N-terminal domain of mouse surfactant protein B with bound lipid, Y59A/H79A mutant

  • Classification: SURFACTANT PROTEIN
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2020-03-04 Released: 2020-11-25 
  • Deposition Author(s): Rapoport, T.A., Bodnar, N.O.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

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Ligand Structure Quality Assessment 

This is version 2.0 of the entry. See complete history


Mechanism of Lamellar Body Formation by Lung Surfactant Protein B.

Sever, N.Milicic, G.Bodnar, N.O.Wu, X.Rapoport, T.A.

(2021) Mol Cell 81: 49-66.e8

  • DOI: https://doi.org/10.1016/j.molcel.2020.10.042
  • Primary Citation of Related Structures:  
    6VYN, 6VZ0, 6VZD, 6VZE, 6W1B, 7MBK

  • PubMed Abstract: 

    Breathing depends on pulmonary surfactant, a mixture of phospholipids and proteins, secreted by alveolar type II cells. Surfactant requires lamellar bodies (LBs), organelles containing densely packed concentric membrane layers, for storage and secretion. LB biogenesis remains mysterious but requires surfactant protein B (SP-B), which is synthesized as a precursor (pre-proSP-B) that is cleaved during trafficking into three related proteins. Here, we elucidate the functions and cooperation of these proteins in LB formation. We show that the N-terminal domain of proSP-B is a phospholipid-binding and -transfer protein whose activities are required for proSP-B export from the endoplasmic reticulum (ER) and sorting to LBs, the conversion of proSP-B into lipoprotein particles, and neonatal viability in mice. The C-terminal domain facilitates ER export of proSP-B. The mature middle domain, generated after proteolytic cleavage of proSP-B, generates the striking membrane layers characteristic of LBs. Together, our results lead to a mechanistic model of LB biogenesis.

  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pulmonary surfactant-associated protein B87Mus musculusMutation(s): 2 
Gene Names: SftpbSftp3
Find proteins for P50405 (Mus musculus)
Explore P50405 
Go to UniProtKB:  P50405
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50405
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PEE

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth E]
L [auth E]
M [auth B]
I [auth A],
J [auth A],
K [auth E],
L [auth E],
M [auth B],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth F],
U [auth H]
C41 H78 N O8 P
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.335α = 90
b = 169.527β = 126.897
c = 73.714γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2020-12-09
    Changes: Database references
  • Version 1.3: 2021-01-20
    Changes: Database references
  • Version 2.0: 2023-10-18
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary