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- EMDB-49945: Structure of Native Bovine Rhodopsin in Complex with Mb7 in the D... -

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Basic information

Entry
Database: EMDB / ID: EMD-49945
TitleStructure of Native Bovine Rhodopsin in Complex with Mb7 in the Dark State
Map data
Sample
  • Complex: Bovin Rhodopsin in complex with Megabody 7 in dark state
    • Protein or peptide: Megabody 7
  • Protein or peptide: Rhodopsin
  • Ligand: RETINAL
Keywordsnanoboy / rhodopsin / native purification / dark state / retinal / ISOMERASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / sperm head plasma membrane / opsin binding / The canonical retinoid cycle in rods (twilight vision) / absorption of visible light / G protein-coupled opsin signaling pathway / 11-cis retinal binding / podosome assembly ...Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / sperm head plasma membrane / opsin binding / The canonical retinoid cycle in rods (twilight vision) / absorption of visible light / G protein-coupled opsin signaling pathway / 11-cis retinal binding / podosome assembly / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / cellular response to light stimulus / rod photoreceptor outer segment / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / response to light intensity / photoreceptor cell maintenance / arrestin family protein binding / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction, visible light / response to light stimulus / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / visual perception / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / cell-cell junction / photoreceptor disc membrane / sperm midpiece / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHuang W / Salom-Arbona D / Suder D / Taylor DJ / Palczewski K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RM1 GM142002 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural analysis of rhodopsin states in megabody complexes.
Authors: David Salom / Diana S Suder / Wei Huang / Arum Wu / Els Pardon / Jan Steyaert / Philip D Kiser / Derek J Taylor / Shane Gonen / Krzysztof Palczewski /
Abstract: Rhodopsin, the most intensively studied G protein-coupled receptor (GPCR), is activated by light-induced isomerization of its chromophore 11--retinal. This study employed cryogenic electron ...Rhodopsin, the most intensively studied G protein-coupled receptor (GPCR), is activated by light-induced isomerization of its chromophore 11--retinal. This study employed cryogenic electron microscopy (cryo-EM) to investigate rhodopsin structure using a megabody (Mb7) as a negative allosteric modulator. Three distinct cryo-EM structures were solved: ground-state rhodopsin, photoactivated rhodopsin, and apo-rhodopsin, all in complex with Mb7. Photoactivated rhodopsin and apo-rhodopsin, both in complex with Mb7, maintain a conformation remarkably similar to ground-state rhodopsin rather than adopting a Meta-II-like conformation. Structural elements, including the conserved residues of the NPxxY motif and the ionic lock, remain in positions corresponding to inactive rhodopsin. The megabody forms extensive interactions with rhodopsin's extracellular loop 2, N terminus, and glycans. The findings demonstrate that Mb7 stabilizes photoactivated rhodopsin in a Meta-I-like conformation, preventing progression to the active Meta-II state through specific immobilization of the extracellular domain. This work establishes a foundation for cryo-EM-guided discovery of ligands modulating rhodopsin.
History
DepositionMar 29, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49945.png

Downloads & links

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Map

FileDownload / File: emd_49945.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 368 pix.
= 393.76 Å		1.07 Å/pix.
x 368 pix.
= 393.76 Å		1.07 Å/pix.
x 368 pix.
= 393.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.42606565 - 0.90696967
Average (Standard dev.)-0.00008635197 (±0.014549784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 393.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49945_half_map_1.map
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Half map: #1

Fileemd_49945_half_map_2.map
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Sample components

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Entire : Bovin Rhodopsin in complex with Megabody 7 in dark state

EntireName: Bovin Rhodopsin in complex with Megabody 7 in dark state
Components
  • Complex: Bovin Rhodopsin in complex with Megabody 7 in dark state
    • Protein or peptide: Megabody 7
  • Protein or peptide: Rhodopsin
  • Ligand: RETINAL

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Supramolecule #1: Bovin Rhodopsin in complex with Megabody 7 in dark state

SupramoleculeName: Bovin Rhodopsin in complex with Megabody 7 in dark state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Megabody 7

MacromoleculeName: Megabody 7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.035657 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VQLVESGGGL V(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)SLRLSCAA SGFTFS RYV MNWVRQAPGK GLEWVSGISR DGSYTDYADS VKGRFTISRD NAKDTLYLQM NSLKPEDTAV YYCSKYNSVV TTPPGQG TQ VTVS

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Macromolecule #2: Rhodopsin

MacromoleculeName: Rhodopsin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 36.466734 KDa
SequenceString: (ACE)MNGTEGPNF YVPFSNKTGV VRSPFEAPQY YLAEPWQFSM LAAYMFLLIM LGFPINFLTL YVTVQHKKLR TPLNYI LLN LAVADLFMVF GGFTTTLYTS LHGYFVFGPT GCNLEGFFAT LGGEIALWSL VVLAIERYVV VCKPMSNFRF GENHAIM GV AFTWVMALAC ...String:
(ACE)MNGTEGPNF YVPFSNKTGV VRSPFEAPQY YLAEPWQFSM LAAYMFLLIM LGFPINFLTL YVTVQHKKLR TPLNYI LLN LAVADLFMVF GGFTTTLYTS LHGYFVFGPT GCNLEGFFAT LGGEIALWSL VVLAIERYVV VCKPMSNFRF GENHAIM GV AFTWVMALAC AAPPLVGWSR YIPEGMQCSC GIDYYTPHEE TNNESFVIYM FVVHFIIPLI VIFFCYGQLV FTVKEAAA Q QQESATTQKA EKEVTRMVII MVIAFLICWL PYAGVAFYIF THQGSDFGPI FMTIPAFFAK TSAVYNPVIY IMMNKQFRN CMVTTLC

UniProtKB: Rhodopsin

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Macromolecule #5: RETINAL

MacromoleculeName: RETINAL / type: ligand / ID: 5 / Number of copies: 2 / Formula: RET
Molecular weightTheoretical: 284.436 Da
Chemical component information

ChemComp-RET:
RETINAL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 8.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 0.01 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: C1 / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 112705
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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