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- PDB-5xtw: Crystal structure of the CysR-CTLD2 fragment of human MR at acidic pH -

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Basic information

Entry
Database: PDB / ID: 5xtw
TitleCrystal structure of the CysR-CTLD2 fragment of human MR at acidic pH
ComponentsMacrophage mannose receptor 1
KeywordsSUGAR BINDING PROTEIN / Collagen binding / Lectin-activity / Endocytic receptor / Immune receptor
Function / homology
Function and homology information


cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / 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 / virus receptor activity / signaling receptor activity ...cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / 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 / 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: 3.2 Å
AuthorsHe, Y. / Hu, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020102 China
National Natural Science Foundation of China31270772 China
CitationJournal: Structure / Year: 2018
Title: Structural Insights into the pH-Dependent Conformational Change and Collagen Recognition of the Human Mannose Receptor
Authors: Hu, Z. / Shi, X. / Yu, B. / Li, N. / Huang, Y. / He, Y.
History
DepositionJun 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 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

Downloads & links

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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
E: Macrophage mannose receptor 1
F: Macrophage mannose receptor 1
G: Macrophage mannose receptor 1
H: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,10622
Polymers435,3038
Non-polymers1,80214
Water0
1
A: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6483
Polymers54,4131
Non-polymers2352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6082
Polymers54,4131
Non-polymers1951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6483
Polymers54,4131
Non-polymers2352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6483
Polymers54,4131
Non-polymers2352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6483
Polymers54,4131
Non-polymers2352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6483
Polymers54,4131
Non-polymers2352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6082
Polymers54,4131
Non-polymers1951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Macrophage mannose receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6483
Polymers54,4131
Non-polymers2352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.819, 164.768, 164.596
Angle α, β, γ (deg.)91.11, 97.56, 97.50
Int Tables number1
Space group name H-MP1

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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.: 8 / Fragment: UNP residues 22-490
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
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% (v/v) tacsimate (pH 6.0), 0.1M MES monohydrate (pH 6.0), 25% (w/v) polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.2→27.942 Å / Num. obs: 72181 / % possible obs: 96.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 7.8
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.091 / Rsym value: 0.382 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data processing
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XTS

5xts


Resolution: 3.2→27.942 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 2006 2.8 %
Rwork0.2108 --
obs0.2118 71602 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→27.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28510 0 102 0 28612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229457
X-RAY DIFFRACTIONf_angle_d0.51839938
X-RAY DIFFRACTIONf_dihedral_angle_d9.81417373
X-RAY DIFFRACTIONf_chiral_restr0.044073
X-RAY DIFFRACTIONf_plane_restr0.0035031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1999-3.27980.33361500.28324694X-RAY DIFFRACTION91
3.2798-3.36840.33691310.26445087X-RAY DIFFRACTION96
3.3684-3.46730.27691400.25844736X-RAY DIFFRACTION95
3.4673-3.5790.33821510.24415077X-RAY DIFFRACTION97
3.579-3.70670.24781550.22344969X-RAY DIFFRACTION97
3.7067-3.85470.27691330.21885029X-RAY DIFFRACTION97
3.8547-4.02970.25121400.20625107X-RAY DIFFRACTION98
4.0297-4.24140.24231540.19064977X-RAY DIFFRACTION98
4.2414-4.50610.23191540.18225070X-RAY DIFFRACTION97
4.5061-4.85240.20281400.17715103X-RAY DIFFRACTION98
4.8524-5.33760.17631500.17135029X-RAY DIFFRACTION97
5.3376-6.1030.21931420.19925047X-RAY DIFFRACTION98
6.103-7.66280.29251430.2164962X-RAY DIFFRACTION97
7.6628-27.94350.19851230.21414709X-RAY DIFFRACTION91

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