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- PDB-9qy1: Endo180 (uPARAP) carbohydrate-recognition domain 2 with bound met... -

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Basic information

Entry
Database: PDB / ID: 9qy1
TitleEndo180 (uPARAP) carbohydrate-recognition domain 2 with bound methyl fucoside
ComponentsMannose receptor C type 2
KeywordsSUGAR BINDING PROTEIN / Lectin Endocytosis Endothelial cells
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / collagen catabolic process / collagen binding / endocytosis / carbohydrate binding / membrane
Similarity search - Function
MRC2-like, N-terminal cysteine-rich domain / CD209-like, C-type lectin-like 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 / : / C-type lectin, conserved site ...MRC2-like, N-terminal cysteine-rich domain / CD209-like, C-type lectin-like 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 / : / 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
methyl alpha-L-fucopyranoside / Mannose receptor C-type 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDrickamer, K. / Feinberg, H. / Weis, W.I. / Taylor, M.E. / Jegouzo, S.A.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/V014137/1 United Kingdom
CitationJournal: To Be Published
Title: Sugar binding activity of the endothelial receptor Endo180
Authors: Jegouzo, S.A.F. / Feinberg, H. / Lasanajak, Y. / Smith, D.H. / Weis, W.I. / Drickamer, K. / Taylor, M.E.
History
DepositionApr 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannose receptor C type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2204
Polymers14,9621
Non-polymers2583
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, This is a fragment constituting one folded domain from a larger polypeptide
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-23 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.650, 66.560, 37.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Mannose receptor C type 2


Mass: 14961.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: MRC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3Q1M5H7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.89 Å3/Da / Density % sol: 34.93 %
Crystal growTemperature: 289.5 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Drop: 5.2 mg/ml protein 5 mM CaCl2 10 mM Tris-Cl, pH 8.0 25mM NaCl 50mM alpha-Methyl-Fucoside Reservoir 26% polyethylene glycol 8K 0.1 M Tris-Cl, pH 8.0.

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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: Dec 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 9435 / % possible obs: 100 % / Redundancy: 24.7 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.99 / Rsym value: 0.125 / Net I/σ(I): 21.08
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 22.4 % / Num. unique obs: 922 / CC1/2: 0.992 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.65 Å / SU ML: 0.1898 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.2236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2386 472 5.03 %
Rwork0.1837 8913 -
obs0.1865 9385 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.92 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 14 67 1117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581096
X-RAY DIFFRACTIONf_angle_d0.80541485
X-RAY DIFFRACTIONf_chiral_restr0.0564154
X-RAY DIFFRACTIONf_plane_restr0.0062189
X-RAY DIFFRACTIONf_dihedral_angle_d13.464398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.170.24411540.18392907X-RAY DIFFRACTION99.71
2.18-2.740.27221550.2122917X-RAY DIFFRACTION99.64
2.74-37.650.22481630.17363089X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 9.77750118094 Å / Origin y: 11.4569054019 Å / Origin z: 11.1400383382 Å
111213212223313233
T0.153199167465 Å2-0.0214478960848 Å2-0.000212805574231 Å2-0.181901508825 Å20.00824081621446 Å2--0.223642881584 Å2
L3.2569426406 °20.713088153415 °2-0.234645138704 °2-4.1269059069 °2-0.19061457131 °2--2.10513826244 °2
S-0.0411010200323 Å °0.18351715735 Å °0.0189591627724 Å °-0.0467080784318 Å °0.031689806186 Å °-0.269511239709 Å °-0.0775211944767 Å °0.0259281201237 Å °-0.0260886120554 Å °
Refinement TLS groupSelection details: all

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