03468.76654103
X-RAY DIFFRACTIONr_lrange_other9.03168.76354045
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
2.5-2.5650.3031010.25222090.25423400.9450.96198.71790.246
2.565-2.6350.2871160.22621360.22922830.9440.96798.64210.215
2.635-2.7110.3111070.20420910.20922340.9420.97298.38850.191
2.711-2.7940.2821040.20420120.20821400.9390.97298.87850.189
2.794-2.8860.293970.18919750.19420960.9540.97798.8550.173
2.886-2.9870.271770.17219610.17620630.9580.98198.78820.156
2.987-3.0990.2581160.16618110.17119610.9520.98298.26620.15
3.099-3.2250.2441040.17217410.17618640.9610.98198.98070.157
3.225-3.3680.238850.1617100.16418220.9640.98598.51810.15
3.368-3.5320.22790.16616220.16917380.9750.98797.87110.158
3.532-3.7220.241480.1576740.16216500.9680.98943.75760.155
3.722-3.9460.257490.15810210.16315770.9670.98867.85030.151
3.946-4.2170.237840.13813730.14314680.970.9999.25070.134
4.217-4.5520.143930.10412640.10713750.9890.99598.69090.102
4.552-4.9830.158660.112010.10312720.9820.99499.60690.099
4.983-5.5650.214560.11710780.12211550.9780.99398.18180.114
5.565-6.4140.212570.1449490.14810300.9770.99197.66990.138
6.414-7.8270.237370.1418240.1468710.9810.9998.85190.138
7.827-10.950.115300.1056580.1056920.9940.99499.4220.111
10.95-52.8040.17260.1923800.194140.9750.97498.06760.21
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)
10.5173-0.26510.1650.354-0.04010.07920.01-0.09070.1482-0.1134-0.0219-0.16810.0259-0.05690.0120.1634-0.00540.01210.04790.01410.093642.49636.100113.2878
20.55920.0114-0.39630.05350.0570.38940.04730.02970.07380.07350.0499-0.02510.12220.0198-0.09710.24690.0306-0.06530.0495-0.01080.031416.38512.351163.5843
30.367-0.0268-0.2790.00430.01550.45690.08160.10790.00060.0087-0.0152-0.0007-0.0019-0.0659-0.06640.17210.0208-0.04180.0654-0.01370.02516.53970.950349.8736
Refinement TLS groupSelection: ALL

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