[English] 日本語
Yorodumi
- EMDB-14991: Human PRPH2-ROM1 hetero-dimer -

+
Open data


ID or keywords:

Loading...

-
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: NanobodySingle-domain antibody
      • Protein or peptide: NanobodySingle-domain antibody
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 / plasma membrane => GO:0005886 / 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 / plasma membrane => GO:0005886 / photoreceptor outer segment / photoreceptor inner segment / visual perception / protein homooligomerization / retina development in camera-type eye / regulation of gene expression / membrane => GO:0016020 / cell adhesion / protein homodimerization activity
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

-
Structure visualization

Supplemental images

emd_14991.png

Downloads & links

-
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 °

-
Supplemental data

-
Additional map: Sharpened map

Fileemd_14991_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_14991_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_14991_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: NanobodySingle-domain antibody
      • Protein or peptide: NanobodySingle-domain antibody

-
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

-
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)

-
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)

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more