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- PDB-2oya: Crystal structure analysis of the dimeric form of the SRCR domain... -

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Basic information

Entry
Database: PDB / ID: 2oya
TitleCrystal structure analysis of the dimeric form of the SRCR domain of mouse MARCO
ComponentsMacrophage receptor MARCO
KeywordsLIGAND BINDING PROTEIN / Extracellular matrix / Scavenger receptor cysteine-rich (SRCR) / macrophage receptor / ligand binding / basic cluster / acidic cluster / sulfate binding / dimer
Function / homology
Function and homology information


Scavenging by Class A Receptors / collagen trimer / apoptotic cell clearance / cargo receptor activity / phagocytosis, engulfment / amyloid-beta clearance / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / extracellular matrix / receptor-mediated endocytosis / G protein-coupled receptor binding ...Scavenging by Class A Receptors / collagen trimer / apoptotic cell clearance / cargo receptor activity / phagocytosis, engulfment / amyloid-beta clearance / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / extracellular matrix / receptor-mediated endocytosis / G protein-coupled receptor binding / endocytosis / amyloid-beta binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / innate immune response / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
: / Mac-2 Binding Protein / SRCR-like domain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich ...: / Mac-2 Binding Protein / SRCR-like domain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Roll / Alpha Beta
Similarity search - Domain/homology
Macrophage receptor MARCO
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsOjala, J.R.M. / Pikkarainen, T. / Tuuttila, A. / Sandalova, T. / Tryggvason, K.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the cysteine-rich domain of scavenger receptor MARCO reveals the presence of a basic and an acidic cluster that both contribute to ligand recognition.
Authors: Ojala, J.R. / Pikkarainen, T. / Tuuttila, A. / Sandalova, T. / Tryggvason, K.
History
DepositionFeb 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 31, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_biol ...entity_src_gen / struct_biol / struct_ref_seq_dif / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Macrophage receptor MARCO
B: Macrophage receptor MARCO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9635
Polymers22,6752
Non-polymers2883
Water3,459192
1
A: Macrophage receptor MARCO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5293
Polymers11,3371
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrophage receptor MARCO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4332
Polymers11,3371
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-42 kcal/mol
Surface area9760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)31.087, 36.553, 44.605
Angle α, β, γ (deg.)116.30, 90.35, 96.41
Int Tables number1
Space group name H-MP1
DetailsBiological unit is a monomer. There are two biological units in the asymmetric unit (chains A & B)

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Components

#1: Protein Macrophage receptor MARCO / Macrophage receptor with collagenous structure


Mass: 11337.281 Da / Num. of mol.: 2
Fragment: C-terminal domain, scavenger receptor cysteine-rich domain (SRCR)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: Marco / Plasmid: pCEP-PU / Cell (production host): embryonic kidney cells / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human) / References: UniProt: Q60754
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7% PEG 4000, 0.1M Bis-Tris, 0.1M Lithium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.097 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.097 Å / Relative weight: 1
ReflectionResolution: 1.77→14.912 Å / Num. all: 17081 / Num. obs: 16364 / % possible obs: 95.4 % / Observed criterion σ(F): 0.013 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 13.8
Reflection shellResolution: 1.77→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 9.1 / Num. measured all: 7835 / Num. unique all: 2282 / Rsym value: 0.074 / % possible all: 89.4

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Phasing

Phasing MRRfactor: 0.428 / Cor.coef. Fo:Fc: 0.519
Highest resolutionLowest resolution
Rotation3 Å14.91 Å
Translation3 Å14.91 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OY3

2oy3


Resolution: 1.77→14.912 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.108 / SU ML: 0.069 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1644 10 %RANDOM
Rwork0.15 ---
obs0.154 16364 95.81 %-
all-17081 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.18 Å2-0.04 Å2
2--0.08 Å2-0.06 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.77→14.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 15 192 1791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211695
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.8952316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82824.34399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45315245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.791516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021398
X-RAY DIFFRACTIONr_nbd_refined0.1880.2808
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.233
X-RAY DIFFRACTIONr_mcbond_it0.7611.51060
X-RAY DIFFRACTIONr_mcangle_it1.20321649
X-RAY DIFFRACTIONr_scbond_it2.1373753
X-RAY DIFFRACTIONr_scangle_it3.0984.5667
LS refinement shellResolution: 1.77→1.815 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 110 -
Rwork0.184 1072 -
obs-1182 90.23 %

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