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- PDB-6inv: Crystal structure of the CysR-CTLD2 fragment of human MR at acidi... -

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Basic information

Entry
Database: PDB / ID: 6inv
TitleCrystal structure of the CysR-CTLD2 fragment of human MR at acidic pH (pH 4.0)
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 / 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: 3.3 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 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage mannose receptor 1


Theoretical massNumber of molelcules
Total (without water)54,4131
Polymers54,4131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.392, 238.394, 104.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 1
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

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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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M lithium chloride, 0.1 M citric acid (pH 4.0), 10% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 8092 / % possible obs: 95.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 2.109
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.283 / Num. unique obs: 738

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XTS

5xts


Resolution: 3.3→39.732 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 30.47
RfactorNum. reflection% reflection
Rfree0.2849 807 9.99 %
Rwork0.2424 --
obs0.2468 8079 93.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→39.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 0 0 3515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023622
X-RAY DIFFRACTIONf_angle_d0.4974913
X-RAY DIFFRACTIONf_dihedral_angle_d10.4222126
X-RAY DIFFRACTIONf_chiral_restr0.038504
X-RAY DIFFRACTIONf_plane_restr0.003616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2882-3.49410.35021070.2895964X-RAY DIFFRACTION76
3.4941-3.76370.31541320.2571183X-RAY DIFFRACTION93
3.7637-4.14210.2811370.25141228X-RAY DIFFRACTION96
4.1421-4.74060.26021410.22471264X-RAY DIFFRACTION98
4.7406-5.96940.26791400.24281281X-RAY DIFFRACTION97
5.9694-39.73520.28551500.23091352X-RAY DIFFRACTION98

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