4M18

Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Molecular mechanisms of inhibition of influenza by surfactant protein d revealed by large-scale molecular dynamics simulation.

Goh, B.C.Rynkiewicz, M.J.Cafarella, T.R.White, M.R.Hartshorn, K.L.Allen, K.Crouch, E.C.Calin, O.Seeberger, P.H.Schulten, K.Seaton, B.A.

(2013) Biochemistry 52: 8527-8538

  • DOI: https://doi.org/10.1021/bi4010683
  • Primary Citation of Related Structures:  
    4M17, 4M18

  • PubMed Abstract: 

    Surfactant protein D (SP-D), a mammalian C-type lectin, is the primary innate inhibitor of influenza A virus (IAV) in the lung. Interactions of SP-D with highly branched viral N-linked glycans on hemagglutinin (HA), an abundant IAV envelope protein and critical virulence factor, promote viral aggregation and neutralization through as yet unknown molecular mechanisms. Two truncated human SP-D forms, wild-type (WT) and double mutant D325A+R343V, representing neck and carbohydrate recognition domains are compared in this study. Whereas both WT and D325A+R343V bind to isolated glycosylated HA, WT does not inhibit IAV in neutralization assays; in contrast, D325A+R343V neutralization compares well with that of full-length native SP-D. To elucidate the mechanism for these biochemical observations, we have determined crystal structures of D325A+R343V in the presence and absence of a viral nonamannoside (Man9). On the basis of the D325A+R343V-Man9 structure and other crystallographic data, models of complexes between HA and WT or D325A+R343V were produced and subjected to molecular dynamics. Simulations reveal that whereas WT and D325A+R343V both block the sialic acid receptor site of HA, the D325A+R343V complex is more stable, with stronger binding caused by additional hydrogen bonds and hydrophobic interactions with HA residues. Furthermore, the blocking mechanism of HA differs for WT and D325A+R343V because of alternate glycan binding modes. The combined results suggest a mechanism through which the mode of SP-D-HA interaction could significantly influence viral aggregation and neutralization. These studies provide the first atomic-level molecular view of an innate host defense lectin inhibiting its viral glycoprotein target.


  • Organizational Affiliation

    Beckman Institute and Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pulmonary surfactant-associated protein D
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
147Homo sapiensMutation(s): 2 
Gene Names: COLEC7PSPDSFTP4SFTPD
UniProt & NIH Common Fund Data Resources
Find proteins for P35247 (Homo sapiens)
Explore P35247 
Go to UniProtKB:  P35247
PHAROS:  P35247
GTEx:  ENSG00000133661 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35247
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
M, N, P, Q, R
M, N, P, Q, R, S, T, U, W, X
3N/A
Glycosylation Resources
GlyTouCan:  G25559RS
GlyCosmos:  G25559RS
GlyGen:  G25559RS
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
O, V
2N/A
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth I]
BA [auth A]
BB [auth J]
CA [auth B]
AA [auth A],
AB [auth I],
BA [auth A],
BB [auth J],
CA [auth B],
CB [auth J],
DA [auth B],
DB [auth J],
EA [auth B],
EB [auth K],
FA [auth C],
FB [auth K],
GA [auth C],
GB [auth K],
HA [auth C],
HB [auth L],
IA [auth D],
IB [auth L],
JA [auth D],
JB [auth L],
KA [auth D],
LA [auth E],
MA [auth E],
NA [auth E],
OA [auth F],
PA [auth F],
QA [auth F],
RA [auth G],
SA [auth G],
TA [auth G],
UA [auth G],
VA [auth H],
WA [auth H],
XA [auth H],
Y [auth A],
YA [auth I],
Z [auth A],
ZA [auth I]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.833α = 90
b = 159.454β = 90
c = 159.894γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary