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- PDB-8oxw: Transglutaminase 3 in complex with DH patient-derived Fab DH63-B02 -

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Basic information

Entry
Database: PDB / ID: 8oxw
TitleTransglutaminase 3 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 / antibody / dermatitis herpetiformis
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / extrinsic component of cytoplasmic side of plasma membrane / hair follicle morphogenesis / acyltransferase activity / keratinization / catalytic activity / keratinocyte differentiation / protein modification process ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / extrinsic component of cytoplasmic side of plasma membrane / hair follicle morphogenesis / acyltransferase activity / keratinization / 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
Protein-glutamine gamma-glutamyltransferase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)124,80718
Polymers123,9693
Non-polymers83815
Water20,7351151
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-35 kcal/mol
Surface area45260 Å2
Unit cell
Length a, b, c (Å)81.505, 93.488, 90.644
Angle α, β, γ (deg.)90.000, 92.632, 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, 1166 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1151 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.82 Å3/Da / Density % sol: 56.38 %
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, 10 mM CaCl2, 10 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.7→50.02 Å / Num. obs: 146920 / % possible obs: 98.7 % / Redundancy: 3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.058 / Rrim(I) all: 0.083 / Net I/σ(I): 7.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.024 / Num. unique obs: 7313 / CC1/2: 0.359 / Rpim(I) all: 1.005 / Rrim(I) all: 1.436

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimless0.7.9data scaling
Coot0.9.8.7model building
PHASER2.8.3phasing
DIALS2.2.10data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.315 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.5 / SU ML: 0.099 / Cross valid method: FREE R-VALUE / ESU R: 0.095 / ESU R Free: 0.098
Details: TLS. Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2101 7468 5.092 %
Rwork0.1724 139188 -
all0.174 --
obs-146656 98.422 %
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: 33.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.277 Å2
2--1.752 Å20 Å2
3----1.291 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8615 0 48 1151 9814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0128991
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168347
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.64212199
X-RAY DIFFRACTIONr_angle_other_deg0.5941.56619270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6151146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.264551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.285101480
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.5210383
X-RAY DIFFRACTIONr_chiral_restr0.0850.21356
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022061
X-RAY DIFFRACTIONr_nbd_refined0.1980.21474
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.27621
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24314
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.24780
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2863
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1050.23
X-RAY DIFFRACTIONr_metal_ion_refined0.2740.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2550.210
X-RAY DIFFRACTIONr_nbd_other0.1960.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.228
X-RAY DIFFRACTIONr_mcbond_it3.3822.7294547
X-RAY DIFFRACTIONr_mcbond_other3.3812.7294547
X-RAY DIFFRACTIONr_mcangle_it4.7864.8755693
X-RAY DIFFRACTIONr_mcangle_other4.7864.8795694
X-RAY DIFFRACTIONr_scbond_it4.2673.0734444
X-RAY DIFFRACTIONr_scbond_other4.2663.0744445
X-RAY DIFFRACTIONr_scangle_it6.1925.4376503
X-RAY DIFFRACTIONr_scangle_other6.1915.4376504
X-RAY DIFFRACTIONr_lrange_it8.7329.76810083
X-RAY DIFFRACTIONr_lrange_other8.64728.2629769
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
1.7-1.7440.355430.344103640.344109490.8940.89599.61640.346
1.744-1.7920.3255410.315100490.315106430.9120.91399.5020.316
1.792-1.8440.295370.398250.3104130.9280.92399.51020.3
1.844-1.90.2954640.2795930.271101080.9340.93999.49540.266
1.9-1.9630.2674450.23693010.23797920.9490.95799.53020.227
1.963-2.0310.2444160.2390110.23194840.9490.96299.3990.219
2.031-2.1080.254410.20186610.20391680.9550.97199.28010.187
2.108-2.1940.2244460.18282620.18487950.9660.97899.01080.168
2.194-2.2910.2164330.16779710.16985010.9690.98298.8590.154
2.291-2.4020.2064310.15974970.16180710.9730.98498.22820.147
2.402-2.5320.2234130.14770730.15176830.970.98697.43590.136
2.532-2.6850.2023800.14365730.14672640.9740.98795.71860.135
2.685-2.870.1913390.1561120.15268380.9760.98694.34040.145
2.87-3.0990.1913470.14855880.15164200.9780.98792.44550.144
3.099-3.3930.2072740.1655560.16258730.9730.98699.26780.16
3.393-3.7910.1923130.16249920.16453410.980.98799.3260.164
3.791-4.3720.1692330.13344340.13547080.9830.9999.12910.139
4.372-5.3420.1732400.13137290.13440100.9870.99298.97760.138
5.342-7.5030.1931600.17129240.17231360.9820.98798.34180.177
7.503-45.3150.231720.16916730.17218030.9710.9896.78310.203
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)
10.3924-0.0610.03640.021-0.05670.27420.02730.0627-0.04310.007-0.0211-0.0014-0.0140.0617-0.00620.0470.0255-0.03940.0972-0.00760.041427.5065-0.15327.3011
20.5642-0.0603-0.63320.03240.00410.92340.0486-0.14110.0358-0.04030.02780.0157-0.00830.0836-0.07640.07790.0021-0.03230.1289-0.01040.0202-0.52473.360974.1785
30.4394-0.0783-0.1630.01860.05160.2362-0.0043-0.0020.0445-0.010.002-0.00260.02170.00220.00240.10620.0019-0.01460.03770.01680.0486-10.78751.611761.1377
Refinement TLS groupSelection: ALL

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