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- PDB-3jqh: Structure of the neck region of the glycan-binding receptor DC-SIGNR -

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Basic information

Entry
Database: PDB / ID: 3jqh
TitleStructure of the neck region of the glycan-binding receptor DC-SIGNR
ComponentsC-type lectin domain family 4 member M
KeywordsSUGAR BINDING PROTEIN / DC-SIGNR / four-helix bundle / oligomerization domain / Alternative splicing / Calcium / Cell membrane / Disulfide bond / Endocytosis / Glycoprotein / Host-virus interaction / Immune response / Lectin / Mannose-binding / Membrane / Metal-binding / Polymorphism / Receptor / Secreted / Signal-anchor / Transmembrane
Function / homology
Function and homology information


cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding ...cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding / receptor-mediated endocytosis of virus by host cell / viral genome replication / peptide antigen binding / calcium-dependent protein binding / signaling receptor activity / host cell / virus receptor activity / carbohydrate binding / adaptive immune response / receptor-mediated virion attachment to host cell / intracellular signal transduction / immune response / symbiont entry into host cell / external side of plasma membrane / innate immune response / virion attachment to host cell / extracellular region / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / 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
Similarity search - Domain/homology
C-type lectin domain family 4 member M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.201 Å
AuthorsFeinberg, H. / Tso, C.K.W. / Taylor, M.E. / Drickamer, K. / Weis, W.I.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Segmented helical structure of the neck region of the glycan-binding receptor DC-SIGNR.
Authors: Feinberg, H. / Tso, C.K. / Taylor, M.E. / Drickamer, K. / Weis, W.I.
History
DepositionSep 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-type lectin domain family 4 member M


Theoretical massNumber of molelcules
Total (without water)19,1391
Polymers19,1391
Non-polymers00
Water37821
1
A: C-type lectin domain family 4 member M
x 24


Theoretical massNumber of molelcules
Total (without water)459,33324
Polymers459,33324
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_557x,y,z+21
crystal symmetry operation1_558x,y,z+31
crystal symmetry operation1_559x,y,z+41
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation2_566-x,-y+1,z+11
crystal symmetry operation2_567-x,-y+1,z+21
crystal symmetry operation2_568-x,-y+1,z+31
crystal symmetry operation2_569-x,-y+1,z+41
crystal symmetry operation2_564-x,-y+1,z-11
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation3_556-y+1/2,x+1/2,z+11
crystal symmetry operation3_557-y+1/2,x+1/2,z+21
crystal symmetry operation3_558-y+1/2,x+1/2,z+31
crystal symmetry operation3_559-y+1/2,x+1/2,z+41
crystal symmetry operation3_554-y+1/2,x+1/2,z-11
crystal symmetry operation4_455y-1/2,-x+1/2,z1
crystal symmetry operation4_456y-1/2,-x+1/2,z+11
crystal symmetry operation4_457y-1/2,-x+1/2,z+21
crystal symmetry operation4_458y-1/2,-x+1/2,z+31
crystal symmetry operation4_459y-1/2,-x+1/2,z+41
crystal symmetry operation4_454y-1/2,-x+1/2,z-11
Buried area4670 Å2
ΔGint-52 kcal/mol
Surface area5660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.17, 34.17, 36.72
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-142-

HOH

21A-160-

HOH

DetailsThe biological assembly is a four helix bundle, extending 7 repeats along c axis. Symmetry operations for 6 repeats are shown while last repeat is disordered.

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Components

#1: Protein C-type lectin domain family 4 member M / CD209 antigen-like protein 1 / Dendritic cell-specific ICAM-3-grabbing non-integrin 2 / DC-SIGN2 / ...CD209 antigen-like protein 1 / Dendritic cell-specific ICAM-3-grabbing non-integrin 2 / DC-SIGN2 / DC-SIGN-related protein / DC-SIGNR / Liver/lymph node-specific ICAM-3-grabbing non-integrin / L-SIGN


Mass: 19138.871 Da / Num. of mol.: 1 / Fragment: UNP residues 101-264, neck domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC4M, CD209L, CD209L1, CD299 / Plasmid: pT5T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 / References: UniProt: Q9H2X3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE COMPLETE SEQUENCE HAS 7 REPEATS AND THE ASYMMETRIC UNIT CONTAINS 1 REPEAT OF 23 RESIDUES. THE ...THE COMPLETE SEQUENCE HAS 7 REPEATS AND THE ASYMMETRIC UNIT CONTAINS 1 REPEAT OF 23 RESIDUES. THE MODEL IN COORDINATES REPRESENTS THE AVERAGE OF FIRST 6 REPEATS WITH ALTERNATE CONFORMATION AT 1 AND 15. THE 7TH REPEAT IS DISORDERED. GELSEKSKLQEIYQELTQLKAAVGEL PEKSKLQEIYQELTRLKAAVGEL PEKSKLQEIYQELTRLKAAVGEL PEKSKLQEIYQELTRLKAAVGEL PEKSKLQEIYQELTELKAAVGEL PEKSKLQEIYQELTQLKAAVGEL PDQSKQQQIYQELTDLKTAFERLGHH

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 2.8 mg/ml protein, 10 mM Tris-Cl, pH 8.0, and 25 mM NaCl. Reservoir solution: 9% polyethylene glycol 6000, 1.25 M NaCl and 0.1 Bis-Tris, pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.2→36.719 Å / Num. obs: 1283 / % possible obs: 99.9 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.126 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
PHENIXmodel building
CNSrefinement
Blu-Iceicedata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.201→36.719 Å / SU ML: 0.53 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 64 5.03 %
Rwork0.1936 --
obs0.195 1272 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 124.697 Å2 / ksol: 0.385 e/Å3
Refinement stepCycle: LAST / Resolution: 2.201→36.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms217 0 0 21 238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007223
X-RAY DIFFRACTIONf_angle_d0.957298
X-RAY DIFFRACTIONf_dihedral_angle_d14.39194
X-RAY DIFFRACTIONf_chiral_restr0.04233
X-RAY DIFFRACTIONf_plane_restr0.00339
LS refinement shellResolution: 2.201→2.32 Å / Num. reflection Rwork: 1208

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