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- PDB-8oxy: Transglutaminase 3 without calcium in complex with DH patient-der... -

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Basic information

Entry
Database: PDB / ID: 8oxy
TitleTransglutaminase 3 without calcium 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 / IGHV3-9 / IGLV6-57
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
PHOSPHATE ION / Protein-glutamine gamma-glutamyltransferase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 6, 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)124,74715
Polymers123,9693
Non-polymers77812
Water14,934829
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint8 kcal/mol
Surface area44400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.022, 92.275, 90.359
Angle α, β, γ (deg.)90.000, 92.310, 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
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 841 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bicine-Tris pH 8.5, 22% Ethylene glycol, 11% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 24, 2023
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2→60.43 Å / Num. obs: 88598 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.1 / Rrim(I) all: 0.151 / Net I/σ(I): 5.5
Reflection shellResolution: 2→2.04 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.92 / Num. unique obs: 4358 / CC1/2: 0.599 / Rpim(I) all: 0.812 / Rrim(I) all: 1.231

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimless0.7.9data scaling
PHASER2.8.3phasing
Coot0.9.8.7model building
DIALS3.12.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→58.765 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.205 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.155
Details: TLS refinement. Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2261 4529 5.114 %
Rwork0.1758 84032 -
all0.178 --
obs-88561 99.873 %
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: 33.537 Å2
Baniso -1Baniso -2Baniso -3
1--1.572 Å20 Å2-0.236 Å2
2--1.435 Å20 Å2
3---0.155 Å2
Refinement stepCycle: LAST / Resolution: 2→58.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8600 0 49 829 9478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128876
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168240
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.64212054
X-RAY DIFFRACTIONr_angle_other_deg0.5631.56619013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.89951124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.678549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.041101450
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.19210379
X-RAY DIFFRACTIONr_chiral_restr0.0750.21344
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210433
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022031
X-RAY DIFFRACTIONr_nbd_refined0.2050.21629
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.28125
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24383
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.25020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2790
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.110.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.225
X-RAY DIFFRACTIONr_nbd_other0.2160.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2310.220
X-RAY DIFFRACTIONr_mcbond_it2.8862.6724493
X-RAY DIFFRACTIONr_mcbond_other2.8862.6724493
X-RAY DIFFRACTIONr_mcangle_it4.3834.7775618
X-RAY DIFFRACTIONr_mcangle_other4.3834.7785619
X-RAY DIFFRACTIONr_scbond_it4.0833.0244383
X-RAY DIFFRACTIONr_scbond_other3.9583.024380
X-RAY DIFFRACTIONr_scangle_it6.1195.3356436
X-RAY DIFFRACTIONr_scangle_other6.1085.336431
X-RAY DIFFRACTIONr_lrange_it8.58830.68310140
X-RAY DIFFRACTIONr_lrange_other8.49129.8769922
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
2-2.0520.3053570.29562060.29665730.9230.92799.84790.298
2.052-2.1080.3013350.26359870.26563280.9370.94499.90520.265
2.108-2.1690.2923150.24558230.24761430.9430.95599.91860.245
2.169-2.2360.2572840.23457510.23560380.950.9699.95030.231
2.236-2.3090.2553330.21355130.21558510.9540.96799.91450.209
2.309-2.390.2552930.19753120.256100.9610.97499.91090.191
2.39-2.480.2282770.18151350.18454230.9680.97999.79720.173
2.48-2.5810.2082480.1750200.17252790.9690.98199.79160.162
2.581-2.6960.2332740.15647100.1649880.9660.98599.91980.145
2.696-2.8270.2432390.15345940.15748370.9640.98699.91730.144
2.827-2.9790.2071980.14543910.14745900.9730.98799.97820.137
2.979-3.160.2012110.14740890.1543020.9770.98899.95350.141
3.16-3.3770.2061880.15338790.15640720.9750.98899.87720.151
3.377-3.6470.2151960.16936110.17138130.9750.98799.84260.171
3.647-3.9930.2181610.17433300.17634960.9760.98599.8570.178
3.993-4.4620.1981890.14530080.14831970.9760.9891000.153
4.462-5.1470.1671400.13426600.13628080.9850.99199.71510.144
5.147-6.2920.241260.18722400.1923710.9830.98999.78910.195
6.292-8.8480.2531100.18417580.18818770.9710.98799.52050.193
8.848-58.7650.21550.1610140.16210730.9820.98399.62720.211
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)
10.5128-0.08270.24940.0302-0.09120.28590.02080.04520.0111-0.0018-0.01910.00870.00440.0484-0.00170.00470.01960.00450.1098-0.00210.071927.82620.059927.171
20.5207-0.0071-0.53650.045-0.08370.81110.0566-0.08410.0712-0.03620.06280.0120.05730.0399-0.11940.0515-0.0177-0.01440.1469-0.00760.03770.05053.304873.6421
30.3736-0.10990.20710.0329-0.06830.37110.11790.00720.0301-0.03280.008-0.00640.0649-0.0533-0.12590.0507-0.0077-0.00850.03720.03060.1113-10.4321.42760.8428
Refinement TLS groupSelection: ALL

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