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- PDB-7l68: C-type carbohydrate-recognition domain 4 of the mannose receptor -

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Basic information

Entry
Database: PDB / ID: 7l68
TitleC-type carbohydrate-recognition domain 4 of the mannose receptor
ComponentsMacrophage mannose receptor 1
KeywordsSUGAR BINDING PROTEIN / GLYCOBIOLOGY / CARBOHYDRATE-BINDING PROTEIN / C-TYPE LECTIN
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: 1.4 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
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
B: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0664
Polymers30,9862
Non-polymers802
Water6,792377
1
A: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5332
Polymers15,4931
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5332
Polymers15,4931
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.623, 58.718, 62.383
Angle α, β, γ (deg.)90.000, 97.660, 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22897
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.85 Å3/Da / Density % sol: 33.6 %
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 10mM Man9GlcNAc2. Reservoir solution: 2.5% 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: 1.4→31.34 Å / Num. obs: 42022 / % possible obs: 94.4 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.022 / Rrim(I) all: 0.061 / Net I/σ(I): 23.6 / Num. measured all: 309250 / Scaling rejects: 240
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
1.4-1.427.30.1111475420090.990.0440.1212.492.6
7.67-31.346.60.08218772840.9720.0380.09232.497.9

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Processing

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

7jub


Resolution: 1.4→31.34 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1749 2000 4.76 %
Rwork0.1548 40000 -
obs0.1558 42000 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.83 Å2 / Biso mean: 12.7885 Å2 / Biso min: 3.88 Å2
Refinement stepCycle: final / Resolution: 1.4→31.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 2 377 2552
Biso mean--6.49 21.65 -
Num. residues----268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.430.20611400.1622798293893
1.43-1.470.20031410.16352825296694
1.47-1.520.17231440.1542883302795
1.52-1.570.16581420.15222849299195
1.57-1.620.18931430.15612845298894
1.62-1.690.17241440.14842864300895
1.69-1.760.17561380.15632774291292
1.76-1.860.18291330.15782649278287
1.86-1.970.18331440.1562903304796
1.97-2.130.17111460.15062920306697
2.13-2.340.18421480.15462956310497
2.34-2.680.17081470.17212943309096
2.68-3.370.17671360.15892726286289
3.37-31.340.15911540.14273065321999
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)
11.2721-2.31321.66858.0764-6.18864.84680.07040.1638-0.3176-0.40510.06110.4550.1348-0.9533-0.1190.2361-0.0106-0.04520.2794-0.02230.1722.029316.865346.5817
21.5841-0.2989-0.73332.05160.75791.34990.02510.04160.0438-0.1138-0.04830.1607-0.0875-0.08860.01940.0440.0024-0.01070.05040.00170.04845.856628.797162.611
35.4918-2.58662.08788.5601-1.81024.12220.08510.2172-0.0414-0.352-0.08640.03450.1544-0.09680.02660.0794-0.0184-0.0080.07520.00320.02159.907925.400547.8708
42.08630.9025-0.36031.39660.9512.12090.05180.0526-0.1868-0.02370.0178-0.11550.18460.1424-0.03320.060.0040.00130.065-0.00890.04617.63324.769960.7665
51.6042-0.31960.67250.54460.56041.4410.00240.05220.0455-0.0378-0.00750.0022-0.02570.04540.00570.0461-0.00750.0070.03350.00970.032818.574931.835660.9555
60.9205-0.36380.3416.4742-0.84010.20460.03520.1903-0.0948-0.2496-0.04280.13890.0801-0.02320.01960.07830.0018-0.00710.0796-0.01690.0516-3.045817.981722.0271
71.4029-1.2708-0.53891.68320.69670.609-0.0685-0.0266-0.09250.12840.02710.0790.1014-0.02470.03240.0551-0.01060.00670.04830.00430.0374-1.909327.653933.9509
85.19890.3951.24814.5181-1.19285.41610.00490.0822-0.0881-0.1431-0.01040.04530.0561-0.10730.01790.06380.00220.01140.04860.00340.00022.38629.100916.6453
92.55080.8243-0.70581.99420.89691.66490.05670.0422-0.0596-0.1096-0.00420.0150.02770.0289-0.06040.0592-0.00330.02190.01740.00850.01057.444832.208131.4457
101.50760.34530.24060.91730.29491.4669-0.02430.01660.0252-0.0067-0.0008-0.0706-0.05440.08670.02940.03820.00530.0050.03390.01040.04658.190334.191330.8163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 629 through 640 )A629 - 640
2X-RAY DIFFRACTION2chain 'A' and (resid 641 through 674 )A641 - 674
3X-RAY DIFFRACTION3chain 'A' and (resid 675 through 688 )A675 - 688
4X-RAY DIFFRACTION4chain 'A' and (resid 689 through 720 )A689 - 720
5X-RAY DIFFRACTION5chain 'A' and (resid 721 through 761 )A721 - 761
6X-RAY DIFFRACTION6chain 'B' and (resid 627 through 645 )B627 - 645
7X-RAY DIFFRACTION7chain 'B' and (resid 646 through 674 )B646 - 674
8X-RAY DIFFRACTION8chain 'B' and (resid 675 through 688 )B675 - 688
9X-RAY DIFFRACTION9chain 'B' and (resid 689 through 709 )B689 - 709
10X-RAY DIFFRACTION10chain 'B' and (resid 710 through 761 )B710 - 761

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