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- EMDB-14991: Human PRPH2-ROM1 hetero-dimer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-14991
TitleHuman PRPH2-ROM1 hetero-dimer
Map dataNon-sharpened map
Sample
  • Complex: Human PRPH2-ROM1 hetero-dimer
    • Complex: Human PRPH2-ROM1 hetero-dimer
      • Protein or peptide: Peripherin-2
      • Protein or peptide: Rod outer segment membrane protein 1
    • Complex: Nanobody
      • Protein or peptide: Nanobody
Function / homology
Function and homology information


protein localization to photoreceptor outer segment / camera-type eye photoreceptor cell differentiation / response to low light intensity stimulus / photoreceptor cell outer segment organization / detection of light stimulus involved in visual perception / retina vasculature development in camera-type eye / protein heterooligomerization / photoreceptor outer segment membrane / protein maturation / photoreceptor outer segment ...protein localization to photoreceptor outer segment / camera-type eye photoreceptor cell differentiation / response to low light intensity stimulus / photoreceptor cell outer segment organization / detection of light stimulus involved in visual perception / retina vasculature development in camera-type eye / protein heterooligomerization / photoreceptor outer segment membrane / protein maturation / photoreceptor outer segment / photoreceptor inner segment / visual perception / protein localization to plasma membrane / protein homooligomerization / retina development in camera-type eye / regulation of gene expression / cell adhesion / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Peripherin/rom-1 / Peripherin/rom-1, conserved site / Peripherin, extracellular domain / Peripherin / rom-1 signature. / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family
Similarity search - Domain/homology
Peripherin-2 / Rod outer segment membrane protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama (mammal)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsEl Mazouni D / Gros P
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)BC.000795.1European Union
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-EM structures of peripherin-2 and ROM1 suggest multiple roles in photoreceptor membrane morphogenesis.
Authors: Dounia El Mazouni / Piet Gros /
Abstract: Mammalian peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) are retina-specific tetraspanins that partake in the constant renewal of stacked membrane discs of photoreceptor cells ...Mammalian peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) are retina-specific tetraspanins that partake in the constant renewal of stacked membrane discs of photoreceptor cells that enable vision. Here, we present single-particle cryo-electron microscopy structures of solubilized PRPH2-ROM1 heterodimers and higher-order oligomers. High-risk PRPH2 and ROM1 mutations causing blindness map to the protein-dimer interface. Cysteine bridges connect dimers forming positive-curved oligomers, whereas negative-curved oligomers were observed occasionally. Hexamers and octamers exhibit a secondary micelle that envelopes four carboxyl-terminal helices, supporting a potential role in membrane remodeling. Together, the data indicate multiple structures for PRPH2-ROM1 in creating and maintaining compartmentalization of photoreceptor cells.
History
DepositionMay 17, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14991.png

Downloads & links

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Map

FileDownload / File: emd_14991.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 432 pix.
= 283.392 Å		0.66 Å/pix.
x 432 pix.
= 283.392 Å		0.66 Å/pix.
x 432 pix.
= 283.392 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.076656096 - 0.22285856
Average (Standard dev.)9.954237e-06 (±0.00746569)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 283.392 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_14991_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14991_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14991_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human PRPH2-ROM1 hetero-dimer

EntireName: Human PRPH2-ROM1 hetero-dimer
Components
  • Complex: Human PRPH2-ROM1 hetero-dimer
    • Complex: Human PRPH2-ROM1 hetero-dimer
      • Protein or peptide: Peripherin-2
      • Protein or peptide: Rod outer segment membrane protein 1
    • Complex: Nanobody
      • Protein or peptide: Nanobody

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Supramolecule #1: Human PRPH2-ROM1 hetero-dimer

SupramoleculeName: Human PRPH2-ROM1 hetero-dimer / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 76 kDa/nm

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Supramolecule #2: Human PRPH2-ROM1 hetero-dimer

SupramoleculeName: Human PRPH2-ROM1 hetero-dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: Nanobody

SupramoleculeName: Nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Lama (mammal)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Peripherin-2

MacromoleculeName: Peripherin-2 / type: protein_or_peptide / ID: 1
Details: HHHHHH = tag of purification Sequence of the protein starts at A-L-L (Aminoacids 2-3-4)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.054137 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHGSAL LKVKFDQKKR VKLAQGLWLM NWFSVLAGII IFSLGLFLKI ELRKRSDVMN NSESHFVPNS LIGMGVLSCV FNSLAGKIC YDALDPAKYA RWKPWLKPYL AICVLFNIIL FLVALCCFLL RGSLENTLGQ GLKNGMKYYR DTDTPGRSFM K KTIDMLQI ...String:
HHHHHHGSAL LKVKFDQKKR VKLAQGLWLM NWFSVLAGII IFSLGLFLKI ELRKRSDVMN NSESHFVPNS LIGMGVLSCV FNSLAGKIC YDALDPAKYA RWKPWLKPYL AICVLFNIIL FLVALCCFLL RGSLENTLGQ GLKNGMKYYR DTDTPGRSFM K KTIDMLQI EFKCCGNNGF RDWFEIQWIS NRYLDFSSKE VKDRIKSNVD GRYLVDGVPF SCCNPSSPRP CIQYQITNNS AH YSYDHQT EELNLWVRGC RAALLSYYSS LMNSMGVVTL LIWLFEVTIT IGLRYLQTSL DGVSNPEESE SESEGWLLEK SVP ETWKAF LESVKKLGKG NQVEAEGAGA GQAPEAG

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Macromolecule #2: Rod outer segment membrane protein 1

MacromoleculeName: Rod outer segment membrane protein 1 / type: protein_or_peptide / ID: 2
Details: The protein sequence starts at A-P-V-L, residues 2-3-4-5
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.249828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSAPVLPLVL PLQPRIRLAQ GLWLLSWLLA LAGGVILLCS GHLLVQLRHL GTFLAPSCQF PVLPQAALAA GAVALGTGLV GVGASRASL NAALYPPWRG VLGPLLVAGT AGGGGLLVVG LGLALALPGS LDEALEEGLV TALAHYKDTE VPGHCQAKRL V DELQLRYH ...String:
GSAPVLPLVL PLQPRIRLAQ GLWLLSWLLA LAGGVILLCS GHLLVQLRHL GTFLAPSCQF PVLPQAALAA GAVALGTGLV GVGASRASL NAALYPPWRG VLGPLLVAGT AGGGGLLVVG LGLALALPGS LDEALEEGLV TALAHYKDTE VPGHCQAKRL V DELQLRYH CCGRHGYKDW FGVQWVSSRY LDPGDRDVAD RIQSNVEGLY LTDGVPFSCC NPHSPRPCLQ NRLSDSYAHP LF DPRQPNQ NLWAQGCHEV LLEHLQDLAG TLGSMLAVTF LLQALVLLGL RYLQTALEGL GGVIDAGGET QGYLFPSGLK DML KTAWLQ GGVACRPAPE EAPPGEAPPK EDLSEA

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Macromolecule #3: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama (mammal)
Molecular weightTheoretical: 14.646134 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SQVQLQESGG GLVQAGGSLR LSCAASTRTT SRYTVGWFCQ APGKEREFVA AVHWSGGSTW YADSVKGRFT ISRDNAKNTV YLQMNSLKQ EDTAVYYCAA AEPRRYSYYM RPDEYNYWGQ GTQVTVSSAA PLE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 2.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93727
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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