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- PDB-8oxv: Transglutaminase 3 zymogen in complex with DH patient-derived Fab... -

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Basic information

Entry
Database: PDB / ID: 8oxv
TitleTransglutaminase 3 zymogen in complex with 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 / zymogen / antibody / dermatitis herpetiformis
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / catalytic activity / keratinocyte differentiation / extrinsic component of cytoplasmic side of plasma membrane / protein modification process ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / catalytic activity / keratinocyte differentiation / extrinsic component of cytoplasmic side of plasma membrane / 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/protease-like homologues ...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
Protein-glutamine gamma-glutamyltransferase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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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)124,31110
Polymers123,9693
Non-polymers3427
Water24,2481346
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-63 kcal/mol
Surface area46150 Å2
Unit cell
Length a, b, c (Å)81.659, 94.040, 91.143
Angle α, β, γ (deg.)90.000, 93.463, 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: 76706.570 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: 24112.951 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 , 4 types, 1353 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1346 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1M HEPES-MOPS pH7.1, 15% ethylene glycol, 7.5% PEG8000, 6 mM CaCl2, 6 mM MgCl2. 20% Ethylene glycol in the cryo solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 25, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.8→41.806 Å / Num. obs: 127215 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.987 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.074 / Rrim(I) all: 0.122 / Net I/σ(I): 6.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.167 / Num. unique obs: 6308 / CC1/2: 0.457 / Rpim(I) all: 0.952 / Rrim(I) all: 1.513

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimless0.7.9data scaling
DIALS2.2.10data reduction
PHASER2.8.3phasing
Coot0.9.8.7model building
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.806 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.567 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.121
Details: TLS. Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.229 6326 4.975 %
Rwork0.1854 120828 -
all0.188 --
obs-127154 99.91 %
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: 33.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.155 Å2-0 Å2-0.527 Å2
2--0.379 Å2-0 Å2
3----0.159 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8632 0 16 1346 9994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0128983
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168314
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.6412205
X-RAY DIFFRACTIONr_angle_other_deg0.5781.56619203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.77451148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.942550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.769101485
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.09810386
X-RAY DIFFRACTIONr_chiral_restr0.0830.21357
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022056
X-RAY DIFFRACTIONr_nbd_refined0.2010.21531
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.27792
X-RAY DIFFRACTIONr_nbtor_refined0.180.24309
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.24796
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2992
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1810.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.214
X-RAY DIFFRACTIONr_nbd_other0.1610.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.229
X-RAY DIFFRACTIONr_mcbond_it3.1352.3994552
X-RAY DIFFRACTIONr_mcbond_other3.1352.3994552
X-RAY DIFFRACTIONr_mcangle_it4.6454.2855698
X-RAY DIFFRACTIONr_mcangle_other4.6454.2885699
X-RAY DIFFRACTIONr_scbond_it3.642.6484431
X-RAY DIFFRACTIONr_scbond_other3.642.6494432
X-RAY DIFFRACTIONr_scangle_it5.484.7016503
X-RAY DIFFRACTIONr_scangle_other5.4794.7016504
X-RAY DIFFRACTIONr_lrange_it8.82926.97110294
X-RAY DIFFRACTIONr_lrange_other8.72525.0669874
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
1.8-1.8470.3465010.32788910.32894020.9140.91799.89360.332
1.847-1.8970.3385020.31186270.31291340.9190.92999.94530.314
1.897-1.9520.3164260.28184320.28288640.930.94599.93230.282
1.952-2.0120.2844290.25381840.25586160.9460.95699.96520.251
2.012-2.0780.2514270.23579270.23683560.9590.96299.97610.228
2.078-2.1510.2714390.22176490.22380920.9490.96899.95060.211
2.151-2.2320.2353440.19474150.19677700.9650.97699.85840.183
2.232-2.3220.2513310.19571850.19875230.960.97599.9070.183
2.322-2.4250.243050.17669270.17972360.9660.9899.94470.164
2.425-2.5430.2373420.17765550.1869010.9650.9899.9420.166
2.543-2.680.2193830.16761810.1765690.970.98399.92390.156
2.68-2.8420.2172720.16559360.16862120.970.98399.93560.157
2.842-3.0370.2253100.1755670.17358780.9680.98499.9830.165
3.037-3.2790.2172720.17751660.17954430.9730.98399.90810.174
3.279-3.590.2192290.18447720.18650060.9740.98499.90010.184
3.59-4.010.2112230.16443390.16745680.9740.98599.86870.166
4.01-4.6230.1621760.12938370.13140190.9840.98999.85070.136
4.623-5.6450.21900.15432370.15634280.9770.98999.97080.166
5.645-7.9120.2491280.17825560.18226840.9680.9871000.188
7.912-41.8060.206970.19814450.19915570.9770.9699.03660.447
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)
10.4645-0.14210.07050.1192-0.17180.31090.07280.0536-0.0622-0.012-0.05310.0227-0.01960.0732-0.01980.09940.0405-0.06820.10630.00210.151926.9798-0.207227.6119
20.9179-0.1448-0.6330.0405-0.00851.37560.0335-0.17190.019-0.02810.0360.0123-0.11290.075-0.06950.2381-0.0273-0.0930.0479-0.01430.0986-1.41763.04174.691
30.5333-0.1003-0.15050.04890.12010.3272-0.04690.020.10170.0098-0.00050.00380.04150.00290.04750.1854-0.003-0.0180.00360.02660.2032-11.49281.453961.4262
Refinement TLS groupSelection: ALL

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