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- PDB-5qu2: Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY -

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Basic information

Entry
Database: PDB / ID: 5qu2
TitleCrystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY
Components
  • ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2
  • Cytoplasmic protein NCK1
KeywordsSIGNALING PROTEIN / SH3 DOMAIN / ADAPTOR / PEPTIDE BINDING / DOMAIN SWAP
Function / homology
Function and homology information


positive regulation of cap-dependent translational initiation / regulation of translation initiation in response to endoplasmic reticulum stress / eukaryotic initiation factor eIF2 binding / positive regulation of translation in response to endoplasmic reticulum stress / gamma-delta T cell receptor complex / protein phosphatase type 1 complex / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of cap-independent translational initiation / T cell anergy / positive regulation of cell-cell adhesion mediated by integrin ...positive regulation of cap-dependent translational initiation / regulation of translation initiation in response to endoplasmic reticulum stress / eukaryotic initiation factor eIF2 binding / positive regulation of translation in response to endoplasmic reticulum stress / gamma-delta T cell receptor complex / protein phosphatase type 1 complex / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of cap-independent translational initiation / T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of T cell anergy / gamma-delta T cell activation / CD4-positive, alpha-beta T cell proliferation / cytoskeletal anchor activity / negative thymic T cell selection / substrate-dependent cell migration, cell extension / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / positive thymic T cell selection / signal complex assembly / Activation of RAC1 / Nephrin family interactions / DCC mediated attractive signaling / vesicle membrane / lamellipodium assembly / positive regulation of cell-matrix adhesion / T cell receptor complex / RHOV GTPase cycle / negative regulation of T cell receptor signaling pathway / smoothened signaling pathway / protein kinase inhibitor activity / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of interleukin-4 production / positive regulation of actin filament polymerization / negative regulation of PERK-mediated unfolded protein response / dendrite development / RHOU GTPase cycle / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / T cell receptor binding / T cell costimulation / ephrin receptor binding / signaling adaptor activity / positive regulation of T cell proliferation / antiviral innate immune response / positive regulation of interleukin-2 production / Downstream signal transduction / positive regulation of calcium-mediated signaling / negative regulation of insulin receptor signaling pathway / protein sequestering activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cell surface receptor protein tyrosine kinase signaling pathway / regulation of cell migration / response to endoplasmic reticulum stress / T cell activation / actin filament organization / cerebellum development / negative regulation of smoothened signaling pathway / FCGR3A-mediated phagocytosis / apoptotic signaling pathway / calcium-mediated signaling / molecular condensate scaffold activity / PKR-mediated signaling / receptor tyrosine kinase binding / positive regulation of neuron projection development / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / VEGFA-VEGFR2 Pathway / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / Downstream TCR signaling / cell migration / cell-cell junction / T cell receptor signaling pathway / signaling receptor complex adaptor activity / cell body / protein-containing complex assembly / protein-macromolecule adaptor activity / regulation of apoptotic process / dendritic spine / adaptive immune response / Potential therapeutics for SARS / cell surface receptor signaling pathway / ribosome / cadherin binding / G protein-coupled receptor signaling pathway / protein domain specific binding / external side of plasma membrane / signaling receptor binding / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / : / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM ...Nck1, SH3 domain 1 / Nck1, SH3 domain 2 / Nck1, SH3 domain 3 / Nck1, SH2 domain / Cytoplasmic protein NCK / : / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / SH3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 epsilon chain / SH2/SH3 adapter protein NCK1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsRudolph, M.G.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Small molecule AX-024 reduces T cell proliferation independently of CD3ε/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain.
Authors: Richter, K. / Rufer, A.C. / Muller, M. / Burger, D. / Casagrande, F. / Grossenbacher, T. / Huber, S. / Hug, M.N. / Koldewey, P. / D'Osualdo, A. / Schlatter, D. / Stoll, T. / Rudolph, M.G.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 26, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1May 12, 2021Group: Derived calculations / Structure summary / Category: pdbx_deposit_group / struct_conn
Item: _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_type ..._pdbx_deposit_group.group_description / _pdbx_deposit_group.group_type / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_value_order / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.2Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 2.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytoplasmic protein NCK1
B: Cytoplasmic protein NCK1
D: ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2
E: ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7317
Polymers16,4434
Non-polymers2883
Water3,117173
1
A: Cytoplasmic protein NCK1
D: ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5095
Polymers8,2212
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-31 kcal/mol
Surface area4620 Å2
MethodPISA
2
B: Cytoplasmic protein NCK1
E: ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2


