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- PDB-7zw1: Human PRPH2-ROM1 hetero-dimer -

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Basic information

Entry
Database: PDB / ID: 7zw1
TitleHuman PRPH2-ROM1 hetero-dimer
Components
  • Nanobody
  • Peripherin-2
  • Rod outer segment membrane protein 1
KeywordsMEMBRANE PROTEIN / PRPH2 / peripherin-2 / ROM1 / hetero-complex / tetraspanin
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 / retina vasculature development in camera-type eye / detection of light stimulus involved in visual perception / protein heterooligomerization / photoreceptor outer segment membrane / photoreceptor outer segment / photoreceptor inner segment ...protein localization to photoreceptor outer segment / camera-type eye photoreceptor cell differentiation / response to low light intensity stimulus / photoreceptor cell outer segment organization / retina vasculature development in camera-type eye / detection of light stimulus involved in visual perception / protein heterooligomerization / photoreceptor outer segment membrane / photoreceptor outer segment / photoreceptor inner segment / visual perception / protein maturation / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Peripherin-2 / Rod outer segment membrane protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama (mammal)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsEl Mazouni, D. / Gros, P.
Funding supportEuropean Union, 1items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Nov 16, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 16, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peripherin-2
B: Rod outer segment membrane protein 1
C: Nanobody


Theoretical massNumber of molelcules
Total (without water)91,9503
Polymers91,9503
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3750 Å2
ΔGint-17 kcal/mol
Surface area37800 Å2

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Components

#1: Protein Peripherin-2 / Retinal degeneration slow protein / Tetraspanin-22 / Tspan-22


Mass: 40054.137 Da / Num. of mol.: 1 / Mutation: C150S
Source method: isolated from a genetically manipulated source
Details: HHHHHH = tag of purification Sequence of the protein starts at A-L-L (Aminoacids 2-3-4)
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPH2, PRPH, RDS, TSPAN22 / Production host: Homo sapiens (human) / References: UniProt: P23942
#2: Protein Rod outer segment membrane protein 1 / ROSP1 / Tetraspanin-23 / Tspan-23


Mass: 37249.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein sequence starts at A-P-V-L, residues 2-3-4-5
Source: (gene. exp.) Homo sapiens (human) / Gene: ROM1, TSPAN23 / Production host: Homo sapiens (human) / References: UniProt: Q03395
#3: Antibody Nanobody


Mass: 14646.134 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama (mammal) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human PRPH2-ROM1 hetero-dimerCOMPLEXall0RECOMBINANT
2Human PRPH2-ROM1 hetero-dimerCOMPLEX#1-#21RECOMBINANT
3NanobodyCOMPLEX#31RECOMBINANT
Molecular weightValue: 76 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Lama (mammal)9839
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
4cryoSPARC2.2CTF correction
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93727 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026067
ELECTRON MICROSCOPYf_angle_d0.4838239
ELECTRON MICROSCOPYf_dihedral_angle_d3.564828
ELECTRON MICROSCOPYf_chiral_restr0.035907
ELECTRON MICROSCOPYf_plane_restr0.0031050

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