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- PDB-4bfe: Structure of the extracellular portion of mouse CD200RLa -

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Basic information

Entry
Database: PDB / ID: 4bfe
TitleStructure of the extracellular portion of mouse CD200RLa
ComponentsCELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 4
KeywordsIMMUNE SYSTEM / PAIRED RECEPTOR / IG DOMAINS / VIRAL MIMICRY / LEUKAEMIA
Function / homology
Function and homology information


regulation of neuroinflammatory response / signaling receptor activity / external side of plasma membrane
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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CYSTEINE / Cell surface glycoprotein CD200 receptor 4
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 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 1.4Oct 23, 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 ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 4
B: CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 4
C: CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,64231
Polymers73,0123
Non-polymers4,63028
Water11,079615
1
A: CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7579
Polymers24,3371
Non-polymers1,4198
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,85310
Polymers24,3371
Non-polymers1,5159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,03312
Polymers24,3371
Non-polymers1,69611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.590, 157.590, 167.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-2068-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.27144, 0.91928, -0.28503), (-0.07914, 0.27383, 0.95852), (0.9592, 0.28274, -0.00158)14.82477, 35.66623, -52.97234
2given(-0.24956, -0.10291, 0.96288), (0.93669, 0.22655, 0.26699), (-0.24562, 0.96855, 0.03985)58.12469, -5.4725, -32.83457

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Components

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Protein / Sugars , 2 types, 18 molecules ABC

#1: Protein CELL SURFACE GLYCOPROTEIN CD200 RECEPTOR 4 / CD200 CELL SURFACE GLYCOPROTEIN RECEPTOR-LIKE 4 / CD200 RECEPTOR-LIKE 4 / CD200 CELL SURFACE ...CD200 CELL SURFACE GLYCOPROTEIN RECEPTOR-LIKE 4 / CD200 RECEPTOR-LIKE 4 / CD200 CELL SURFACE GLYCOPROTEIN RECEPTOR-LIKE A / CD200RLA / CELL SURFACE GLYCOPROTEIN OX2 RECEPTOR 4


Mass: 24337.213 Da / Num. of mol.: 3 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-238
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: Q6XJV4
#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.: 15
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, 628 molecules

#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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 ...NUMBERING IN THE PDB IS BASED ON THE START OF THE MATURE SEQUENCE, AS DETERMINED BY N-TERMINAL SEQUENCING ON THE HOMOLOGUE MCD200R.

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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: 3.72 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growpH: 6.5
Details: 2.0M AMMONIUM SULFATE, 0.1M SODIUM CACODYLATE, 0.2M SODIUM CHLORIDE, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→168.02 Å / Num. obs: 42242 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 56.43 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.9526 / Cor.coef. Fo:Fc free: 0.9332 / SU R Cruickshank DPI: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.246 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 2115 5.07 %RANDOM
Rwork0.1714 ---
obs0.1731 41716 97.51 %-
Displacement parametersBiso mean: 48.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.2215 Å20 Å20 Å2
2---2.2215 Å20 Å2
3---4.4431 Å2
Refine analyzeLuzzati coordinate error obs: 0.274 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 284 615 5195
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014701HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.236456HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1626SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes674HARMONIC5
X-RAY DIFFRACTIONt_it4701HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion16.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion704SEMIHARMONIC5
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_contact5121SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2911 137 4.6 %
Rwork0.2481 2840 -
all0.2501 2977 -
obs--97.51 %

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