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

ID or keywords:

Entry

Database: PDB / ID: 8rmy

Title

Transglutaminase 3 in complex with inhibitor Z-don and DH patient-derived Fab DH63-A02

Components

(Antibody Fab fragment ...) x 2
P6S-ONL-VAL-PRO-MLL
Protein-glutamine gamma-glutamyltransferase E

Keywords

TRANSFERASE / transglutaminase / tg3 / tgm3 / inhibitor / antibody / calcium

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 / keratinization / acyltransferase activity / catalytic activity / keratinocyte differentiation / protein modification process ...
Similarity search - Function

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Heggelund, J.E. / Sollid, L.M.

Funding support

Norway, 3items

Organization	Grant number	Country
Other government	south eastern norway regional health authority (project 2020027)	Norway
Other private	Stiftelsen KG Jebsen (project SKGJ-MED-017)	Norway
Other government	University of Oslo World-leading research program on human immunology (WL-IMMUNOLOGY).	Norway

Citation

Journal: 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

Deposition	Jan 9, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 12, 2025	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2025	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8rmy.cif.gz	368.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8rmy.ent.gz	288.2 KB	Display	PDB format
PDBx/mmJSON format	8rmy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rm/8rmy ftp://data.pdbj.org/pub/pdb/validation_reports/rm/8rmy	HTTPS FTP

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Related structure data

Related structure data	8rmxC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15151/ESRF-ES-1022934233 / Data set type: other data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (13) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (13)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

F: Antibody Fab fragment light chain IGKV4-1

C: Antibody Fab fragment light chain IGKV4-1

A: Protein-glutamine gamma-glutamyltransferase E

D: Protein-glutamine gamma-glutamyltransferase E

E: Antibody Fab fragment heavy chain IGHV2-5

B: Antibody Fab fragment heavy chain IGHV2-5

J: P6S-ONL-VAL-PRO-MLL

K: P6S-ONL-VAL-PRO-MLL

hetero molecules

200 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

F: Antibody Fab fragment light chain IGKV4-1

D: Protein-glutamine gamma-glutamyltransferase E

E: Antibody Fab fragment heavy chain IGHV2-5

K: P6S-ONL-VAL-PRO-MLL

hetero molecules

defined by author
100 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Antibody Fab fragment light chain IGKV4-1

A: Protein-glutamine gamma-glutamyltransferase E

B: Antibody Fab fragment heavy chain IGHV2-5

J: P6S-ONL-VAL-PRO-MLL

hetero molecules

defined by author
100 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.184, 260.191, 139.024
Angle α, β, γ (deg.)	90, 95.1, 90
Int Tables number	5
Space group name H-M	I121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	F
2	1	C
3	2	A
4	2	D
5	3	E
6	3	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ILE	ILE	ARG	ARG	F	A	2 - 216	2 - 216
2	1	1	ILE	ILE	ARG	ARG	C	B	2 - 216	2 - 216
3	2	2	ALA	ALA	LYS	LYS	A	C	2 - 459	2 - 459
4	2	2	ALA	ALA	LYS	LYS	D	D	2 - 459	2 - 459
5	3	3	ILE	ILE	VAL	VAL	E	E	2 - 216	2 - 216
6	3	3	ILE	ILE	VAL	VAL	B	F	2 - 216	2 - 216

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

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Antibody , 2 types, 4 molecules FCEB

#1: 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)
#3: Antibody	Antibody Fab fragment heavy chain IGHV2-5 Mass: 23642.766 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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Protein / Protein/peptide , 2 types, 4 molecules ADJK

#2: 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 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q08188, protein-glutamine gamma-glutamyltransferase
#4: Protein/peptide	P6S-ONL-VAL-PRO-MLL Mass: 602.717 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#2: 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 / Cell line (production host): Sf9 / Production host:

Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08188, protein-glutamine gamma-glutamyltransferase

#4: Protein/peptide

P6S-ONL-VAL-PRO-MLL

Mass: 602.717 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 57 molecules

#5: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅O₇
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.33 Å³/Da / Density % sol: 71.56 %
Crystal grow	Temperature: 293 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8856 Å / Relative weight: 1
Reflection	Resolution: 2.9→69.2 Å / Num. obs: 73407 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC_1/2: 0.983 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.09 / R_rim(I) all: 0.153 / Χ²: 0.99 / Net I/σ(I): 5.9
Reflection shell	Resolution: 2.9→2.96 Å / Redundancy: 5.3 % / R_merge(I) obs: 1.857 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4520 / CC_1/2: 0.185 / R_pim(I) all: 1.41 / R_rim(I) all: 2.345 / Χ²: 0.93 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
DIALS	3.12.1	data reduction
Aimless	0.7.13	data scaling
PHASER	2.8.3	phasing
Coot	0.9.8.92	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→69.2 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.945 / SU B: 21.279 / SU ML: 0.348 / Cross valid method: FREE R-VALUE / ESU R: 0.573 / ESU R Free: 0.32
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2425	3722	5.078 %
R_work	0.1947	69572	-
all	0.197	-	-
obs	-	73294	99.678 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 111.633 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.018 Å²	-0 Å²	2.423 Å²
2-	-	-4.602 Å²	-0 Å²
3-	-	-	4.086 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→69.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13713	0	131	46	13890

