6SP2 | pdb_00006sp2

CryoEM structure of SERINC from Drosophila melanogaster


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6SP2

This is version 1.4 of the entry. See complete history

Literature

A bipartite structural organization defines the SERINC family of HIV-1 restriction factors.

Pye, V.E.Rosa, A.Bertelli, C.Struwe, W.B.Maslen, S.L.Corey, R.Liko, I.Hassall, M.Mattiuzzo, G.Ballandras-Colas, A.Nans, A.Takeuchi, Y.Stansfeld, P.J.Skehel, J.M.Robinson, C.V.Pizzato, M.Cherepanov, P.

(2020) Nat Struct Mol Biol 27: 78-83

  • DOI: https://doi.org/10.1038/s41594-019-0357-0
  • Primary Citation Related Structures: 
    6SP2

  • PubMed 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 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.


  • Organizational Affiliation
    • Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK.

Macromolecule Content 

  • Total Structure Weight: 353.93 kDa 
  • Atom Count: 18,498 
  • Modeled Residue Count: 2,190 
  • Deposited Residue Count: 3,078 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Membrane protein TMS1d
A, B, C, D, E
A, B, C, D, E, F
513Drosophila melanogasterMutation(s): 0 
Gene Names: TMS1CG4672
Membrane Entity: Yes 
UniProt
Find proteins for Q9U6P4 (Drosophila melanogaster)
Explore Q9U6P4 
Go to UniProtKB:  Q9U6P4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U6P4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
AA [auth F]
I [auth A]
K [auth B]
O [auth C]
S [auth D]
AA [auth F],
I [auth A],
K [auth B],
O [auth C],
S [auth D],
W [auth E]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
LMN

Query on LMN



Download:Ideal Coordinates CCD File
BA [auth F]
CA [auth F]
G [auth A]
J [auth A]
L [auth B]
BA [auth F],
CA [auth F],
G [auth A],
J [auth A],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
T [auth D],
U [auth D],
X [auth E],
Y [auth E]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
P5S

Query on P5S



Download:Ideal Coordinates CCD File
DA [auth F]
H [auth A]
N [auth B]
R [auth C]
V [auth D]
DA [auth F],
H [auth A],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC001061
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50 AI150481

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references
  • Version 1.2: 2020-01-22
    Changes: Database references
  • Version 1.3: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2024-11-06
    Changes: Data collection, Structure summary