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- PDB-4caj: Crystallographic structure of the mouse SIGN-R1 CRD domain in com... -

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Basic information

Entry
Database: PDB / ID: 4caj
TitleCrystallographic structure of the mouse SIGN-R1 CRD domain in complex with sialic acid
ComponentsCD209 ANTIGEN-LIKE PROTEIN B
KeywordsIMMUNE SYSTEM / C-LECTIN CRD / SIGN-R1 / CAPSULAR POLYSACCHARIDE
Function / homology
Function and homology information


detection of yeast / (1->3)-beta-D-glucan binding / fucose binding / phagocytosis, recognition / polysaccharide binding / D-mannose binding / detection of bacterium / positive regulation of phagocytosis / endocytosis / positive regulation of tumor necrosis factor production ...detection of yeast / (1->3)-beta-D-glucan binding / fucose binding / phagocytosis, recognition / polysaccharide binding / D-mannose binding / detection of bacterium / positive regulation of phagocytosis / endocytosis / positive regulation of tumor necrosis factor production / immune response / external side of plasma membrane / membrane / metal ion binding
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) / C-type lectin-like/link domain superfamily ...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
N-acetyl-alpha-neuraminic acid / CD209 antigen-like protein B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.191 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. / Rodriguez, A. / Ramirez, E. / Chacon, P. / Anthony, R.M. / Park, C.G. / Hermoso, J.A.
History
DepositionOct 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: 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)75,93443
Polymers71,8934
Non-polymers4,04139
Water8,395466
1
A: CD209 ANTIGEN-LIKE PROTEIN B
B: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,21823
Polymers35,9472
Non-polymers2,27121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-211.1 kcal/mol
Surface area13650 Å2
MethodPISA
2
C: CD209 ANTIGEN-LIKE PROTEIN B
D: CD209 ANTIGEN-LIKE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,71620
Polymers35,9472
Non-polymers1,77018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-211 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.200, 94.470, 76.140
Angle α, β, γ (deg.)90.00, 121.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2066-

HOH

21B-2076-

HOH

31C-2086-

HOH

41D-2075-

HOH

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Components

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Protein / Sugars , 2 types, 7 molecules ABCD

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


Mass: 17973.301 Da / Num. of mol.: 4 / Fragment: CRD, RESIDUES 191-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: Q8CJ91
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 502 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

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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: 3.67 Å3/Da / Density % sol: 66.49 % / 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 BISTRISPH 5.5 AND 1.6 M (NH4)2SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→42.95 Å / Num. obs: 50858 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 30.84 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZHG

