9LR2 | pdb_00009lr2

Cryo-EM structure of the JN241-9-bound APLNR dimer-Gi complex

PDB DOI: https://doi.org/10.2210/pdb9LR2/pdb
EM Map EMD-63313: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Spodoptera frugiperda, Trichoplusia ni
Mutation(s): Yes

Deposited: 2025-01-28 Released: 2026-02-04
Deposition Author(s): Ji, S., Wang, W., Yang, Y., Shen, Q., Zhang, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of the JN241-9-bound APLNR dimer-Gi complex

Ji, S., Wang, W., Yang, Y., Shen, Q., Zhang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 232.8 kDa
Atom Count: 13,115
Modeled Residue Count: 1,671
Deposited Residue Count: 2,039
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 4 Gene Names: GNAI1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Apelin receptor	B [auth R], C [auth Q]	380	Homo sapiens	Mutation(s): 0 Gene Names: APLNR, AGTRL1, APJ
UniProt & NIH Common Fund Data Resources
Find proteins for P35414 (Homo sapiens) Explore P35414 Go to UniProtKB: P35414
PHAROS: P35414 GTEx: ENSG00000134817
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35414
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
JN241-9	D, E [auth C]	130	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	F [auth B]	345	Homo sapiens	Mutation(s): 0 Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873 Go to UniProtKB: P62873
PHAROS: P62873 GTEx: ENSG00000078369
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62873
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	70	Homo sapiens	Mutation(s): 0 Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768 Go to UniProtKB: P59768
PHAROS: P59768 GTEx: ENSG00000186469
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
single Fab chain(scFv16)	H [auth S]	250	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCF Query on PCF Download Ideal Coordinates CCD File SDF format, chain I [auth R] SDF format, chain Q MOL2 format, chain I [auth R] MOL2 format, chain Q mmCIF format, chain I [auth R] mmCIF format, chain Q	I [auth R], Q	1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE C₄₀ H₈₀ N O₈ P KILNVBDSWZSGLL-KXQOOQHDSA-N		Interactions Focus chain I [auth R] Focus chain Q Interactions & Density Focus chain I [auth R] Focus chain Q
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain J [auth R] SDF format, chain K [auth R] SDF format, chain L [auth R] SDF format, chain M [auth R] SDF format, chain N [auth R] SDF format, chain O [auth R] SDF format, chain P [auth R] SDF format, chain R [auth Q] SDF format, chain S [auth Q] SDF format, chain T [auth Q] SDF format, chain U [auth Q] SDF format, chain V [auth Q] SDF format, chain W [auth Q] SDF format, chain X [auth Q] MOL2 format, chain J [auth R] MOL2 format, chain K [auth R] MOL2 format, chain L [auth R] MOL2 format, chain M [auth R] MOL2 format, chain N [auth R] MOL2 format, chain O [auth R] MOL2 format, chain P [auth R] MOL2 format, chain R [auth Q] MOL2 format, chain S [auth Q] MOL2 format, chain T [auth Q] MOL2 format, chain U [auth Q] MOL2 format, chain V [auth Q] MOL2 format, chain W [auth Q] MOL2 format, chain X [auth Q] mmCIF format, chain J [auth R] mmCIF format, chain K [auth R] mmCIF format, chain L [auth R] mmCIF format, chain M [auth R] mmCIF format, chain N [auth R] mmCIF format, chain O [auth R] mmCIF format, chain P [auth R] mmCIF format, chain R [auth Q] mmCIF format, chain S [auth Q] mmCIF format, chain T [auth Q] mmCIF format, chain U [auth Q] mmCIF format, chain V [auth Q] mmCIF format, chain W [auth Q] mmCIF format, chain X [auth Q]	J [auth R] K [auth R] L [auth R] M [auth R] N [auth R] J [auth R], K [auth R], L [auth R], M [auth R], N [auth R], O [auth R], P [auth R], R [auth Q], S [auth Q], T [auth Q], U [auth Q], V [auth Q], W [auth Q], X [auth Q]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain J [auth R] Focus chain K [auth R] Focus chain L [auth R] Focus chain M [auth R] Focus chain N [auth R] Focus chain O [auth R] Focus chain P [auth R] Focus chain R [auth Q] Focus chain S [auth Q] Focus chain T [auth Q] Focus chain U [auth Q] Focus chain V [auth Q] Focus chain W [auth Q] Focus chain X [auth Q] Interactions & Density Focus chain J [auth R] Focus chain K [auth R] Focus chain L [auth R] Focus chain M [auth R] Focus chain N [auth R] Focus chain O [auth R] Focus chain P [auth R] Focus chain R [auth Q] Focus chain S [auth Q] Focus chain T [auth Q] Focus chain U [auth Q] Focus chain V [auth Q] Focus chain W [auth Q] Focus chain X [auth Q]