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- PDB-8rmx: Transglutaminase 3 in complex with DH patient-derived Fab DH63-A02 -

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Basic information

Entry
Database: PDB / ID: 8rmx
TitleTransglutaminase 3 in complex with DH patient-derived Fab DH63-A02
Components
  • (Antibody Fab fragment ...) x 2
  • Protein-glutamine gamma-glutamyltransferase E
KeywordsTRANSFERASE / Transglutaminase / autoantibody / 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
PHOSPHATE ION / Protein-glutamine gamma-glutamyltransferase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsHeggelund, J.E. / Sollid, L.M.
Funding support Norway, 3items
OrganizationGrant numberCountry
Other privateSKGJ-MED-017 Norway
Other government2020027 Norway
Other governmentWL-IMMUNOLOGY Norway
CitationJournal: Nat Commun / Year: 2025
Title: Enzyme-activating B-cell receptors boost antigen presentation to pathogenic T cells in gluten-sensitive autoimmunity.
Authors: Iversen, R. / Heggelund, J.E. / Das, S. / Hoydahl, L.S. / Sollid, L.M.
History
DepositionJan 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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
E: Antibody Fab fragment heavy chain IGHV2-5
F: Antibody Fab fragment light chain IGKV4-1
D: Protein-glutamine gamma-glutamyltransferase E
B: Antibody Fab fragment heavy chain IGHV2-5
C: Antibody Fab fragment light chain IGKV4-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,10120
Polymers198,1016
Non-polymers1,00014
Water1,29772
1
A: Protein-glutamine gamma-glutamyltransferase E
B: Antibody Fab fragment heavy chain IGHV2-5
C: Antibody Fab fragment light chain IGKV4-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4569
Polymers99,0513
Non-polymers4056
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Antibody Fab fragment heavy chain IGHV2-5
F: Antibody Fab fragment light chain IGKV4-1
D: Protein-glutamine gamma-glutamyltransferase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,64611
Polymers99,0513
Non-polymers5958
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.031, 264.004, 148.7
Angle α, β, γ (deg.)90, 106.289, 90
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
32E
42B
53F
63C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALALYSLYSAA2 - 4612 - 461
211ALAALALYSLYSDD2 - 4612 - 461
322GLNGLNGLUGLUEB1 - 2171 - 217
422GLNGLNGLUGLUBE1 - 2171 - 217
533ASPASPGLYGLYFC1 - 2171 - 217
633ASPASPGLYGLYCF1 - 2171 - 217

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Protein-glutamine gamma-glutamyltransferase E / Transglutaminase E / TG(E) / TGE / TGase E / Transglutaminase-3 / TGase-3


Mass: 51369.211 Da / Num. of mol.: 2
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, protein-glutamine gamma-glutamyltransferase

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Antibody , 2 types, 4 molecules EBFC

#2: Antibody Antibody Fab fragment heavy chain IGHV2-5


Mass: 23539.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Antibody Fab fragment light chain IGKV4-1


Mass: 24141.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 86 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.15 M phosphate-citrate pH 5.0, 40% ethanol and 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.8→132.002 Å / Num. obs: 83425 / % possible obs: 99.3 % / Redundancy: 7.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.108 / Rrim(I) all: 0.207 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
14.57-1326.30.0516230.9870.0320.06
2.8-2.867.12.83140640.3951.7473.336

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
DIALSdata reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
Coot0.9.8.92model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.803→132 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.94 / SU B: 21.004 / SU ML: 0.342 / Cross valid method: FREE R-VALUE / ESU R: 0.448 / ESU R Free: 0.299
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2503 4243 5.086 %
Rwork0.205 79174 -
all0.207 --
obs-83417 99.314 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 107.009 Å2
Baniso -1Baniso -2Baniso -3
1--4.769 Å20 Å23.479 Å2
2---7.571 Å20 Å2
3---8.803 Å2
Refinement stepCycle: LAST / Resolution: 2.803→132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13743 0 46 72 13861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01214141
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612953
X-RAY DIFFRACTIONr_ext_dist_refined_b0.0550.1123363
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.78719190
X-RAY DIFFRACTIONr_angle_other_deg0.3891.74729853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.01951768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.746572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.816102273
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.66110613
X-RAY DIFFRACTIONr_chiral_restr0.060.22126
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023340
X-RAY DIFFRACTIONr_nbd_refined0.2070.22341
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.211883
X-RAY DIFFRACTIONr_nbtor_refined0.1830.26905
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.27475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0840.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1850.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.212
X-RAY DIFFRACTIONr_nbd_other0.2880.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3240.29
X-RAY DIFFRACTIONr_mcbond_it14.11310.7067106
X-RAY DIFFRACTIONr_mcbond_other14.10810.7077106
X-RAY DIFFRACTIONr_mcangle_it18.08119.2358856
X-RAY DIFFRACTIONr_mcangle_other18.0819.2368857
X-RAY DIFFRACTIONr_scbond_it15.0410.9157035
X-RAY DIFFRACTIONr_scbond_other14.70810.897002
X-RAY DIFFRACTIONr_scangle_it19.37519.94410334
X-RAY DIFFRACTIONr_scangle_other19.09919.90810287
X-RAY DIFFRACTIONr_lrange_it21.858205.266151226
X-RAY DIFFRACTIONr_lrange_other21.858205.252151212
X-RAY DIFFRACTIONr_ncsr_local_group_10.0830.0515201
X-RAY DIFFRACTIONr_ncsr_local_group_20.1360.055654
X-RAY DIFFRACTIONr_ncsr_local_group_30.1190.056542
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.082730.05009
12DX-RAY DIFFRACTIONLocal ncs0.082730.05009
23EX-RAY DIFFRACTIONLocal ncs0.135810.05008
24BX-RAY DIFFRACTIONLocal ncs0.135810.05008
35FX-RAY DIFFRACTIONLocal ncs0.119230.05008
36CX-RAY DIFFRACTIONLocal ncs0.119230.05008
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
2.803-2.8760.4392480.41653510.41761680.8040.82590.7750.428
2.876-2.9550.4673080.40657410.40960490.7980.8261000.415
2.955-3.0410.3932980.38656060.38759040.8580.8571000.393
3.041-3.1340.3833080.36253770.36356850.8580.8831000.366
3.134-3.2370.3572690.32952840.3355530.9060.9141000.326
3.237-3.350.3312770.29150470.29353240.9210.9361000.285
3.35-3.4770.2862470.24449350.24651820.9430.9581000.236
3.477-3.6190.2942650.2347210.23349860.9390.9651000.222
3.619-3.7790.2482280.20245230.20447510.9610.9741000.196
3.779-3.9640.2422450.18242980.18545430.9640.9791000.178
3.964-4.1780.2162230.15841280.1643510.9680.9841000.156
4.178-4.4310.2122200.13739010.14141210.9720.9881000.14
4.431-4.7370.2082030.14136560.14538590.9730.9871000.148
4.737-5.1160.221920.14633950.14935870.9750.9881000.155
5.116-5.6030.2331940.15231270.15633210.9740.9891000.162
5.603-6.2630.2281400.17128550.17329950.9690.9841000.183
6.263-7.2290.2111120.16925430.17126550.9740.9841000.184
7.229-8.8470.1961180.15121080.15322260.9750.9871000.17
8.847-12.4840.147950.14916550.14917500.9880.9891000.167
12.484-1320.241530.2719230.279830.9540.92199.28790.777

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