8Y02 | pdb_00008y02

Cryo-EM structure of Short-wave-sensitive opsin 1

PDB DOI: https://doi.org/10.2210/pdb8Y02/pdb
EM Map EMD-38801: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens, Bos taurus
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes MemProtMD

Deposited: 2024-01-21 Released: 2025-06-11
Deposition Author(s): Peng, Q., Jiang, H.H., Cheng, X.Y., Li, J., Zhang, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.61 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Cryo-electron microscopy structures of human cone visual pigments

Peng, Q., Li, J., Jiang, H., Cheng, X., Nag, P., Kleinau, G., Lamb, T.D., Busche, L., Lu, Q., Zhou, S., Liu, Y., Zhang, Y., Lv, S., Wan, S., Yang, T., Chen, Y., Zhang, W., Nan, W., Fu, Y., Che, T., Li, Y., Liao, H., Duan, J., Schapiro, I., Scheerer, P., Zhang, J.

(2026) Science

DOI: https://doi.org/10.1126/science.adz8141

Macromolecule Content

Total Structure Weight: 153.84 kDa
Atom Count: 8,666
Modeled Residue Count: 1,125
Deposited Residue Count: 1,380
Unique protein chains: 5

Macromolecules

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| 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): 5 Gene Names: GNAI1 EC: 3.6.5 Membrane Entity: Yes
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	340	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	71	Bos taurus	Mutation(s): 0 Gene Names: GNG2 Membrane Entity: Yes
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212 Go to UniProtKB: P63212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63212
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-wave-sensitive opsin 1	D [auth R]	348	Homo sapiens	Mutation(s): 1 Gene Names: OPN1SW, BCP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P03999 (Homo sapiens) Explore P03999 Go to UniProtKB: P03999
PHAROS: P03999 GTEx: ENSG00000128617
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03999
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv Recombinant Human Monoclonal Antibody (scFv16)	E [auth S]	267	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET (Subject of Investigation/LOI) Query on RET Download:Ideal Coordinates CCD File SDF format, chain F [auth R] MOL2 format, chain F [auth R] mmCIF format, chain F [auth R]	F [auth R]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.61 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-06-11
Type: Initial release
Version 1.1: 2025-07-23
Changes: Data collection
Version 2.0: 2026-02-18
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2026-06-24
Changes: Data collection, Database references