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

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Basic information

Entry
Database: PDB / ID: 7juf
TitleC-type carbohydrate-recognition domain 4 of the mannose receptor complexed with Man-alpha1-2Man
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
DI(HYDROXYETHYL)ETHER / Macrophage mannose receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionAug 19, 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 1.3Apr 3, 2024Group: 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
B: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8978
Polymers30,9862
Non-polymers9116
Water6,089338
1
A: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0225
Polymers15,4931
Non-polymers5294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8753
Polymers15,4931
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.414, 56.376, 61.370
Angle α, β, γ (deg.)90.000, 100.920, 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRC1, CLEC13D, CLEC13DL, MRC1L1 / Plasmid: pT5T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22897
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.89 Å3/Da / Density % sol: 34.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 6.0mg/ml protein in 5mM CaCl2, 10mM Tris, pH 8.0, 25mM NaCl, and30 mM Man-alpha1-2-Man; Reservoir solution: 15% Peg 400, 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: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.4→33.8 Å / Num. obs: 44557 / % possible obs: 98 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.025 / Rrim(I) all: 0.049 / Net I/σ(I): 18
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
1.4-1.423.50.123759021420.9810.0750.1457.995.8
7.66-33.793.70.03111323030.9980.0190.03629.699.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: partially refined model in different symmetry

Resolution: 1.4→33.8 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / Phase error: 15.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1705 2000 4.49 %
Rwork0.1344 42536 -
obs0.136 44536 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.69 Å2 / Biso mean: 14.4917 Å2 / Biso min: 4.83 Å2
Refinement stepCycle: final / Resolution: 1.4→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 57 340 2482
Biso mean--16.43 26.95 -
Num. residues----256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.43440.19881430.1237304196
1.4344-1.47320.16731380.1151293998
1.4732-1.51650.16781410.1062300897
1.5165-1.56550.16741420.1066301996
1.5655-1.62140.16321410.1089300298
1.6214-1.68640.16841440.114304998
1.6864-1.76310.17021420.1229303098
1.7631-1.85610.15831410.1294300497
1.8561-1.97230.17081440.1312304399
1.9723-2.12460.15851450.1313310199
2.1246-2.33840.17321420.142300697
2.3384-2.67660.21671460.1545310299
2.6766-3.37180.16821440.1532305498
3.3718-33.80.15381470.1372313899

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