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- PDB-1dqo: Crystal structure of the cysteine rich domain of mannose receptor... -

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Basic information

Entry
Database: PDB / ID: 1dqo
TitleCrystal structure of the cysteine rich domain of mannose receptor complexed with Acetylgalactosamine-4-sulfate
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 / 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
Chem-ASG / Macrophage mannose receptor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)15,8602
Polymers15,5581
Non-polymers3011
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.430, 41.480, 100.300
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 CELL / Production host: Homo sapiens (human) / References: UniProt: Q61830
#2: Sugar ChemComp-ASG / 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose / 2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE / N-acetyl-4-O-sulfo-beta-D-galactosamine / 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactose / 2-acetamido-2-deoxy-4-O-sulfo-D-galactose / 2-acetamido-2-deoxy-4-O-sulfo-galactose


Type: D-saccharide, beta linking / Mass: 301.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO9S
IdentifierTypeProgram
DGalpNAc[4S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-4-sulfo-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpNAc4SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.33 %
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

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 8984 / Num. obs: 8984 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.105 / % possible all: 95.5
Reflection
*PLUS
Num. measured all: 86630
Reflection shell
*PLUS
% possible obs: 95.5 % / Mean I/σ(I) obs: 11.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQG

1dqg


Resolution: 2.2→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.232 483 RANDOM
Rwork0.211 --
all0.213 8639 -
obs0.213 8639 -
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 18 153 1256
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.49
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 25 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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