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- PDB-2pkd: Crystal structure of CD84: Insite into SLAM family function -

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Basic information

Entry
Database: PDB / ID: 2pkd
TitleCrystal structure of CD84: Insite into SLAM family function
ComponentsSLAM family member 5
KeywordsSIGNALING PROTEIN / SLAM / signaling lymphocyte activation molecule / IgV / immunoglobulin variable / IgC / immunoglobulin constant
Function / homology
Function and homology information


negative regulation of granulocyte macrophage colony-stimulating factor production / negative regulation of interleukin-18 production / negative regulation of mast cell degranulation / regulation of store-operated calcium entry / negative regulation of mast cell activation / leukocyte migration / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / Cell surface interactions at the vascular wall / defense response ...negative regulation of granulocyte macrophage colony-stimulating factor production / negative regulation of interleukin-18 production / negative regulation of mast cell degranulation / regulation of store-operated calcium entry / negative regulation of mast cell activation / leukocyte migration / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / Cell surface interactions at the vascular wall / defense response / autophagy / adaptive immune response / innate immune response / intracellular membrane-bounded organelle / identical protein binding / plasma membrane
Similarity search - Function
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
SLAM family member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.043 Å
AuthorsYan, Q. / Malashkevich, V.N. / Fedorov, A. / Cao, E. / Lary, J.W. / Cole, J.L. / Nathenson, S.G. / Almo, S.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of CD84 provides insight into SLAM family function.
Authors: Yan, Q. / Malashkevich, V.N. / Fedorov, A. / Fedorov, E. / Cao, E. / Lary, J.W. / Cole, J.L. / Nathenson, S.G. / Almo, S.C.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SLAM family member 5
B: SLAM family member 5
C: SLAM family member 5
D: SLAM family member 5
E: SLAM family member 5
F: SLAM family member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0148
Polymers75,9436
Non-polymers712
Water7,080393
1
A: SLAM family member 5
B: SLAM family member 5


Theoretical massNumber of molelcules
Total (without water)25,3142
Polymers25,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SLAM family member 5
E: SLAM family member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3854
Polymers25,3142
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: SLAM family member 5
F: SLAM family member 5


Theoretical massNumber of molelcules
Total (without water)25,3142
Polymers25,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.013, 170.982, 148.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-556-

HOH

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Components

#1: Protein
SLAM family member 5 / Signaling lymphocytic activation molecule 5 / Leukocyte differentiation antigen CD84 / CD84 antigen ...Signaling lymphocytic activation molecule 5 / Leukocyte differentiation antigen CD84 / CD84 antigen / Cell surface antigen MAX.3 / Hly9-beta


Mass: 12657.157 Da / Num. of mol.: 6 / Fragment: CD84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD84, SLAMF5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UIB8
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 0.3 M MgCl2, 0.1 M, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.961, 0.9797, 0.9794
SYNCHROTRONNSLS X29A21.1
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDSep 26, 2005X9A
ADSC QUANTUM 3152CCDSep 26, 2005X29A
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1X9AMADMx-ray1
2X29ASINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9611
20.97971
30.97941
41.11
Reflection

D res low: 40 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
8.91122897830.0721.072.363244099.7
8.92142868940.0631.132.363236499.5
7.7311.62612920.0621.052.3233974100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.084099.910.0481.7898.8
4.035.0810010.051.119.2
3.524.0310010.0621.0459.3
3.23.5210010.0771.0419.3
2.973.210010.1041.0339.3
2.82.9710010.1420.9389.2
2.662.810010.1950.9489
2.542.6610010.2560.9388.7
2.442.5410010.3410.8978.5
2.362.4496.710.3630.8797.9
5.084099.720.0461.9218.7
4.035.0810020.0451.2899.1
3.524.0310020.0541.1899.2
3.23.5210020.0651.0729.2
2.973.210020.0851.0739.2
2.82.9710020.1140.9639.1
2.662.810020.1490.9458.9
2.542.6610020.190.9388.7
2.442.5499.920.2470.9038.5
2.362.4495.320.2660.887.9
54099.930.0331.5027.5
3.97510030.0341.0527.8
3.473.9710030.0481.0047.9
3.153.4710030.0670.9927.9
2.923.1510030.1070.9857.9
2.752.9210030.1640.9577.9
2.612.7510030.2381.0047.8
2.52.6110030.3310.9947.6
2.42.510030.4321.0187.5
2.322.410030.4581.0047.1
ReflectionResolution: 1.98→50 Å / Num. obs: 39739 / % possible obs: 90.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Χ2: 2.127 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.98-2.051.30.4068100.52415.1
2.05-2.131.60.27818880.61735.2
2.13-2.2320.26431070.67357.5
2.23-2.352.50.25339670.86573.3
2.35-2.492.90.21945810.96885.1
2.49-2.693.30.18550291.05292.8
2.69-2.963.60.13651751.31995.4
2.96-3.393.60.09852642.18495.9
3.39-4.263.60.08254643.95999.2
4.26-503.60.05856743.599.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVE2.09phasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.043→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.841 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1999 5 %RANDOM
Rwork0.197 ---
obs0.201 39654 79.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.174 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.043→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5243 0 2 393 5638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225366
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9477344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8215649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46623.712264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9115855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5921542
X-RAY DIFFRACTIONr_chiral_restr0.1360.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024166
X-RAY DIFFRACTIONr_nbd_refined0.2410.22280
X-RAY DIFFRACTIONr_nbtor_refined0.3210.23523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2306
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.230
X-RAY DIFFRACTIONr_mcbond_it1.561.53346
X-RAY DIFFRACTIONr_mcangle_it2.6825371
X-RAY DIFFRACTIONr_scbond_it3.41232329
X-RAY DIFFRACTIONr_scangle_it5.374.51973
LS refinement shellResolution: 2.043→2.096 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 50 -
Rwork0.241 862 -
obs-912 25.5 %

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