8REW | pdb_00008rew

CryoEM structure of human GARP-lTGFbeta1 in complex with a Fab fragment derived from an activating antibody.

PDB DOI: https://doi.org/10.2210/pdb8REW/pdb
EM Map EMD-19110: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Lama glama
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-12-12 Released: 2025-03-26
Deposition Author(s): Felix, J., Lambert, F., Marien, L., van der Woning, B., Savvides, S.N., Lucas, S.
Funding Organization(s): Other private, Other government, Fonds National de la Recherche Scientifique (FNRS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

TGF-beta1 activating antibodies as novel immunotherapeutics for graft-versus-host disease.

Lambert, F., Felix, J., Wautier, S., Gaignage, M., Dupre, E., Marien, L., Lesage, M., van der Woning, B., Coulie, P.G., Savvides, S.N., Lucas, S.

To be published.

Macromolecule Content

Total Structure Weight: 356.57 kDa
Atom Count: 12,428
Modelled Residue Count: 1,609
Deposited Residue Count: 3,204
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming growth factor beta-1	A, B, C, D	390	Homo sapiens	Mutation(s): 0 Gene Names: TGFB1, TGFB
UniProt & NIH Common Fund Data Resources
Find proteins for P01137 (Homo sapiens) Explore P01137 Go to UniProtKB: P01137
PHAROS: P01137 GTEx: ENSG00000105329
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01137
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C	Go to GlyGen: P01137-1
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming growth factor beta activator LRRC32	E	674	Homo sapiens	Mutation(s): 0 Gene Names: LRRC32, D11S833E
UniProt & NIH Common Fund Data Resources
Find proteins for Q14392 (Homo sapiens) Explore Q14392 Go to UniProtKB: Q14392
PHAROS: Q14392 GTEx: ENSG00000137507
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14392
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain E	Go to GlyGen: Q14392-1
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
hFab LHT-22, Light Chain	F, I	238	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
hFab LHT-22, Heavy Chain	G, H	247	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, K	4		N-Glycosylation	Interactions Focus chain J Focus chain K Interactions & Density Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	2		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain P [auth E] SDF format, chain Q [auth E] MOL2 format, chain M [auth A] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] mmCIF format, chain M [auth A] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth E]	M [auth A], N [auth C], O [auth C], P [auth E], Q [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth E] Interactions & Density Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.19.2-4158

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		Fondation contre le Cancer / 2020-079
Other government	Belgium	ARC / 19/24-098
Fonds National de la Recherche Scientifique (FNRS)	Belgium	PDR / T.0145.21
Fonds National de la Recherche Scientifique (FNRS)	Belgium	WELBIO / CR2019A-02R
Other private		Salus Sanguinis