[English] 日本語
Yorodumi
- PDB-6h6a: Crystal structure of UNC119 in complex with LCK peptide -

+
Open data


ID or keywords:

Loading...

-
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 / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation ...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 / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion / Interleukin-2 signaling / CD28 dependent Vav1 pathway / lipoprotein transport / Regulation of KIT signaling / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / intercellular bridge / leukocyte migration / 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 / RHOH GTPase cycle / hemopoiesis / Generation of second messenger molecules / immunological synapse / positive regulation of protein tyrosine kinase activity / T cell differentiation / mitotic cytokinesis / PD-1 signaling / spindle midzone / phosphatidylinositol 3-kinase binding / T cell receptor binding / positive regulation of intrinsic apoptotic signaling pathway / peptidyl-tyrosine autophosphorylation / release of sequestered calcium ion into cytosol / extrinsic component of cytoplasmic side of plasma membrane / GPVI-mediated activation cascade / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / visual perception / phosphotyrosine residue binding / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / platelet activation / spindle pole / peptidyl-tyrosine phosphorylation / endocytosis / Constitutive Signaling by Aberrant PI3K in Cancer / activation of cysteine-type endopeptidase activity involved in apoptotic process / Downstream TCR signaling / positive regulation of T cell activation / PIP3 activates AKT signaling / DAP12 signaling / nervous system development / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / chemical synaptic transmission / protein phosphatase binding / protein tyrosine kinase activity / intracellular signal transduction / response to xenobiotic stimulus / membrane raft / protein phosphorylation / 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 / Distorted Sandwich / SH2 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 / Distorted Sandwich / SH2 domain / 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 / Immunoglobulin E-set / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010D59 - 238
2010G59 - 238
1020D59 - 238
2020J59 - 238
1030G59 - 238
2030J59 - 238

NCS ensembles :
ID
1
2
3

-
Components

-
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

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more