Theoretical massNumber of molelcules
Total (without water)8,2212
Polymers8,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-8 kcal/mol
Surface area4360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.650, 63.340, 99.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

21A-273-

HOH

31A-276-

HOH

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Components

#1: Protein Cytoplasmic protein NCK1 / NCK adaptor protein 1 / Nck-1 / SH2/SH3 adaptor protein NCK-alpha


Mass: 7202.144 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCK1, NCK / Plasmid: PET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16333
#2: Protein/peptide ACE-PRO-PRO-PRO-VAL-PRO-ASN-PRO-ASP-TYR-NH2


Mass: 1019.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P07766*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris/HCl pH 6.5, 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 1.05→49.89 Å / Num. obs: 67794 / % possible obs: 90.5 % / Redundancy: 6.57 % / Biso Wilson estimate: 18.642 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.075 / Χ2: 0.792 / Net I/σ(I): 9.61 / Num. measured all: 445579 / Scaling rejects: 407
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.05-1.085.9094.5590.3221739548636790.2254.99167.1
1.08-1.116.7887.1610.2729984536244170.3417.7582.4
1.11-1.146.7613.540.5729641516743840.4883.83584.8
1.14-1.176.3372.4650.827982509544160.5992.68586.7
1.17-1.216.8141.9681.0829172489442810.7022.1387.5
1.21-1.266.8281.471.4328799472842180.781.5989.2
1.26-1.36.6221.181.8327745459741900.8261.2891.1
1.3-1.366.3470.9632.0826262442041380.8991.04993.6
1.36-1.426.8910.6143.4627702423940200.9520.66394.8
1.42-1.486.90.4514.6226716405638720.9710.48795.5
1.48-1.576.7740.2956.725272387937310.9850.31996.2
1.57-1.666.3910.1979.1622617366335390.9910.21596.6
1.66-1.777.0690.13913.423687344933510.9950.1597.2
1.77-1.926.7670.09418.5421146322031250.9970.10297
1.92-2.16.4320.06924.7818628296728960.9970.07597.6
2.1-2.355.7470.05329.1915265271526560.9970.05997.8
2.35-2.716.6230.04535.8315583239223530.9980.04998.4
2.71-3.326.2530.03740.6412675205320270.9990.0498.7
3.32-4.75.7210.03242.19028160715780.9980.03598.2
4.7-49.896.4310.0345.5959369439230.9990.03297.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.04→49.89 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.575 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2156 4.9 %RANDOM
Rwork0.1659 ---
obs0.1679 41808 57.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.79 Å2 / Biso mean: 14.791 Å2 / Biso min: 7.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.89 Å2
Refinement stepCycle: final / Resolution: 1.04→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 30 176 1309
Biso mean--23.7 28.11 -
Num. residues----132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131220
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171110
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.6681666
X-RAY DIFFRACTIONr_angle_other_deg1.6231.5982598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85222.15279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.87715215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8541510
X-RAY DIFFRACTIONr_chiral_restr0.10.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021341
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02261
X-RAY DIFFRACTIONr_rigid_bond_restr4.9132328
LS refinement shellResolution: 1.045→1.072 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 15 -
Rwork0.384 239 -
all-254 -
obs--4.57 %

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