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- PDB-7yqe: Structure of human SRC regulatory domains in complex with the C-t... -

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Basic information

Entry
Database: PDB / ID: 7yqe
TitleStructure of human SRC regulatory domains in complex with the C-terminal PRRP motifs of GPR54.
ComponentsProto-oncogene tyrosine-protein kinase Src,KiSS-1 receptor
KeywordsSIGNALING PROTEIN / PROTEIN KINASE-LIKE / SIGNALING / COMPLEX
Function / homology
Function and homology information


neuropeptide receptor activity / regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium ...neuropeptide receptor activity / regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / regulation of cell-cell adhesion / response to mineralocorticoid / positive regulation of dephosphorylation / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / entry of bacterium into host cell / positive regulation of protein transport / Regulation of gap junction activity / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / regulation of vascular permeability / Activated NTRK2 signals through FYN / positive regulation of integrin activation / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / : / intestinal epithelial cell development / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / G protein-coupled peptide receptor activity / response to acidic pH / focal adhesion assembly / signal complex assembly / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / podosome / regulation of bone resorption / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / branching involved in mammary gland duct morphogenesis / adherens junction organization / DCC mediated attractive signaling / myoblast proliferation / EPH-Ephrin signaling / odontogenesis / negative regulation of mitochondrial depolarization / Ephrin signaling / cellular response to peptide hormone stimulus / osteoclast development / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / Regulation of KIT signaling / Signaling by ALK / postsynaptic specialization, intracellular component / Receptor Mediated Mitophagy / CTLA4 inhibitory signaling / GP1b-IX-V activation signalling / oogenesis / interleukin-6-mediated signaling pathway / leukocyte migration / phospholipase activator activity / DNA biosynthetic process / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of hippo signaling / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / positive regulation of Notch signaling pathway / Signaling by EGFR / cellular response to platelet-derived growth factor stimulus / stress fiber assembly / positive regulation of epithelial cell migration / positive regulation of smooth muscle cell migration / progesterone receptor signaling pathway / RUNX2 regulates osteoblast differentiation / regulation of heart rate by cardiac conduction / Recycling pathway of L1 / dendritic growth cone / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / uterus development / phospholipase binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Long-term potentiation / neurotrophin TRK receptor signaling pathway / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / negative regulation of telomere maintenance via telomerase / negative regulation of anoikis
Similarity search - Function
KiSS-1 peptide receptor / SH3 domain / 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. ...KiSS-1 peptide receptor / SH3 domain / 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 / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase Src / KiSS-1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsSong, G. / Xu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Kisspeptin-10 binding to Gpr54 in osteoclasts prevents bone loss by activating Dusp18-mediated dephosphorylation of Src.
Authors: Li, Z. / Yang, X. / Fu, R. / Wu, Z. / Xu, S. / Jiao, J. / Qian, M. / Zhang, L. / Wu, C. / Xie, T. / Yao, J. / Wu, Z. / Li, W. / Ma, G. / You, Y. / Chen, Y. / Zhang, H.K. / Cheng, Y. / Tang, ...Authors: Li, Z. / Yang, X. / Fu, R. / Wu, Z. / Xu, S. / Jiao, J. / Qian, M. / Zhang, L. / Wu, C. / Xie, T. / Yao, J. / Wu, Z. / Li, W. / Ma, G. / You, Y. / Chen, Y. / Zhang, H.K. / Cheng, Y. / Tang, X. / Wu, P. / Lian, G. / Wei, H. / Zhao, J. / Xu, J. / Ai, L. / Siwko, S. / Wang, Y. / Ding, J. / Song, G. / Luo, J. / Liu, M. / Xiao, J.
History
DepositionAug 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src,KiSS-1 receptor
B: Proto-oncogene tyrosine-protein kinase Src,KiSS-1 receptor


Theoretical massNumber of molelcules
Total (without water)42,8102
Polymers42,8102
Non-polymers00
Water00
1
A: Proto-oncogene tyrosine-protein kinase Src,KiSS-1 receptor