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	14205
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	13030
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.037	0.1	115249
X-RAY DIFFRACTION	r_angle_refined_deg	1.012	1.789	19263
X-RAY DIFFRACTION	r_angle_other_deg	0.349	1.746	30027
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.733	5	1765
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.043	5	84
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.74	10	2265
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.176	10	610
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	2131
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	16918
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3354
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	2479
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.231	0.2	11948
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	6856
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	7514
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	265
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.017	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.169	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.204	0.2	45
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.191	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	15.888	11.248	7097
X-RAY DIFFRACTION	r_mcbond_other	15.877	11.249	7094
X-RAY DIFFRACTION	r_mcangle_it	21.249	20.227	8841
X-RAY DIFFRACTION	r_mcangle_other	21.251	20.228	8842
X-RAY DIFFRACTION	r_scbond_it	15.231	11.332	7108
X-RAY DIFFRACTION	r_scbond_other	15.217	11.328	7105
X-RAY DIFFRACTION	r_scangle_it	21.04	20.773	10422
X-RAY DIFFRACTION	r_scangle_other	21.022	20.766	10417
X-RAY DIFFRACTION	r_lrange_it	23.648	209.177	144857
X-RAY DIFFRACTION	r_lrange_other	23.649	209.181	144853
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.17	0.05	6043
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.083	0.05	14902
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.173	0.05	5270

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	F	X-RAY DIFFRACTION	Local ncs	0.16984	0.05007
1	2	C	X-RAY DIFFRACTION	Local ncs	0.16984	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08325	0.05009
2	4	D	X-RAY DIFFRACTION	Local ncs	0.08325	0.05009
3	5	E	X-RAY DIFFRACTION	Local ncs	0.17333	0.05007
3	6	B	X-RAY DIFFRACTION	Local ncs	0.17333	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.9-2.975	0.393	275	0.382	5095	0.383	5449	0.883	0.889	98.5502	0.396
2.975-3.056	0.376	264	0.376	4948	0.376	5243	0.889	0.891	99.4087	0.388
3.056-3.144	0.397	275	0.356	4851	0.358	5150	0.888	0.908	99.534	0.365
3.144-3.241	0.362	269	0.339	4712	0.34	4996	0.906	0.925	99.6998	0.35
3.241-3.347	0.341	263	0.312	4562	0.314	4834	0.912	0.935	99.8138	0.319
3.347-3.464	0.341	243	0.282	4440	0.285	4688	0.92	0.947	99.8933	0.279
3.464-3.595	0.338	196	0.25	4289	0.254	4487	0.925	0.96	99.9554	0.246
3.595-3.741	0.31	207	0.232	4160	0.235	4372	0.937	0.968	99.8856	0.23
3.741-3.907	0.29	214	0.211	3957	0.215	4178	0.946	0.975	99.8325	0.206
3.907-4.097	0.255	197	0.187	3796	0.19	3996	0.959	0.979	99.9249	0.183
4.097-4.318	0.208	178	0.166	3581	0.168	3763	0.971	0.984	99.8937	0.166
4.318-4.578	0.194	170	0.147	3397	0.149	3582	0.974	0.987	99.5812	0.15
4.578-4.893	0.193	183	0.123	3210	0.126	3395	0.976	0.991	99.9411	0.124
4.893-5.283	0.189	166	0.133	2990	0.136	3158	0.979	0.989	99.9367	0.136
5.283-5.784	0.238	145	0.149	2746	0.153	2892	0.968	0.987	99.9654	0.152
5.784-6.461	0.196	134	0.155	2477	0.157	2615	0.974	0.986	99.847	0.159
6.461-7.449	0.284	118	0.167	2210	0.173	2330	0.962	0.984	99.9142	0.174
7.449-9.097	0.159	106	0.143	1859	0.144	1973	0.985	0.987	99.5945	0.155
9.097-12.756	0.144	78	0.137	1460	0.138	1541	0.987	0.989	99.8053	0.155
12.756-69.2	0.244	41	0.27	832	0.269	883	0.967	0.898	98.8675	1.057

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