7RUG | pdb_00007rug

Human SERINC3-DeltaICL4

• PDB DOI: https://doi.org/10.2210/pdb7RUG/pdb
• EM Map EMD-24705: EMDB EMDataResource

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2021-08-17 Released: 2022-08-24 
• Deposition Author(s): Purdy, M.D., Leonhardt, S.A., Yeager, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry.

Leonhardt, S.A., Purdy, M.D., Grover, J.R., Yang, Z., Poulos, S., McIntire, W.E., Tatham, E.A., Erramilli, S.K., Nosol, K., Lai, K.K., Ding, S., Lu, M., Uchil, P.D., Finzi, A., Rein, A., Kossiakoff, A.A., Mothes, W., Yeager, M.

(2023) Nat Commun 14: 4368-4368

• PubMed: 37474505 
• DOI: https://doi.org/10.1038/s41467-023-39262-2
• Primary Citation Related Structures: 
  7RU6, 7RUG


• PubMed Abstract: 
  

  The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). Here, we determine cryoEM maps of full-length human SERINC3 and an ICL4 deletion construct, which reveal that hSERINC3 is comprised of two α-helical bundles connected by a ~ 40-residue, highly tilted, "crossmember" helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes induce flipping of phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. Furthermore, SERINC3, SERINC5 and the scramblase TMEM16F expose PS on the surface of HIV-1 and reduce infectivity, with similar results in MLV. SERINC effects in HIV-1 and MLV are counteracted by Nef and GlycoGag, respectively. Our results demonstrate that SERINCs are membrane transporters that flip lipids, resulting in a loss of membrane asymmetry that is strongly correlated with changes in Env conformation and loss of infectivity.

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Organizational Affiliation: 
• The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA.
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
Molecular Electron Microscopy Core, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 535, Frederick, MD, 21702, USA.
Centre de Recherche du CHUM (CRCHUM), Montreal, QC, Canada.
Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, TX, USA.
Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada.
Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA. [e-mail].
The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA. [e-mail].
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA. [e-mail].
Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA. [e-mail].
Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA. [e-mail].
Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA. [e-mail].
Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA. [e-mail].
Department of Medicine, Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 78.1 kDa 
• Atom Count: 2,701 
• Modeled Residue Count: 331 
• Deposited Residue Count: 709 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine incorporator 3	A	468	Homo sapiens	Mutation(s): 0  Gene Names: SERINC3, DIFF33, TDE1, SBBI99 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q13530 (Homo sapiens) Explore Q13530  Go to UniProtKB:  Q13530
PHAROS:  Q13530 GTEx:  ENSG00000132824

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SiA	B [auth L]	241	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.20.1-4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Purdy, M.D., Leonhardt, S.A., Yeager, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5P50AI150464-15

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references