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- PDB-6inn: Crystal structure of the CysR-CTLD3 fragment of human MR at acidi... -

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Basic information

Entry
Database: PDB / ID: 6inn
TitleCrystal structure of the CysR-CTLD3 fragment of human MR at acidic pH (pH 5.6)
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 / 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 / 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 / virus 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. ...: / 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: 3.001 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 26, 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
B: Macrophage mannose receptor 1
C: Macrophage mannose receptor 1
D: Macrophage mannose receptor 1


Theoretical massNumber of molelcules
Total (without water)283,8454
Polymers283,8454
Non-polymers00
Water00
1
A: Macrophage mannose receptor 1


Theoretical massNumber of molelcules
Total (without water)70,9611
Polymers70,9611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrophage mannose receptor 1


Theoretical massNumber of molelcules
Total (without water)70,9611
Polymers70,9611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Macrophage mannose receptor 1


Theoretical massNumber of molelcules
Total (without water)70,9611
Polymers70,9611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Macrophage mannose receptor 1


Theoretical massNumber of molelcules
Total (without water)70,9611
Polymers70,9611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)235.867, 235.867, 129.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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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: 70961.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / 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: 6.54 Å3/Da / Density % sol: 81.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate (pH 5.6), 1.0 M lithium sulfate monohydrate

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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 6M / Detector: PIXEL / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 266852 / % possible obs: 98.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 7.42
Reflection shellResolution: 3→3 Å / Rmerge(I) obs: 0.473 / Num. unique obs: 13195

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Processing

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

5xts


Resolution: 3.001→29.988 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 28.62
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 3850 1.44 %RANDOM
Rwork0.2556 ---
obs0.256 266754 95.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.001→29.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19258 0 0 0 19258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219862
X-RAY DIFFRACTIONf_angle_d0.44926943
X-RAY DIFFRACTIONf_dihedral_angle_d10.91511653
X-RAY DIFFRACTIONf_chiral_restr0.0382749
X-RAY DIFFRACTIONf_plane_restr0.0033404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0013-3.03790.43171290.39038158X-RAY DIFFRACTION84
3.0379-3.07630.37971270.37868511X-RAY DIFFRACTION86
3.0763-3.11670.37871220.36838558X-RAY DIFFRACTION88
3.1167-3.15940.30631280.36928728X-RAY DIFFRACTION88
3.1594-3.20450.39991300.35698715X-RAY DIFFRACTION90
3.2045-3.25230.38171340.34648925X-RAY DIFFRACTION91
3.2523-3.3030.35431410.3359073X-RAY DIFFRACTION92
3.303-3.35710.31521270.32339109X-RAY DIFFRACTION93
3.3571-3.41490.30141350.31169333X-RAY DIFFRACTION94
3.4149-3.47690.31531300.30089329X-RAY DIFFRACTION96
3.4769-3.54370.31451390.29149460X-RAY DIFFRACTION96
3.5437-3.61590.31751320.27519479X-RAY DIFFRACTION97
3.6159-3.69440.29341390.27589661X-RAY DIFFRACTION98
3.6944-3.78020.27271350.26419537X-RAY DIFFRACTION98
3.7802-3.87450.3151440.26119726X-RAY DIFFRACTION98
3.8745-3.9790.27761330.24089704X-RAY DIFFRACTION99
3.979-4.09590.25691410.24049665X-RAY DIFFRACTION99
4.0959-4.22770.3161490.21599731X-RAY DIFFRACTION99
4.2277-4.37840.22671400.20719754X-RAY DIFFRACTION99
4.3784-4.55310.2281450.19279766X-RAY DIFFRACTION99
4.5531-4.75950.19431370.18659728X-RAY DIFFRACTION99
4.7595-5.00940.2131440.18399804X-RAY DIFFRACTION100
5.0094-5.32160.18431420.19359749X-RAY DIFFRACTION100
5.3216-5.72990.22981400.20669750X-RAY DIFFRACTION99
5.7299-6.30170.25031420.23079725X-RAY DIFFRACTION99
6.3017-7.20250.3011440.23269673X-RAY DIFFRACTION99
7.2025-9.0330.20351460.21059792X-RAY DIFFRACTION100
9.033-29.98950.25381550.23669761X-RAY DIFFRACTION99

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