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- PDB-3zhg: Crystallographic structure of the native mouse SIGN-R1 CRD domain -

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Basic information

Entry
Database: PDB / ID: 3zhg
TitleCrystallographic structure of the native mouse SIGN-R1 CRD domain
Components(CD209 ANTIGEN-LIKE PROTEIN B) x 2
KeywordsIMMUNE SYSTEM / C-LECTIN CRD / CAPSULAR POLYSACCHARIDE.
Function / homology
Function and homology information


detection of yeast / (1->3)-beta-D-glucan binding / phagocytosis, recognition / D-mannose binding / polysaccharide binding / detection of bacterium / positive regulation of phagocytosis / endocytosis / positive regulation of tumor necrosis factor production / external side of plasma membrane ...detection of yeast / (1->3)-beta-D-glucan binding / phagocytosis, recognition / D-mannose binding / polysaccharide binding / detection of bacterium / positive regulation of phagocytosis / endocytosis / positive regulation of tumor necrosis factor production / external side of plasma membrane / metal ion binding / membrane
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) ...CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
CD209 antigen-like protein B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSilva-Martin, N. / Bartual, S.G. / Hermoso, J.A.
CitationJournal: Structure / Year: 2014
Title: Structural Basis for Selective Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor Sign-R1.
Authors: Silva-Martin, N. / Bartual, S.G. / Ramirez-Aportela, E. / Chacon, P. / Park, C.G. / Hermoso, J.A.
History
DepositionDec 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Mar 11, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD209 ANTIGEN-LIKE PROTEIN B
B: CD209 ANTIGEN-LIKE PROTEIN B
C: CD209 ANTIGEN-LIKE PROTEIN B
D: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,81126
Polymers71,9214
Non-polymers1,88922
Water7,314406
1
A: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules

A: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,18016
Polymers35,9472
Non-polymers1,23314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules

B: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,60310
Polymers35,9472
Non-polymers6578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
3
C: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules

C: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,18016
Polymers35,9472
Non-polymers1,23314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
4
D: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules

D: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,65910
Polymers36,0032
Non-polymers6578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Unit cell
Length a, b, c (Å)146.720, 92.770, 77.060
Angle α, β, γ (deg.)90.00, 121.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CD209 ANTIGEN-LIKE PROTEIN B / SIGN-R1 / DC-SIGN-RELATED PROTEIN 1 / DC-SIGNR1 / OTB7 / CD209


Mass: 17973.301 Da / Num. of mol.: 3 / Fragment: CRD, RESIDUES 191-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse)
Cell line (production host): CHINESE HAMSTER OVARY (CHO) CELLS
Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY / References: UniProt: Q8CJ91
#2: Protein CD209 ANTIGEN-LIKE PROTEIN B / SIGN-R1 / DC-SIGN-RELATED PROTEIN 1 / DC-SIGNR1 / OTB7 / CD209


Mass: 18001.314 Da / Num. of mol.: 1 / Fragment: CRD RESIDUES 190-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse)
Cell line (production host): CHINESE HAMSTER OVARY (CHO) CELLS
Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY / References: UniProt: Q8CJ91
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.19 % / Description: NONE
Crystal growDetails: CRYSTALS GROWN BY MIXING 1 UL OF CRD_SIGN-R1 (4 MG/ML IN 20 MM TRIS/HCL PH 7.5 AND 100 MM NACL) WITH 1UL OF PRECIPITANT CONSISTING IN 0.1 M BISTRIS PH 5.5 AND 1.6 M (NH4)2SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 1.87→74.53 Å / Num. obs: 52474 / % possible obs: 93 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 1.87→1.98 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / % possible all: 72

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→27.627 Å / SU ML: 0.27 / σ(F): 1.36 / Phase error: 30.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 3711 7.08 %
Rwork0.2045 --
obs0.2072 52388 72.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.747 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.5068 Å20 Å2-5.0463 Å2
2--9.7241 Å20 Å2
3----2.2172 Å2
Refinement stepCycle: LAST / Resolution: 1.87→27.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4303 0 94 406 4803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114541
X-RAY DIFFRACTIONf_angle_d1.0736148
X-RAY DIFFRACTIONf_dihedral_angle_d18.0561588
X-RAY DIFFRACTIONf_chiral_restr0.074611
X-RAY DIFFRACTIONf_plane_restr0.005758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8701-1.93690.38981050.28451430X-RAY DIFFRACTION21
1.9369-2.01450.2891590.25271993X-RAY DIFFRACTION30
2.0145-2.10610.28092070.25172704X-RAY DIFFRACTION41
2.1061-2.21710.2462660.21113723X-RAY DIFFRACTION55
2.2171-2.35590.27134500.2185336X-RAY DIFFRACTION80
2.3559-2.53770.26515030.21996619X-RAY DIFFRACTION98
2.5377-2.79290.26215150.22596636X-RAY DIFFRACTION99
2.7929-3.19650.26915110.22526703X-RAY DIFFRACTION99
3.1965-4.02530.21864950.17186709X-RAY DIFFRACTION99
4.0253-27.63030.21015000.18046824X-RAY DIFFRACTION99

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