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- PDB-1dqg: CRYSTAL STRUCTURE OF THE CYSTEINE RICH DOMAIN OF MANNOSE RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1dqg
TitleCRYSTAL STRUCTURE OF THE CYSTEINE RICH DOMAIN OF MANNOSE RECEPTOR
ComponentsMANNOSE RECEPTOR
KeywordsSUGAR BINDING PROTEIN / beta trefoil / multilectin receptor / pituitary hormones / sulfated carbohydrate
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / cargo receptor activity / D-mannose binding / receptor-mediated endocytosis / cellular response to interleukin-4 / cellular response to type II interferon / transmembrane signaling receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane ...Cross-presentation of soluble exogenous antigens (endosomes) / cargo receptor activity / D-mannose binding / receptor-mediated endocytosis / cellular response to interleukin-4 / cellular response to type II interferon / transmembrane signaling receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane / cell surface / plasma membrane
Similarity search - Function
MRC2-like, N-terminal cysteine-rich domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / : / Ricin-type beta-trefoil lectin domain / C-type lectin, conserved site ...MRC2-like, N-terminal cysteine-rich domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / : / Ricin-type beta-trefoil lectin domain / C-type lectin, conserved site / C-type lectin domain signature. / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / C-type lectin fold / Kringle-like fold / Mainly Beta
Similarity search - Domain/homology
Macrophage mannose receptor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.7 Å
AuthorsLiu, Y. / Chirino, A.J. / Misulovin, Z. / Leteux, C. / Feizi, T. / Nussenzweig, M.C. / Bjorkman, P.J.
CitationJournal: J.Exp.Med. / Year: 2000
Title: Crystal structure of the cysteine-rich domain of mannose receptor complexed with a sulfated carbohydrate ligand.
Authors: Liu, Y. / Chirino, A.J. / Misulovin, Z. / Leteux, C. / Feizi, T. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionJan 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANNOSE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6552
Polymers15,5581
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.580, 41.280, 98.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MANNOSE RECEPTOR


Mass: 15558.486 Da / Num. of mol.: 1 / Fragment: CYSTEINE RICH DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell: MACROPHAGE / Cell line: EPITHELIAL CELLS / Production host: Homo sapiens (human) / References: UniProt: Q61830
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
210 mMHEPES1drop
310 mM1dropNaCl
430 %(w/v)PEG80001reservoir
50.2 Mammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS II1IMAGE PLATEOct 1, 1998
RIGAKU RAXIS II2IMAGE PLATEMay 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. all: 152280 / Num. obs: 18536 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21
Reflection shellResolution: 1.7→1.77 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.205 / Num. unique all: 1641 / % possible all: 91.3
Reflection
*PLUS
Num. measured all: 152280
Reflection shell
*PLUS
% possible obs: 91.3 % / Mean I/σ(I) obs: 5.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.7→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.208 1078 RANDOM
Rwork0.196 --
all0.198 18132 -
obs0.198 18132 -
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 5 0 1090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.89
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 25 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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