1RTM | pdb_00001rtm

TRIMERIC STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.270 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Trimeric structure of a C-type mannose-binding protein.

Weis, W.I.Drickamer, K.

(1994) Structure 2: 1227-1240

  • DOI: https://doi.org/10.1016/S0969-2126(94)00124-3
  • Primary Citation Related Structures: 
    1RTM

  • PubMed Abstract: 

    Mannose-binding proteins (MBPs) are C-type (Ca(2+)-dependent) animal lectins found in serum. They recognize cell-surface oligosaccharide structures characteristic of pathogenic bacteria and fungi, and trigger the neutralization of these organisms. Like most lectins, MBPs display weak intrinsic affinity for monovalent sugar ligands, but bind avidly to multivalent ligands. We report physical studies in solution and the crystal structure determined at 1.8 A Bragg spacings of a trimeric fragment of MBP-A, containing the carbohydrate-recognition domain (CRD) and the neck domain that links the carboxy-terminal CRD to the collagen-like portion of the intact molecule. The neck consists of a parallel triple-stranded coiled coil of alpha-helices linked by four residues to the CRD. The isolated neck peptide does not form stable helices in aqueous solution. The previously characterized carbohydrate-binding sites lie at the distal end of the trimer and are separated from each other by 53 A. The carbohydrate-binding sites in MBP-A are too far apart for a single trimer to bind multivalently to a typical mammalian high-mannose oligosaccharide. Thus MBPs can recognize pathogens selectively by binding avidly only to the widely spaced, repetitive sugar arrays on pathogenic cell surfaces. Sequence alignments reveal that other C-type lectins are likely to have a similar oligomeric structure, but differences in their detailed organization will have an important role in determining their interactions with oligosaccharides.


  • Organizational Affiliation
    • Department of Structural Biology, Stanford University School of Medicine, CA 94305.

Macromolecule Content 

  • Total Structure Weight: 51.28 kDa 
  • Atom Count: 4,061 
  • Modeled Residue Count: 447 
  • Deposited Residue Count: 447 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MANNOSE-BINDING PROTEIN-AA [auth 1],
B [auth 2],
C [auth 3]
149Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P19999 (Rattus norvegicus)
Explore P19999 
Go to UniProtKB:  P19999
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19999
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on GOL



Download:Ideal Coordinates CCD File
BA [auth 3]
CA [auth 3]
DA [auth 3]
H [auth 1]
I [auth 1]
BA [auth 3],
CA [auth 3],
DA [auth 3],
H [auth 1],
I [auth 1],
J [auth 1],
K [auth 1],
L [auth 1],
M [auth 1],
N [auth 1],
O [auth 1],
P [auth 1],
U [auth 2],
V [auth 2],
W [auth 2]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth 1]
E [auth 1]
F [auth 1]
Q [auth 2]
R [auth 2]
D [auth 1],
E [auth 1],
F [auth 1],
Q [auth 2],
R [auth 2],
S [auth 2],
X [auth 3],
Y [auth 3],
Z [auth 3]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth 3],
G [auth 1],
T [auth 2]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.270 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80α = 90
b = 85.1β = 106.3
c = 98.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-10-30
    Changes: Structure summary