[English] 日本語
Yorodumi
- PDB-6sp2: CryoEM structure of SERINC from Drosophila melanogaster -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sp2
TitleCryoEM structure of SERINC from Drosophila melanogaster
ComponentsMembrane protein TMS1d
KeywordsMEMBRANE PROTEIN / Anti-retroviral / TM10 / SERINC fold / novel fold
Function / homologySerine incorporator/TMS membrane protein / Serine incorporator (Serinc) / membrane / CARDIOLIPIN / Chem-P5S / Membrane protein TMS1d
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsPye, V.E. / Nans, A. / Cherepanov, P.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001061 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150481 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: A bipartite structural organization defines the SERINC family of HIV-1 restriction factors.
Authors: Valerie E Pye / Annachiara Rosa / Cinzia Bertelli / Weston B Struwe / Sarah L Maslen / Robin Corey / Idlir Liko / Mark Hassall / Giada Mattiuzzo / Allison Ballandras-Colas / Andrea Nans / ...Authors: Valerie E Pye / Annachiara Rosa / Cinzia Bertelli / Weston B Struwe / Sarah L Maslen / Robin Corey / Idlir Liko / Mark Hassall / Giada Mattiuzzo / Allison Ballandras-Colas / Andrea Nans / Yasuhiro Takeuchi / Phillip J Stansfeld / J Mark Skehel / Carol V Robinson / Massimo Pizzato / Peter Cherepanov /
Abstract: The human integral membrane protein SERINC5 potently restricts HIV-1 infectivity and sensitizes the virus to antibody-mediated neutralization. Here, using cryo-EM, we determine the structures of ...The human integral membrane protein SERINC5 potently restricts HIV-1 infectivity and sensitizes the virus to antibody-mediated neutralization. Here, using cryo-EM, we determine the structures of human SERINC5 and its orthologue from Drosophila melanogaster at subnanometer and near-atomic resolution, respectively. The structures reveal a novel fold comprised of ten transmembrane helices organized into two subdomains and bisected by a long diagonal helix. A lipid binding groove and clusters of conserved residues highlight potential functional sites. A structure-based mutagenesis scan identified surface-exposed regions and the interface between the subdomains of SERINC5 as critical for HIV-1-restriction activity. The same regions are also important for viral sensitization to neutralizing antibodies, directly linking the antiviral activity of SERINC5 with remodeling of the HIV-1 envelope glycoprotein.
History
DepositionAug 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10279
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Membrane protein TMS1d
B: Membrane protein TMS1d
C: Membrane protein TMS1d
D: Membrane protein TMS1d
E: Membrane protein TMS1d
F: Membrane protein TMS1d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,92930
Polymers328,3306
Non-polymers25,59924
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, larger MWt peak on gel filtration; higher bands visible in SDS PAGE and shift in native PAGE; hexamer seen by negative stain EM and this cryoEM structure.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area32380 Å2
ΔGint-350 kcal/mol
Surface area91730 Å2
MethodPISA

-
Components

#1: Protein
Membrane protein TMS1d


Mass: 54721.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: TMS1, CG4672 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9U6P4
#2: Chemical
ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
#3: Chemical
ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H82NO10P
#4: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: SERINC homo-hexamer / Type: COMPLEX
Details: homo-hexamer of SERINC from Drosophila melanogaster recombinantly expressed and purified in detergent micelle; imaged as single particle.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.32805646 MDa / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.04 Msodium chlorideNaCl1
20.01 MHEPESC8H18N2O4S-NaOH1
30.5 mMTCEPC9H15O6P1
40.5 mMDTTHSCH2CH(OH)CH(OH)CH2SH1
50.0003 %LMNGC47H88O221
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Freshly purified mono-dispersed sample
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: wait 60 seconds, blot for 3-4 seconds

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Details: 5,807 movies were collected

-
Processing

EM software
IDNameVersionCategoryDetails
1RELION2.1particle selection
7Cootmodel fitting
9cryoSPARC2initial Euler assignment
10cryoSPARC2final Euler assignmentab initio
11RELION2.1classification
12cryoSPARC23D reconstructionNuRefinement
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1857080
Details: A sub-set of particles semi-automatically picked in EMAN2 Boxer were used to generate the starting 2D class averages, which, upon low-pass filtering to 20 A, served as templates for auto- ...Details: A sub-set of particles semi-automatically picked in EMAN2 Boxer were used to generate the starting 2D class averages, which, upon low-pass filtering to 20 A, served as templates for auto-picking of the entire dataset.
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159252 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 150.6 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient

+
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