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- PDB-7l63: C-type carbohydrate-recognition domain 4 of the mannose receptor ... -

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Basic information

Entry
Database: PDB / ID: 7l63
TitleC-type carbohydrate-recognition domain 4 of the mannose receptor complexed with L-fucose-(alpha 1-2)-D-galactose-(beta1-4)-D-glucose
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 / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity ...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 / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane / cell surface / plasma membrane
Similarity search - Function
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 ...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 / C-type lectin fold / Kringle-like fold
Similarity search - Domain/homology
Macrophage mannose receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0223
Polymers15,4931
Non-polymers5292
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.514, 54.479, 37.172
Angle α, β, γ (deg.)90.000, 101.310, 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: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 6mg/ml protein in 5mM CaCl2, 10mM Tris, pH 8.0, 25mM NaCl, and 15mM L-fucose-(alpha 1-2)-D-galactose-(beta1-4)-D-glucose. Reservoir solution: 12.5% 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: 1.65→36.45 Å / Num. obs: 16058 / % possible obs: 98.4 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Net I/σ(I): 17.9 / Num. measured all: 113470 / Scaling rejects: 85
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
1.65-1.6870.30354927870.9830.1240.3285.199.4
9.04-36.456.80.0397361080.9990.0160.04235.197.9

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Processing

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

7jub


Resolution: 1.65→36.45 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 813 5.07 %
Rwork0.176 15230 -
obs0.1777 16043 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.77 Å2 / Biso mean: 27.985 Å2 / Biso min: 13.86 Å2
Refinement stepCycle: final / Resolution: 1.65→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 34 132 1234
Biso mean--33.01 36.2 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.750.2461370.19622501263898
1.75-1.890.21211280.18622494262297
1.89-2.080.20351410.18042554269599
2.08-2.380.21931330.1852551268499
2.38-30.21681350.1952530266598
3-36.450.19681390.15822600273999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.06210.21051.52435.1299-0.27934.84360.166-0.3651-0.3516-0.8565-0.029-0.88860.48910.6324-0.07020.51590.1040.0260.4833-0.03370.484410.92692.93160.9734
22.99350.6121-0.65881.97790.62262.68660.02220.59210.3405-0.5621-0.0203-0.076-0.1380.3082-0.00560.2685-0.0139-0.0040.18640.0510.19881.151216.0273-4.1742
33.6143-1.27791.96333.9424-0.73674.96460.08810.0365-0.2347-0.42080.03220.26580.3758-0.2284-0.12720.2064-0.0314-0.00690.1452-0.00050.1408-3.91247.50421.0841
42.6822.3565-2.10752.5445-0.18887.77560.06340.1282-0.186-0.09970.0669-0.47270.16240.5797-0.06880.15380.0167-0.00330.2332-0.0160.239511.02512.82628.5081
55.0569-0.6129-0.12073.2224-0.14634.6742-0.1279-0.32290.06810.16870.0860.16230.3742-0.05970.04680.1420.0221-0.01290.1202-0.01690.1351-4.447411.967610.7313
63.2504-0.3255-0.78011.86550.24753.36250.0498-0.12230.2772-0.11230.04270.0655-0.0778-0.0389-0.08690.1095-0.0048-0.01260.1158-0.00750.1648-5.35818.50858.9519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 627 through 640 )A627 - 640
2X-RAY DIFFRACTION2chain 'A' and (resid 641 through 654 )A641 - 654
3X-RAY DIFFRACTION3chain 'A' and (resid 655 through 674 )A655 - 674
4X-RAY DIFFRACTION4chain 'A' and (resid 675 through 688 )A675 - 688
5X-RAY DIFFRACTION5chain 'A' and (resid 689 through 721 )A689 - 721
6X-RAY DIFFRACTION6chain 'A' and (resid 722 through 761 )A722 - 761

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