3zhg


Resolution: 2.191→14.948 Å / SU ML: 0.45 / σ(F): 1.33 / Phase error: 34.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2812 2273 5.1 %
Rwork0.2053 --
obs0.2093 44455 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.191→14.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 0 219 466 4976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184629
X-RAY DIFFRACTIONf_angle_d1.4416280
X-RAY DIFFRACTIONf_dihedral_angle_d13.2491575
X-RAY DIFFRACTIONf_chiral_restr0.059626
X-RAY DIFFRACTIONf_plane_restr0.008758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.191-2.23850.36321300.36822482X-RAY DIFFRACTION91
2.2385-2.29040.40531530.34762472X-RAY DIFFRACTION94
2.2904-2.34750.38481300.32312552X-RAY DIFFRACTION95
2.3475-2.41070.35051290.31172556X-RAY DIFFRACTION96
2.4107-2.48130.35691440.29282614X-RAY DIFFRACTION97
2.4813-2.5610.32291370.28162633X-RAY DIFFRACTION98
2.561-2.65210.39751390.27922642X-RAY DIFFRACTION99
2.6521-2.75770.34481370.2662657X-RAY DIFFRACTION99
2.7577-2.88230.31641460.25692672X-RAY DIFFRACTION100
2.8823-3.03310.34271500.24332698X-RAY DIFFRACTION100
3.0331-3.22130.26091370.20352708X-RAY DIFFRACTION100
3.2213-3.46720.30021530.17632688X-RAY DIFFRACTION100
3.4672-3.81080.23981240.13682683X-RAY DIFFRACTION100
3.8108-4.35040.16991540.12432704X-RAY DIFFRACTION100
4.3504-5.43680.20151540.12132697X-RAY DIFFRACTION100
5.4368-14.94820.2921560.18192724X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.46820.53290.79490.86140.06340.25910.0109-0.2029-0.08530.0908-0.0041-0.0258-0.0093-0.1284-0.06550.2430.0091-0.19670.70950.05630.41728.85330.269528.4049
23.8579-1.8193-2.35943.11324.51487.1932-0.0596-0.5889-0.17440.46320.5285-0.74190.42890.6437-0.49660.17260.064-0.04960.63490.05780.51520.94783.568615.7006
32.5023-0.37411.25011.0977-0.69381.3939-0.0013-0.0153-0.24010.0562-0.0821-0.1656-0.0420.0228-0.01680.0710.0522-0.06920.3481-0.07590.210814.864-6.47717.3471
40.23740.25390.14430.38160.26840.20470.0369-0.0422-0.1211-0.11050.06170.15610.02130.03980.19310.29220.0797-0.1890.64750.03220.37857.66032.340412.9111
56.7673-0.46164.0143.3152-1.04344.46460.21260.5558-0.4712-0.36290.08620.08130.39420.5805-0.30410.35870.0182-0.2450.6863-0.0530.49889.7504-12.15565.1925
66.3902-2.77913.84681.2086-1.67282.31540.15780.0061-0.3478-0.4064-0.11120.71930.1587-0.36860.04920.437-0.1846-0.2210.7536-0.09150.5861-0.2313-6.99588.0466
76.2035-0.08073.62012.18970.97273.40920.06630.88080.0992-0.3268-0.0510.0143-0.02090.40370.11060.22190.0267-0.08860.77640.10540.40612.00950.64313.5335
82.52291.9401-0.19535.6293-3.5493.01030.256-1.29790.18250.4797-0.15870.51050.0084-0.6536-0.090.2412-0.1247-0.03520.839-0.01520.31388.0538-5.012427.4337
92.6848-0.54372.19051.4268-0.46571.7878-0.06830.13960.1837-0.1249-0.09710.059-0.04840.1566-0.04280.20170.0443-0.14140.60050.0610.340410.308411.958826.4589
105.4652-5.2677-1.09845.58890.32451.2743-0.3894-0.05180.61870.26750.2539-0.56950.18920.58370.14990.38830.1885-0.10190.7190.21430.53463.92139.248143.6822
114.91690.40753.42471.83710.53982.4216-0.17130.07670.2101-0.07770.0655-0.0006-0.17340.35810.14390.22520.0469-0.01590.82210.06360.22922.488718.859637.2108
121.0374-0.68770.0460.4582-0.06230.3049-0.1132-0.1093-0.0475-0.0147-0.06690.1525-0.08810.0975-0.11650.2251-0.0466-0.09940.8430.01620.4422-4.6979.932333.0087
132.92441.1635-0.88072.61370.41061.8536-0.2379-1.39441.04590.3436-0.08350.3028-0.3034-0.47640.27760.27630.0818-0.10970.8574-0.18480.4172-10.833924.53137.927
142.12441.29091.68250.86281.19181.6981-0.06010.24430.0674-0.176-0.01910.1175-0.09740.0460.07130.2952-0.0029-0.22440.74340.03220.6144-12.939118.940628.1367
157.5537-2.25381.79921.8011-0.53420.6351-0.0432-0.9812-0.06710.2029-0.00350.2511-0.0323-0.34380.00650.2211-0.0494-0.02960.92360.02290.3389-11.053511.835541.1756
164.0013.887-0.59117.8783-2.15550.6966-0.15850.6903-0.3504-0.641-0.1412-0.80060.03980.19440.31020.22690.05620.04610.81540.11580.35439.558617.268625.0832
174.869-0.15142.90442.15040.3751.83280.0106-0.6686-0.06190.1741-0.0120.125-0.0137-0.34230.11750.187-0.0084-0.09730.67680.02150.355123.332-2.956838.1343
