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- PDB-6ioe: Crystal structure of the CysR-CTLD2 fragment of human MR at basic... -

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Basic information

Entry
Database: PDB / ID: 6ioe
TitleCrystal structure of the CysR-CTLD2 fragment of human MR at basic pH (pH 8.5)
ComponentsMacrophage mannose receptor 1
KeywordsIMMUNE SYSTEM / CD206 / mannose receptor family / pH-dependent / conformational change / scavenger receptor
Function / homology
Function and homology information


cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / receptor-mediated endocytosis / cellular response to interleukin-4 / cellular response to type II interferon / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / signaling receptor activity / virus receptor activity ...cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / receptor-mediated endocytosis / cellular response to interleukin-4 / cellular response to type II interferon / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / signaling receptor activity / virus 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 / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Macrophage mannose receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHu, Z. / He, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270772 China
Chinese Academy of SciencesXDB08020102 China
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural basis of the pH-dependent conformational change of the N-terminal region of human mannose receptor/CD206.
Authors: Hu, Z. / Wang, Y. / Cheng, C. / He, Y.
History
DepositionOct 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)108,8262
Polymers108,8262
Non-polymers00
Water00
1
A: Macrophage mannose receptor 1


Theoretical massNumber of molelcules
Total (without water)54,4131
Polymers54,4131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrophage mannose receptor 1


Theoretical massNumber of molelcules
Total (without water)54,4131
Polymers54,4131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)241.425, 72.240, 109.529
Angle α, β, γ (deg.)90.00, 114.51, 90.00
Int Tables number5
Space group name H-MC121

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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: 54412.914 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: Trichoplusia ni (cabbage looper) / References: UniProt: P22897
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: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.2 M potassium sodium tartrate tetrahydrate, 0.1 M Tris (pH 8.5)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 37435 / % possible obs: 97.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 11.71
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.463 / Num. unique obs: 3452

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XTS

5xts


Resolution: 2.9→29.846 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 34.58
RfactorNum. reflection% reflection
Rfree0.2842 2006 5.38 %
Rwork0.2364 --
obs0.239 37307 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7242 0 0 0 7242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117465
X-RAY DIFFRACTIONf_angle_d1.22210129
X-RAY DIFFRACTIONf_dihedral_angle_d8.0464333
X-RAY DIFFRACTIONf_chiral_restr0.0581035
X-RAY DIFFRACTIONf_plane_restr0.0061278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8985-2.9710.46971340.35862264X-RAY DIFFRACTION88
2.971-3.05120.36551250.32442390X-RAY DIFFRACTION92
3.0512-3.14090.33491440.30972460X-RAY DIFFRACTION95
3.1409-3.24220.34511490.29322534X-RAY DIFFRACTION98
3.2422-3.35790.32981410.28522519X-RAY DIFFRACTION98
3.3579-3.49220.32891440.27222531X-RAY DIFFRACTION98
3.4922-3.65080.35361380.25212553X-RAY DIFFRACTION98
3.6508-3.84290.31951420.23032546X-RAY DIFFRACTION98
3.8429-4.08310.30481430.21582552X-RAY DIFFRACTION99
4.0831-4.39750.23881430.19352570X-RAY DIFFRACTION99
4.3975-4.83840.23441570.18952598X-RAY DIFFRACTION99
4.8384-5.53460.21831450.19792570X-RAY DIFFRACTION99
5.5346-6.95840.25961480.23892607X-RAY DIFFRACTION99
6.9584-29.84740.2421530.22172607X-RAY DIFFRACTION97

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