[English] 日本語
Yorodumi
- PDB-7yqe: Structure of human SRC regulatory domains in complex with the C-t... -

+
Open data


ID or keywords:

Loading...

-
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


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / neuropeptide receptor activity / negative regulation of telomere maintenance / response to mineralocorticoid ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / neuropeptide receptor activity / negative regulation of telomere maintenance / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / positive regulation of dephosphorylation / regulation of epithelial cell migration / ERBB2 signaling pathway / positive regulation of protein transport / Regulation of gap junction activity / cellular response to progesterone stimulus / BMP receptor binding / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / positive regulation of integrin activation / Activated NTRK2 signals through FYN / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / negative regulation of neutrophil activation / regulation of vascular permeability / positive regulation of glucose metabolic process / transcytosis / osteoclast development / Activated NTRK3 signals through PI3K / connexin binding / focal adhesion assembly / cellular response to fluid shear stress / adherens junction organization / signal complex assembly / positive regulation of small GTPase mediated signal transduction / response to acidic pH / branching involved in mammary gland duct morphogenesis / G protein-coupled peptide receptor activity / positive regulation of Ras protein signal transduction / Co-stimulation by CD28 / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / positive regulation of podosome assembly / EPH-Ephrin signaling / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / myoblast proliferation / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / podosome / odontogenesis / cellular response to peptide hormone stimulus / MET activates PTK2 signaling / Regulation of KIT signaling / cellular response to fatty acid / postsynaptic specialization, intracellular component / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / oogenesis / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / Receptor Mediated Mitophagy / EPHA-mediated growth cone collapse / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / DNA biosynthetic process / positive regulation of Notch signaling pathway / Signaling by EGFR / stress fiber assembly / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / uterus development / regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / Recycling pathway of L1 / phospholipase binding / regulation of heart rate by cardiac conduction / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / dendritic growth cone / platelet-derived growth factor receptor signaling pathway / RHOU GTPase cycle / protein tyrosine kinase activator activity / negative regulation of anoikis / RET signaling / Long-term potentiation / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / positive regulation of bone resorption
Similarity search - Function
KiSS-1 peptide receptor / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains ...KiSS-1 peptide receptor / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / 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
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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
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://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