183.61.855-2.44441.1256-1.78153.26260.05690.08940.1382-0.07670.10530.3094-0.0879-0.2308-0.20550.45470.0996-0.23020.61270.1270.383929.6424-6.151821.0468
191.5393-0.49280.30111.28370.09540.3786-0.05280.05190.0632-0.0461-0.03850.0788-0.1033-0.07670.11020.14950.0364-0.14390.35660.06230.257831.01243.9527.177
203.88472.29293.66031.42632.04953.61760.11610.0111-0.11270.08520.0509-0.24450.11140.0373-0.17770.14120.0529-0.07760.50330.09080.329137.1875-8.233935.9502
212.80820.12260.82610.7037-0.01480.2471-0.02120.18650.2522-0.02530.0169-0.1775-0.03950.1611-0.04140.1716-0.0186-0.08920.7913-0.00020.437142.02940.899327.5808
223.4978-1.05681.7832.0822-0.55890.90910.16550.80770.1299-0.185-0.2585-0.210.02490.52350.17010.17110.0049-0.1010.35910.12990.290822.9175-14.18730.7483
231.3736-0.32420.07370.4983-0.08351.3733-0.0703-0.15670.03860.10580.0897-0.0098-0.0659-0.1807-0.0130.19170.0797-0.06020.68790.05550.333121.758-13.724543.1955
249.23830.5048-0.34583.61470.33332.0484-0.04110.031-0.7396-0.0535-0.0416-0.18830.0238-0.19330.07760.19780.1150.00850.7327-0.08060.339319.0023-21.494347.2391
250.6814-0.37050.12680.7531-0.50280.36310.01030.2511-0.08760.0520.1016-0.07-0.041-0.12960.01960.2671-0.0095-0.12270.88140.05820.413125.9918-12.517251.8144
267.97132.86893.0414.05512.08194.31720.389-0.8028-0.72710.4298-0.2241-0.12690.51-0.5674-0.19660.2309-0.1421-0.13420.55240.06560.498524.406-27.1759.4468
274.08423.01612.82812.75772.2151.98850.0594-0.0074-0.27070.30660.0509-0.58710.04930.3036-0.09710.29450.0431-0.20420.72190.00210.600334.1514-21.520956.8458
284.3407-1.22211.53041.1457-0.37171.29160.0627-0.5636-0.02740.12460.00450.07330.046-0.1402-0.03890.22450.01070.00150.9884-0.01330.261721.6564-14.37361.1514
290.641-0.7018-1.57673.68791.51953.8925-0.05920.26840.1011-0.48470.2403-0.42270.33630.8796-0.16170.32450.04820.00330.8148-0.05410.222825.7294-19.775536.8469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 192 THROUGH 209 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 210 THROUGH 215 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 216 THROUGH 235 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 236 THROUGH 259 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 260 THROUGH 269 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 270 THROUGH 280 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 281 THROUGH 313 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 314 THROUGH 322 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 191 THROUGH 209 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 210 THROUGH 215 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 216 THROUGH 235 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 236 THROUGH 259 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 260 THROUGH 269 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 270 THROUGH 280 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 281 THROUGH 313 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 314 THROUGH 323 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 191 THROUGH 209 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 210 THROUGH 215 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 216 THROUGH 235 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 236 THROUGH 249 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 250 THROUGH 322 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 191 THROUGH 199 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 200 THROUGH 215 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 216 THROUGH 235 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 236 THROUGH 259 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 260 THROUGH 269 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 270 THROUGH 280 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 281 THROUGH 313 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 314 THROUGH 322 )

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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