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- PDB-9ofx: Crystal structure of c-Src SH3 domain in H32 space group mediated... -

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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 / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of integrin activation ...regulation of caveolin-mediated endocytosis / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / cellular response to progesterone stimulus / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of integrin activation / BMP receptor binding / negative regulation of focal adhesion assembly / Activated NTRK2 signals through FYN / intestinal epithelial cell development / focal adhesion assembly / Netrin mediated repulsion signals / negative regulation of neutrophil activation / bone resorption / positive regulation of small GTPase mediated signal transduction / connexin binding / Activated NTRK3 signals through PI3K / signal complex assembly / regulation of vascular permeability / Co-stimulation by CD28 / EPH-Ephrin signaling / podosome / positive regulation of lamellipodium morphogenesis / DCC mediated attractive signaling / regulation of bone resorption / Regulation of RUNX1 Expression and Activity / stress fiber assembly / Ephrin signaling / Signal regulatory protein family interactions / negative regulation of mitochondrial depolarization / leukocyte migration / MET activates PTK2 signaling / Regulation of KIT signaling / cellular response to peptide hormone stimulus / regulation of early endosome to late endosome transport / Signaling by ALK / phospholipase activator activity / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / positive regulation of Rac protein signal transduction / stimulatory C-type lectin receptor signaling pathway / Receptor Mediated Mitophagy / Signaling by EGFR / negative regulation of intrinsic apoptotic signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / regulation of cell-cell adhesion / GRB2:SOS provides linkage to MAPK signaling for Integrins / progesterone receptor signaling pathway / RHOU GTPase cycle / Recycling pathway of L1 / positive regulation of epithelial cell migration / RET signaling / regulation of heart rate by cardiac conduction / FCGR activation / signaling receptor activator activity / negative regulation of anoikis / Long-term potentiation / EPH-ephrin mediated repulsion of cells / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / transforming growth factor beta receptor signaling pathway / GAB1 signalosome / negative regulation of hippo signaling / protein tyrosine kinase activator activity / T cell costimulation / Nuclear signaling by ERBB4 / lactation / osteoclast differentiation / negative regulation of protein-containing complex assembly / ephrin receptor binding / phospholipase binding / Signaling by ERBB2 / Integrin signaling / p38MAPK events / EPHB-mediated forward signaling / positive regulation of TORC1 signaling / peptidyl-tyrosine phosphorylation / NCAM signaling for neurite out-growth / Downstream signal transduction / FCGR3A-mediated IL10 synthesis / ionotropic glutamate receptor binding / positive regulation of glycolytic process / SH2 domain binding / integrin-mediated signaling pathway / response to interleukin-1 / negative regulation of extrinsic apoptotic signaling pathway / Downregulation of ERBB4 signaling / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / InlA-mediated entry of Listeria monocytogenes into host cells / angiotensin-activated signaling pathway
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 / 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
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
Revision 1.2Jan 7, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
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

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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

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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 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

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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

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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

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