  • defined by author
  • Evidence: gel filtration, There is an intermolecular disulfide between the two monomers in the asymmetric unit but this is definitely because of lattice packing as the full length SRC is monomeric ...Evidence: gel filtration, There is an intermolecular disulfide between the two monomers in the asymmetric unit but this is definitely because of lattice packing as the full length SRC is monomeric and the truncation exposed a cysteine that generate the intermolecular disulfide bond. the fragment used for crystallization is monomer.
  • 21.4 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)21,4051
Polymers21,4051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene tyrosine-protein kinase Src,KiSS-1 receptor


Theoretical massNumber of molelcules
Total (without water)21,4051
Polymers21,4051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.245, 95.245, 122.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 87 through 249 or (resid 250...
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 87 through 249 or (resid 250...A87 - 249
121(chain A and (resid 87 through 249 or (resid 250...A250
131(chain A and (resid 87 through 249 or (resid 250...A87 - 344
141(chain A and (resid 87 through 249 or (resid 250...A87 - 344
151(chain A and (resid 87 through 249 or (resid 250...A87 - 344
161(chain A and (resid 87 through 249 or (resid 250...A87 - 344
211chain BB87 - 339

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src,KiSS-1 receptor / Proto-oncogene c-Src / pp60c-src / p60-Src / KiSS-1R / G-protein coupled receptor 54 / G-protein ...Proto-oncogene c-Src / pp60c-src / p60-Src / KiSS-1R / G-protein coupled receptor 54 / G-protein coupled receptor OT7T175 / hOT7T175 / Hypogonadotropin-1 / Kisspeptins receptor / Metastin receptor


Mass: 21404.910 Da / Num. of mol.: 2 / Mutation: C338S,C340S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1, KISS1R, AXOR12, GPR54 / Production host: Escherichia coli (E. coli)
References: UniProt: P12931, UniProt: Q969F8, non-specific protein-tyrosine kinase

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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: 3.76 Å3/Da / Density % sol: 67.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1% v/v 1,4 Dioxane, 0.1 M Tris pH 7.5, 12.5% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 83 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.5→82.9 Å / Num. obs: 8144 / % possible obs: 97.4 % / Redundancy: 19.1 % / Biso Wilson estimate: 129.62 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.039 / Rrim(I) all: 0.167 / Rsym value: 0.167 / Net I/σ(I): 12.7
Reflection shellResolution: 3.5→3.599 Å / Redundancy: 18.4 % / Rmerge(I) obs: 1.536 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 395 / CC1/2: 0.76 / Rpim(I) all: 0.365 / Rrim(I) all: 1.579 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2src

2src


Resolution: 3.5→19.97 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2946 800 9.93 %
Rwork0.2677 7257 -
obs0.2703 8057 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.89 Å2 / Biso mean: 142.0594 Å2 / Biso min: 107.1 Å2
Refinement stepCycle: final / Resolution: 3.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 0 0 2736
Num. residues----341
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1024X-RAY DIFFRACTION4.199TORSIONAL
12B1024X-RAY DIFFRACTION4.199TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.720.42361410.378412271368100
3.72-40.34421000.3405926102673
4-4.40.34861360.315912391375100
4.4-5.030.30881410.260612691410100
5.03-6.30.26711420.271512631405100
6.31-19.970.25341400.22113331473100
Refinement TLS params.Method: refined / Origin x: 27.0864 Å / Origin y: -9.6621 Å / Origin z: -4.8424 Å
111213212223313233
T0.7898 Å20.1614 Å20.0158 Å2-0.8978 Å20.2359 Å2--1.0752 Å2
L2.1449 °2-0.8293 °2-2.2065 °2-1.9502 °22.1643 °2--3.8391 °2
S-0.195 Å °0.0845 Å °0.0909 Å °0.4085 Å °0.2015 Å °-0.424 Å °0.2817 Å °0.1368 Å °0.0919 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA87 - 344
2X-RAY DIFFRACTION1allB87 - 339

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