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- PDB-2ox9: Mouse Scavenger Receptor C-type Lectin carbohydrate-recognition d... -

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Basic information

Entry
Database: PDB / ID: 2ox9
TitleMouse Scavenger Receptor C-type Lectin carbohydrate-recognition domain.
ComponentsCollectin placenta 1
KeywordsSUGAR BINDING PROTEIN / c-type lectin
Function / homology
Function and homology information


plasma membrane raft organization / low-density lipoprotein particle binding / toll-like receptor 3 signaling pathway / scavenger receptor activity / phagocytosis, recognition / collagen trimer / cellular response to exogenous dsRNA / pattern recognition receptor activity / signaling receptor activity / carbohydrate binding ...plasma membrane raft organization / low-density lipoprotein particle binding / toll-like receptor 3 signaling pathway / scavenger receptor activity / phagocytosis, recognition / collagen trimer / cellular response to exogenous dsRNA / pattern recognition receptor activity / signaling receptor activity / carbohydrate binding / collagen-containing extracellular matrix / defense response to bacterium / immune response / membrane / metal ion binding
Similarity search - Function
CD209-like, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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. ...CD209-like, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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
Lewis X antigen, beta anomer / Collectin-12
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWeis, W.I. / Feinberg, H. / Drickamer, K. / Taylor, M.E.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Scavenger receptor C-type lectin binds to the leukocyte cell surface glycan Lewis(x) by a novel mechanism.
Authors: Feinberg, H. / Taylor, M.E. / Weis, W.I.
History
DepositionFeb 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Collectin placenta 1
B: Collectin placenta 1
C: Collectin placenta 1
D: Collectin placenta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,00324
Polymers65,2444
Non-polymers2,75920
Water6,431357
1
A: Collectin placenta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0016
Polymers16,3111
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collectin placenta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0016
Polymers16,3111
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Collectin placenta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0016
Polymers16,3111
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Collectin placenta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0016
Polymers16,3111
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.998, 53.755, 59.084
Angle α, β, γ (deg.)67.75, 76.70, 85.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Collectin placenta 1 / Collectin sub-family member 12


Mass: 16310.888 Da / Num. of mol.: 4 / Fragment: CRD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Colec12, CL-P1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K4Q8
#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis X antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis X antigen, beta anomer
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: The protein solution contained 6mg ml-1 protein, 9mM CaCl2 , 9mM Tris pH=7.8, 22.5mM NaCl and 5mM Lewisx. The reservoir solution contained 30% Peg 8K, 0.2M NaCl and 0.1 M Imidazole, pH 8.5., ...Details: The protein solution contained 6mg ml-1 protein, 9mM CaCl2 , 9mM Tris pH=7.8, 22.5mM NaCl and 5mM Lewisx. The reservoir solution contained 30% Peg 8K, 0.2M NaCl and 0.1 M Imidazole, pH 8.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.95→53.7 Å / Num. obs: 35627 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.109
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 1.9 % / Rsym value: 0.113 / % possible all: 91.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→53.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 911755.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1785 5 %SHELLS
Rwork0.224 ---
obs-35627 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.431 Å2 / ksol: 0.363622 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å2-2.19 Å20.42 Å2
2--2.44 Å22.48 Å2
3----4.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.95→53.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 160 357 4828
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_scangle_it3.362.5
LS refinement shellResolution: 1.95→2.1 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.312 357 5.1 %
Rwork0.253 6652 -
obs--89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4carbohydrate.param_ncarbohydrate.top_new

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