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- PDB-6h6a: Crystal structure of UNC119 in complex with LCK peptide -

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Basic information

Entry
Database: PDB / ID: 6h6a
TitleCrystal structure of UNC119 in complex with LCK peptide
Components
  • (Protein unc-119 homolog ...) x 2
  • GLY-CYS-GLY-CYS-SER-SER
KeywordsIMMUNE SYSTEM / Complex / Transport / Kinase
Function / homology
Function and homology information


negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / Nef and signal transduction / CD4 receptor binding ...negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / Nef and signal transduction / CD4 receptor binding / Nef Mediated CD4 Down-regulation / positive regulation of heterotypic cell-cell adhesion / Interleukin-2 signaling / CD28 dependent Vav1 pathway / lipoprotein transport / Regulation of KIT signaling / leukocyte migration / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / intercellular bridge / phospholipase activator activity / CD8 receptor binding / pericentriolar material / positive regulation of T cell receptor signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / phototransduction / mitotic cytokinesis / hemopoiesis / positive regulation of protein tyrosine kinase activity / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / spindle midzone / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / T cell receptor binding / peptidyl-tyrosine autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / GPVI-mediated activation cascade / release of sequestered calcium ion into cytosol / T cell costimulation / phosphotyrosine residue binding / visual perception / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / non-specific protein-tyrosine kinase / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / : / platelet activation / peptidyl-tyrosine phosphorylation / spindle pole / endocytosis / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of T cell activation / Downstream TCR signaling / PIP3 activates AKT signaling / DAP12 signaling / nervous system development / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / protein phosphatase binding / chemical synaptic transmission / intracellular signal transduction / response to xenobiotic stimulus / protein phosphorylation / membrane raft / innate immune response / signaling receptor binding / centrosome / lipid binding / synapse / protein kinase binding / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 domain / Coagulation Factor XIII; Chain A, domain 1 / : / SH3 domain ...: / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 domain / Coagulation Factor XIII; Chain A, domain 1 / : / SH3 domain / SH2 domain / Distorted Sandwich / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin E-set / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / PHOSPHATE ION / Tyrosine-protein kinase Lck / Protein unc-119 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsYelland, T. / ElMaghloob, Y. / McIlwraith, M. / Stephen, L. / Ismail, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Dev.Cell / Year: 2018
Title: The Ciliary Machinery Is Repurposed for T Cell Immune Synapse Trafficking of LCK.
Authors: Stephen, L.A. / ElMaghloob, Y. / McIlwraith, M.J. / Yelland, T. / Castro Sanchez, P. / Roda-Navarro, P. / Ismail, S.
History
DepositionJul 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Nov 27, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Protein unc-119 homolog A
E: GLY-CYS-GLY-CYS-SER-SER
G: Protein unc-119 homolog A
H: GLY-CYS-GLY-CYS-SER-SER
J: Protein unc-119 homolog A
K: GLY-CYS-GLY-CYS-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,24819
Polymers67,1996
Non-polymers3,05013
Water4,720262
1
D: Protein unc-119 homolog A
E: GLY-CYS-GLY-CYS-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3536
Polymers22,4102
Non-polymers1,9424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-8 kcal/mol
Surface area8760 Å2
MethodPISA
2
G: Protein unc-119 homolog A
H: GLY-CYS-GLY-CYS-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9026
Polymers22,3942
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-3 kcal/mol
Surface area8410 Å2
MethodPISA
3
J: Protein unc-119 homolog A
K: GLY-CYS-GLY-CYS-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9947
Polymers22,3942
Non-polymers6005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-8 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.090, 63.620, 188.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21G
12D
22J
13G
23J

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 59 - 238 / Label seq-ID: 1 - 180

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11DA
21GC
12DA
22JE
13GC
23JE

NCS ensembles :
ID
1
2
3

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Components

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Protein unc-119 homolog ... , 2 types, 3 molecules DGJ

#1: Protein Protein unc-119 homolog A / Retinal protein 4 / hRG4


Mass: 21418.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNC119, RG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13432
#3: Protein Protein unc-119 homolog A / Retinal protein 4 / hRG4


Mass: 21402.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNC119, RG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13432

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Protein/peptide , 1 types, 3 molecules EHK

#2: Protein/peptide GLY-CYS-GLY-CYS-SER-SER


Mass: 992.023 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P06239*PLUS

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Non-polymers , 5 types, 275 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O2
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 20% PEG 3350 200mM KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→94.08 Å / Num. obs: 39393 / % possible obs: 99.8 % / Redundancy: 6.5 % / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2→94.08 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.437 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 2072 5 %RANDOM
Rwork0.17095 ---
obs0.17298 39393 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.557 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20 Å2
2--0.02 Å20 Å2
3----2.75 Å2
Refinement stepCycle: 1 / Resolution: 2→94.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 110 262 4578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194524
X-RAY DIFFRACTIONr_bond_other_d0.0030.024188
X-RAY DIFFRACTIONr_angle_refined_deg0.6911.9676082
X-RAY DIFFRACTIONr_angle_other_deg0.5139668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58823.077234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95115732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2851536
X-RAY DIFFRACTIONr_chiral_restr0.0640.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021122
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0352.4472105
X-RAY DIFFRACTIONr_mcbond_other3.0352.4462103
X-RAY DIFFRACTIONr_mcangle_it4.0593.6292634
X-RAY DIFFRACTIONr_mcangle_other4.0593.6292635
X-RAY DIFFRACTIONr_scbond_it4.7422.9872419
X-RAY DIFFRACTIONr_scbond_other4.7352.9872419
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.964.2643447
X-RAY DIFFRACTIONr_long_range_B_refined8.90420.5195005
X-RAY DIFFRACTIONr_long_range_B_other8.90620.5235006
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D99180.11
12G99180.11
21D97130.1
22J97130.1
31G97870.12
32J97870.12
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 146 -
Rwork0.223 2875 -
obs--99.54 %
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)
10.03080.0338-0.08870.4237-0.08050.50890.0177-0.017-0.02410.0293-0.01140.0355-0.13040.0133-0.00630.03550.00210.01130.02370.0180.0596-5.8843-4.62535.653
20.19670.17610.0320.2057-0.1621.06190.0148-0.02430.0541-0.0252-0.01360.02440.1949-0.0812-0.00120.0403-0.01560.00950.01160.00490.0641-28.4005-36.576825.531
30.2819-0.22180.20920.2790.12471.05640.00940.0297-0.00110.0281-0.00380.01960.18950.0906-0.00560.06760.0135-0.03110.01140.0020.030811.4334-25.4452-36.8875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D59 - 238
2X-RAY DIFFRACTION2G59 - 238
3X-RAY DIFFRACTION3J59 - 238

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