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- PDB-4bfg: Structure of the extracellular portion of mouse CD200R -

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Basic information

Entry
Database: PDB / ID: 4bfg
TitleStructure of the extracellular portion of mouse CD200R
ComponentsCELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 1
KeywordsIMMUNE SYSTEM / PAIRED RECEPTOR / IG DOMAINS / VIRAL MIMICRY / LEUKAEMIA
Function / homology
Function and homology information


negative regulation of T cell migration / negative regulation of macrophage migration / protein binding involved in heterotypic cell-cell adhesion / negative regulation of neuroinflammatory response / regulation of neuroinflammatory response / heterotypic cell-cell adhesion / negative regulation of interleukin-6 production / signaling receptor activity / receptor complex / external side of plasma membrane / cell surface
Similarity search - Function
Cell surface glycoprotein CD200 receptor / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Cell surface glycoprotein CD200 receptor / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / AZIDE ION / CYSTEINE / Cell surface glycoprotein CD200 receptor 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 18, 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 1.5Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5318
Polymers23,5861
Non-polymers9457
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.970, 51.970, 175.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Sugars , 2 types, 4 molecules A

#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: 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.: 3
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 , 4 types, 152 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#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.: 148 / 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 START OF 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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 4
Details: 15% PEG4000, 0.1M SODIUM ACETATE, 0.2M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.08→38.84 Å / Num. obs: 15423 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 34.49 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BFE

4bfe


Resolution: 2.08→15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9204 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.159
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 758 4.99 %RANDOM
Rwork0.1984 ---
obs0.2001 15182 99.86 %-
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.6032 Å20 Å20 Å2
2---5.6032 Å20 Å2
3---11.2064 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: LAST / Resolution: 2.08→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 60 148 1653
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011554HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.322134HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d525SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes225HARMONIC5
X-RAY DIFFRACTIONt_it1554HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.97
X-RAY DIFFRACTIONt_other_torsion17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion234SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1791SEMIHARMONIC4
LS refinement shellResolution: 2.08→2.22 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2696 125 4.7 %
Rwork0.2364 2532 -
all0.238 2657 -
obs--99.86 %

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