8ZXE | pdb_00008zxe

TLR7 in complex with mGrArA (SS)

PDB DOI: https://doi.org/10.2210/pdb8ZXE/pdb
NAKB: 8ZXE
EM Map EMD-60541: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Macaca mulatta, synthetic construct
Expression System: Drosophila melanogaster
Mutation(s): Yes

Deposited: 2024-06-14 Released: 2025-12-17
Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZXE

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

Literature

TLR7 in complex with mGrArA (SS)

Alharbi, A., Sapkota, S., Zhang, Z., Jin, R.

To be published.

Macromolecule Content

Total Structure Weight: 200.07 kDa
Atom Count: 13,020
Modeled Residue Count: 1,532
Deposited Residue Count: 1,652
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 7	A, B	823	Macaca mulatta	Mutation(s): 10 Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta) Explore B3Y653 Go to UniProtKB: B3Y653
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3Y653
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (5'-R((OMG)P(SRA)P*(SRA))-3')	C [auth Q], D [auth R]	3	synthetic construct
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], G [auth E], L [auth J], N [auth L]	3		N-Glycosylation	Interactions Focus chain E [auth C] Focus chain G [auth E] Focus chain L [auth J] Focus chain N [auth L] Interactions & Density Focus chain E [auth C] Focus chain G [auth E] Focus chain L [auth J] Focus chain N [auth L]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	F [auth D], M [auth K]	4		N-Glycosylation	Interactions Focus chain F [auth D] Focus chain M [auth K] Interactions & Density Focus chain F [auth D] Focus chain M [auth K]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F], I [auth G], J [auth H], K [auth I], O [auth M], H [auth F], I [auth G], J [auth H], K [auth I], O [auth M], P [auth N], Q [auth O], R [auth P]	2		N-Glycosylation	Interactions Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth H] Focus chain K [auth I] Focus chain O [auth M] Focus chain P [auth N] Focus chain Q [auth O] Focus chain R [auth P] Interactions & Density Focus chain H [auth F] Focus chain I [auth G] Focus chain J [auth H] Focus chain K [auth I] Focus chain O [auth M] Focus chain P [auth N] Focus chain Q [auth O] Focus chain R [auth P]
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 S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	S [auth A] T [auth A] U [auth A] V [auth B] W [auth B] S [auth A], T [auth A], U [auth A], V [auth B], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.