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- PDB-7l65: C-type carbohydrate-recognition domain 4 of the mannose receptor ... -

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Basic information

Entry
Database: PDB / ID: 7l65
TitleC-type carbohydrate-recognition domain 4 of the mannose receptor complexed with Methyl-GlcNAc
ComponentsMacrophage mannose receptor 1
KeywordsSUGAR BINDING PROTEIN / GLYCOBIOLOGY / CARBOHYDRATE-BINDING PROTEIN / C-TYPE LECTIN / COMPLEX
Function / homology
Function and homology information


cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / signaling receptor activity / cellular response to lipopolysaccharide ...cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / virus receptor activity / 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 / : / C-type lectin, conserved site / C-type lectin domain signature. ...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 / : / 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 / C-type lectin fold / Kringle-like fold
Similarity search - Domain/homology
Chem-2F8 / Macrophage mannose receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 Å
AuthorsWeis, W.I. / Feinberg, H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P005659/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural analysis of carbohydrate binding by the macrophage mannose receptor CD206.
Authors: Feinberg, H. / Jegouzo, S.A.F. / Lasanajak, Y. / Smith, D.F. / Drickamer, K. / Weis, W.I. / Taylor, M.E.
History
DepositionDec 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7683
Polymers15,4931
Non-polymers2752
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.810, 56.326, 34.330
Angle α, β, γ (deg.)90.000, 112.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Macrophage mannose receptor 1 / MMR / C-type lectin domain family 13 member D / C-type lectin domain family 13 member D-like / ...MMR / C-type lectin domain family 13 member D / C-type lectin domain family 13 member D-like / Human mannose receptor / hMR / Macrophage mannose receptor 1-like protein 1


Mass: 15493.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRC1, CLEC13D, CLEC13DL, MRC1L1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22897
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-2F8 / methyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside / methyl 2-(acetylamino)-2-deoxy-alpha-D-glucopyranoside / methyl 2-acetamido-2-deoxy-alpha-D-glucoside / methyl 2-acetamido-2-deoxy-D-glucoside / methyl 2-acetamido-2-deoxy-glucoside


Type: D-saccharide / Mass: 235.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAc[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-N-acetyl-a-D-glucopyranoseCOMMON NAMEGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.9 Å3/Da / Density % sol: 35.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 6mg/ml protein in 5 mM CaCl2, 10 mM Tris, pH 8.0, 25 mM NaCl, and 50mM alpha-MeGlcNAc. Reservoir solution: 15% Peg 8K, 0.1M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.35→30.4 Å / Num. obs: 25247 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 18.8 / Num. measured all: 174816 / Scaling rejects: 423
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.35-1.376.60.116823212470.9890.0490.1269.797.4
7.39-30.45.90.0839771660.9740.0410.09423.796.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7JUB

7jub


Resolution: 1.35→30.4 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / Phase error: 15.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1698 1260 4.99 %
Rwork0.1353 23966 -
obs0.1371 25226 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.19 Å2 / Biso mean: 15.5985 Å2 / Biso min: 5.09 Å2
Refinement stepCycle: final / Resolution: 1.35→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 17 189 1204
Biso mean--21.21 30.02 -
Num. residues----122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.40.17681470.13032625277298
1.4-1.470.1771330.11442677281099
1.47-1.540.1421420.10822642278498
1.54-1.640.16021500.11282649279999
1.64-1.770.17891390.124326602799100
1.77-1.950.1811380.13462662280099
1.95-2.230.16351400.13232644278498
2.23-2.810.14961330.150626962829100
2.81-30.40.18511380.14492711284998

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