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- PDB-5b1r: Crystal structure of mouse CD72a CTLD -

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Basic information

Entry
Database: PDB / ID: 5b1r
TitleCrystal structure of mouse CD72a CTLD
ComponentsB-cell differentiation antigen CD72
KeywordsIMMUNE SYSTEM / C-type lectin / B-cell
Function / homology
Function and homology information


Other semaphorin interactions / transmembrane signaling receptor activity / carbohydrate binding / plasma membrane
Similarity search - Function
B-cell differentiation antigen CD72-like / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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
ACETATE ION / B-cell differentiation antigen CD72
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsShinagawa, K. / Numoto, N. / Tsubata, T. / Ito, N.
CitationJournal: J.Exp.Med. / Year: 2016
Title: CD72 negatively regulates B lymphocyte responses to the lupus-related endogenous toll-like receptor 7 ligand Sm/RNP
Authors: Akatsu, C. / Shinagawa, K. / Numoto, N. / Liu, Z. / Ucar, A.K. / Aslam, M. / Phoon, S. / Adachi, T. / Furukawa, K. / Ito, N. / Tsubata, T.
History
DepositionDec 15, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 8, 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
Revision 1.5Oct 23, 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

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Assembly

Deposited unit
A: B-cell differentiation antigen CD72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3663
Polymers15,2151
Non-polymers1512
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-0 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.472, 65.472, 61.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein B-cell differentiation antigen CD72 / Lyb-2 / Lymphocyte antigen 32 / Ly-32


Mass: 15215.128 Da / Num. of mol.: 1 / Fragment: UNP residues 232-354 / Mutation: C234S, C338S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd72, Ly-32, Ly32, Lyb-2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P21855
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThis sequence is based on GenBank entry AAA37237.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: imidazole, sodium acetate trihydrate, hexamine cobalt (III) chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 46533 / % possible obs: 99.8 % / Redundancy: 11 % / Rsym value: 0.087 / Net I/σ(I): 42.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FM5

1fm5


Resolution: 1.2→26.936 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1479 2354 5.06 %
Rwork0.1284 --
obs0.1294 46487 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 1.2→26.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 10 170 1165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081048
X-RAY DIFFRACTIONf_angle_d1.2061406
X-RAY DIFFRACTIONf_dihedral_angle_d14.12399
X-RAY DIFFRACTIONf_chiral_restr0.075135
X-RAY DIFFRACTIONf_plane_restr0.007175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2001-1.22460.22621500.20582596X-RAY DIFFRACTION100
1.2246-1.25120.24391430.18812567X-RAY DIFFRACTION100
1.2512-1.28030.20991420.17272586X-RAY DIFFRACTION100
1.2803-1.31230.15241370.16022607X-RAY DIFFRACTION100
1.3123-1.34780.15791390.14522566X-RAY DIFFRACTION100
1.3478-1.38740.16881550.12922584X-RAY DIFFRACTION100
1.3874-1.43220.15551420.12092592X-RAY DIFFRACTION100
1.4322-1.48340.13261280.10832595X-RAY DIFFRACTION100
1.4834-1.54280.13051300.09522618X-RAY DIFFRACTION100
1.5428-1.6130.11541260.09262598X-RAY DIFFRACTION100
1.613-1.6980.12291500.09952593X-RAY DIFFRACTION100
1.698-1.80440.11431500.10112587X-RAY DIFFRACTION100
1.8044-1.94370.13261370.10692595X-RAY DIFFRACTION100
1.9437-2.13920.14541380.10862620X-RAY DIFFRACTION100
2.1392-2.44860.14151280.1282612X-RAY DIFFRACTION100
2.4486-3.08420.16781190.14132643X-RAY DIFFRACTION100
3.0842-26.94230.14531400.1452574X-RAY DIFFRACTION97

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