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- PDB-4bfi: Structure of the complex of the extracellular portions of mouse C... -

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Basic information

Entry
Database: PDB / ID: 4bfi
TitleStructure of the complex of the extracellular portions of mouse CD200R and mouse CD200
Components
  • CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 1
  • OX-2 MEMBRANE GLYCOPROTEIN
KeywordsIMMUNE SYSTEM / PAIRED RECEPTOR / IG DOMAINS / VIRAL MIMICRY / LEUKAEMIA MIMICRY / LEUKAEMIA
Function / homology
Function and homology information


negative regulation of macrophage activation / negative regulation of neuroinflammatory response / cell-cell adhesion mediator activity / regulation of neuroinflammatory response / presynaptic active zone / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of immune response / signaling receptor activity / receptor complex / postsynaptic density ...negative regulation of macrophage activation / negative regulation of neuroinflammatory response / cell-cell adhesion mediator activity / regulation of neuroinflammatory response / presynaptic active zone / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of immune response / signaling receptor activity / receptor complex / postsynaptic density / negative regulation of cell population proliferation / external side of plasma membrane / cell surface / plasma membrane
Similarity search - Function
OX-2 membrane glycoprotein / : / Cell surface glycoprotein CD200 receptor / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...OX-2 membrane glycoprotein / : / Cell surface glycoprotein CD200 receptor / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CYSTEINE / OX-2 membrane glycoprotein / Cell surface glycoprotein CD200 receptor 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsHatherley, D. / Lea, S.M. / Johnson, S. / Barclay, A.N.
CitationJournal: Structure / Year: 2013
Title: Structures of Cd200/Cd200 Receptor Family and Implications for Topology, Regulation, and Evolution
Authors: Hatherley, D. / Lea, S.M. / Johnson, S. / Barclay, A.N.
History
DepositionMar 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2May 29, 2013Group: 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 1
B: OX-2 MEMBRANE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,92215
Polymers47,3052
Non-polymers2,61713
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint29.4 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.170, 128.170, 116.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Antibody / Sugars , 3 types, 13 molecules AB

#1: Protein CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 1 / CD200 CELL SURFACE GLYCOPROTEIN RECEPTOR / CELL SURFACE GLYCOPROTEIN OX2 RECEPTOR 1


Mass: 23586.258 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: Q9ES57
#2: Antibody OX-2 MEMBRANE GLYCOPROTEIN / MRC OX-2 ANTIGEN


Mass: 23718.795 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 31-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: O54901
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 29 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsNUMBERING IN THE PDB IS BASED ON THE MATURE SEQUENCE AS DETERMINED BY N-TERMINAL SEQUENCING.

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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: 4.48 Å3/Da / Density % sol: 73 % / Description: NONE
Crystal growpH: 7 / Details: 1.0M IMIDAZOLE PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.984
DetectorType: ADSC CCD / Detector: CCD / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.22→86.04 Å / Num. obs: 16034 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2
Reflection shellResolution: 3.22→3.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSXIA2data reduction
XSCALEXIA2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BFG

4bfg


Resolution: 3.22→86.04 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.879 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.756 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25097 819 5.1 %RANDOM
Rwork0.19894 ---
obs0.20151 15284 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.502 Å2
Baniso -1Baniso -2Baniso -3
1-3.92 Å20 Å20 Å2
2--3.92 Å20 Å2
3----7.85 Å2
Refinement stepCycle: LAST / Resolution: 3.22→86.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 165 27 3220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023274
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9974476
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01125.246122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48715518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.648159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212387
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.221→3.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 42 -
Rwork0.313 990 -
obs--99.33 %

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