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- PDB-4wo1: Crystal structure of the DAP12 transmembrane domain in lipid cubi... -

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Basic information

Entry
Database: PDB / ID: 4wo1
TitleCrystal structure of the DAP12 transmembrane domain in lipid cubic phase
ComponentsTYRO protein tyrosine kinase-binding protein
KeywordsSIGNALING PROTEIN / alpha-helix Transmembrane Signaling
Function / homology
Function and homology information


myeloid leukocyte activation / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of receptor localization to synapse / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / positive regulation of natural killer cell activation / negative regulation of transforming growth factor beta1 production / Other semaphorin interactions / positive regulation of microglial cell mediated cytotoxicity ...myeloid leukocyte activation / stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of receptor localization to synapse / positive regulation of macrophage fusion / positive regulation of osteoclast development / microglial cell activation involved in immune response / positive regulation of natural killer cell activation / negative regulation of transforming growth factor beta1 production / Other semaphorin interactions / positive regulation of microglial cell mediated cytotoxicity / neutrophil activation involved in immune response / positive regulation of protein localization to cell surface / apoptotic cell clearance / Signal regulatory protein family interactions / negative regulation of type I interferon production / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / stimulatory C-type lectin receptor signaling pathway / negative regulation of long-term synaptic potentiation / response to axon injury / cellular defense response / forebrain development / osteoclast differentiation / positive regulation of superoxide anion generation / secretory granule membrane / positive regulation of interleukin-1 beta production / DAP12 interactions / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / actin cytoskeleton organization / molecular adaptor activity / protein stabilization / intracellular signal transduction / signaling receptor binding / Neutrophil degranulation / positive regulation of gene expression / cell surface / signal transduction / protein homodimerization activity / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
TYRO protein tyrosine kinase-binding protein
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / TYRO protein tyrosine kinase-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsCall, M.J. / Call, M.E. / Knoblich, K.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1011352 Australia
veskiVIF12 Australia
Australian Research Council (ARC)DP110104369, FT120100145 Australia
CitationJournal: Cell Rep / Year: 2015
Title: Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly.
Authors: Knoblich, K. / Park, S. / Lutfi, M. / van 't Hag, L. / Conn, C.E. / Seabrook, S.A. / Newman, J. / Czabotar, P.E. / Im, W. / Call, M.E. / Call, M.J.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations / Other / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYRO protein tyrosine kinase-binding protein
B: TYRO protein tyrosine kinase-binding protein
C: TYRO protein tyrosine kinase-binding protein
D: TYRO protein tyrosine kinase-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,50311
Polymers13,3244
Non-polymers2,1797
Water55831
1
A: TYRO protein tyrosine kinase-binding protein
D: TYRO protein tyrosine kinase-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7726
Polymers6,6622
Non-polymers1,1104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-12 kcal/mol
Surface area4770 Å2
MethodPISA
2
B: TYRO protein tyrosine kinase-binding protein
C: TYRO protein tyrosine kinase-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7325
Polymers6,6622
Non-polymers1,0703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-18 kcal/mol
Surface area5230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.797, 43.685, 50.605
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-101-

OLC

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Components

#1: Protein/peptide
TYRO protein tyrosine kinase-binding protein / DNAX-activation protein 12 / Killer-activating receptor-associated protein / KAR-associated protein


Mass: 3331.042 Da / Num. of mol.: 4 / Fragment: UNP residues 35-67 / Mutation: M21V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYROBP, DAP12, KARAP / Production host: Escherichia coli (E. coli) / References: UniProt: O43914
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.07
Details: 0.1 M bis-tris propane chloride pH 6.07, 19.7 %w/v PEG 3350, 0.27 M calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.14→33.12 Å / Num. obs: 6316 / % possible obs: 95.74 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.1374 / Net I/σ(I): 15.46

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WOL

4wol


Resolution: 2.14→33.121 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2957 616 9.76 %1
Rwork0.232 ---
obs0.2382 6310 95.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→33.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 122 31 1033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071003
X-RAY DIFFRACTIONf_angle_d0.9821343
X-RAY DIFFRACTIONf_dihedral_angle_d17.335358
X-RAY DIFFRACTIONf_chiral_restr0.031186
X-RAY DIFFRACTIONf_plane_restr0.004153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.35530.32641400.24551300X-RAY DIFFRACTION90
2.3553-2.6960.27941650.23311457X-RAY DIFFRACTION99
2.696-3.39620.29291550.23981475X-RAY DIFFRACTION99
3.3962-33.12540.29471560.22331462X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.55050.1928-1.00491.1521-0.75635.6678-0.11310.2533-0.19680.0722-0.05220.1870.3628-0.19670.16510.1836-0.00520.0349-0.03150.00580.2245-8.47124.0017-24.7847
22.2073-0.03770.80981.03290.36560.4367-0.3654-0.9377-0.49550.57920.0410.13050.45380.81140.47160.716-0.17320.13210.5310.21520.0035-14.6286.5168-4.1275
31.0340.5615-1.63331.5818-2.41185.2986-0.10790.1189-0.00830.2456-0.2525-0.2284-1.3667-0.49980.42550.2570.0205-0.0960.1345-0.04310.2371-17.392813.8845-26.8809
44.7611-1.0299-3.44934.09724.14637.89210.1641-0.74440.23040.58950.1883-0.017-0.88430.1443-0.31430.41860.0698-0.01360.23170.0635-0.0866-18.89412.3421-4.4645
51.03541.4295-1.69793.097-3.02018.50840.22480.0344-0.0125-0.24170.22790.3122-0.13740.1298-0.32870.19480.0013-0.07150.1136-0.05550.3497-19.83553.6687-28.3311
61.20610.1760.54842.4974-0.80448.47810.12550.062-0.1455-0.045-0.0927-0.27280.22050.30710.02030.1710.0073-0.05020.09950.040.2976-5.890113.8042-24.4581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 40 )
2X-RAY DIFFRACTION2chain 'B' and (resid 9 through 12 )
3X-RAY DIFFRACTION3chain 'B' and (resid 13 through 40 )
4X-RAY DIFFRACTION4chain 'C' and (resid 9 through 14 )
5X-RAY DIFFRACTION5chain 'C' and (resid 15 through 40 )
6X-RAY DIFFRACTION6chain 'D' and (resid 9 through 40 )

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