[English] 日本語
Yorodumi
- PDB-9ofx: Crystal structure of c-Src SH3 domain in H32 space group mediated... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ofx
TitleCrystal structure of c-Src SH3 domain in H32 space group mediated by nickel
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsSIGNALING PROTEIN / SH3 domain / nickel / Src / ATCUN
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / negative regulation of focal adhesion assembly / BMP receptor binding / positive regulation of integrin activation / positive regulation of protein processing / 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 / focal adhesion assembly / connexin binding / osteoclast development / Activated NTRK3 signals through PI3K / cellular response to fluid shear stress / signal complex assembly / positive regulation of small GTPase mediated signal transduction / branching involved in mammary gland duct morphogenesis / Co-stimulation by CD28 / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / EPH-Ephrin signaling / positive regulation of podosome assembly / positive regulation of lamellipodium morphogenesis / regulation of bone resorption / Ephrin signaling / Signal regulatory protein family interactions / odontogenesis / negative regulation of mitochondrial depolarization / podosome / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / Regulation of KIT signaling / regulation of early endosome to late endosome transport / Signaling by ALK / leukocyte migration / phospholipase activator activity / oogenesis / Co-inhibition by CTLA4 / GP1b-IX-V activation signalling / EPHA-mediated growth cone collapse / Receptor Mediated Mitophagy / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / stress fiber assembly / positive regulation of Notch signaling pathway / Signaling by EGFR / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / regulation of cell-cell adhesion / uterus development / PECAM1 interactions / Recycling pathway of L1 / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of heart rate by cardiac conduction / RHOU GTPase cycle / protein tyrosine kinase activator activity / RET signaling / signaling receptor activator activity / negative regulation of anoikis / FCGR activation / Long-term potentiation / positive regulation of epithelial cell migration / progesterone receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / EPH-ephrin mediated repulsion of cells / GAB1 signalosome / ephrin receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / negative regulation of hippo signaling / bone resorption / negative regulation of protein-containing complex assembly / Nuclear signaling by ERBB4 / phospholipase binding / ephrin receptor binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / p38MAPK events / Signaling by ERBB2 / Integrin signaling / EPHB-mediated forward signaling / ionotropic glutamate receptor binding / positive regulation of TORC1 signaling / NCAM signaling for neurite out-growth / Downregulation of ERBB4 signaling / SH2 domain binding
Similarity search - Function
: / 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 / 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 / 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 / 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
NICKEL (II) ION / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsStiegler, A.L. / Calicdan, X. / Ha, B.H. / Fisher, O.S. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
CitationJournal: Protein Pept.Lett. / Year: 2025
Title: Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization.
Authors: Calicdan, X. / Fisher, O.S. / Ha, B.H. / Boggon, T.J. / Stiegler, A.L.
History
DepositionApr 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
C: Proto-oncogene tyrosine-protein kinase Src
D: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,42715
Polymers26,4814
Non-polymers94611
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-42 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.770, 63.770, 271.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-327-

HOH

-
Components

#1: Protein
Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 6620.198 Da / Num. of mol.: 4 / Fragment: c-Src SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Plasmid: pET28a(+)
Details (production host): contains Thrombin and TEV cleavage sequences
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: P12931, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.6 % / Description: rectangular prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7 M Ammonium Sulfate, 5 mM NiCl2, 10% glycerol, 0.1 M HEPES pH 7.5
Temp details: ambient temperature

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cold Nitrogen gas stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979315 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2024
RadiationMonochromator: horizontal bounce Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979315 Å / Relative weight: 1
ReflectionResolution: 1.45→31.95 Å / Num. obs: 73036 / % possible obs: 100 % / Redundancy: 52.6 % / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.012 / Rrim(I) all: 0.087 / Χ2: 1.06 / Net I/av σ(I): 22.9 / Net I/σ(I): 22.9
Reflection shellResolution: 1.45→1.48 Å / % possible obs: 100 % / Redundancy: 46.8 % / Rmerge(I) obs: 3.467 / Num. measured all: 90146 / Num. unique obs: 1925 / CC1/2: 0.784 / Rpim(I) all: 0.509 / Rrim(I) all: 3.505 / Χ2: 1.29 / Net I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimless0.7.15data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→31.89 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 3450 4.72 %Random selection
Rwork0.1625 ---
obs0.1642 73036 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.07 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 56 163 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051985
X-RAY DIFFRACTIONf_angle_d0.8792704
X-RAY DIFFRACTIONf_dihedral_angle_d12.48691
X-RAY DIFFRACTIONf_chiral_restr0.08294
X-RAY DIFFRACTIONf_plane_restr0.005341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.37451370.27882734X-RAY DIFFRACTION100
1.47-1.490.261380.25522794X-RAY DIFFRACTION100
1.49-1.510.28581370.23172807X-RAY DIFFRACTION100
1.51-1.540.27961380.21242757X-RAY DIFFRACTION100
1.54-1.560.24761400.19812799X-RAY DIFFRACTION100
1.56-1.590.23981390.1892796X-RAY DIFFRACTION100
1.59-1.620.2281360.18362737X-RAY DIFFRACTION100
1.62-1.650.22041420.17782803X-RAY DIFFRACTION100
1.65-1.680.20611370.17442765X-RAY DIFFRACTION100
1.68-1.720.23681380.16772798X-RAY DIFFRACTION100
1.72-1.760.20611390.16532764X-RAY DIFFRACTION100
1.76-1.80.32041300.16282790X-RAY DIFFRACTION100
1.8-1.850.23291350.15062797X-RAY DIFFRACTION100
1.85-1.910.19031400.15332771X-RAY DIFFRACTION100
1.91-1.970.19551420.14062776X-RAY DIFFRACTION100
1.97-2.040.17251370.14132811X-RAY DIFFRACTION100
2.04-2.120.20161350.14932803X-RAY DIFFRACTION100
2.12-2.220.20621410.16192774X-RAY DIFFRACTION100
2.22-2.330.18531350.15232800X-RAY DIFFRACTION100
2.33-2.480.25621390.17432759X-RAY DIFFRACTION100
2.48-2.670.22321330.17892806X-RAY DIFFRACTION100
2.67-2.940.19211340.18292776X-RAY DIFFRACTION100
2.94-3.360.17941420.15812797X-RAY DIFFRACTION100
3.36-4.240.15311410.14572789X-RAY DIFFRACTION100
4.24-31.890.18371450.15882783X-RAY DIFFRACTION100

+
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