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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 / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / 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 / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / 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 / response to light stimulus / phototransduction, visible light / phototransduction / G-protein alpha-subunit binding / photoreceptor outer segment / visual perception / guanyl-nucleotide exchange factor activity / sperm midpiece / microtubule cytoskeleton organization / cell-cell junction / photoreceptor disc membrane / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / identical protein binding / membrane / 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.USA / Year: 2026
Title: Structure of Native Bovine Rhodopsin in Complex with Mb7 in the Dark State.
Authors: Huang W / Salom D / Suder DS / Taylor DJ / Palczewski K
History
DepositionMar 29, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 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

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49945_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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