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- PDB-6dm4: Crystal structure of the SH2 domain from RavO (Lpg1129) from Legi... -

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Basic information

Entry
Database: PDB / ID: 6dm4
TitleCrystal structure of the SH2 domain from RavO (Lpg1129) from Legionella pneumophila in complex with Homo sapiens Shc1 phospho-Tyr317 peptide
Components
  • RavO
  • Shc1 phospho-Tyr317 peptide
KeywordsPROTEIN BINDING / SH2 domain / Src homolog 2 domain / Shc1 / phosphopeptide binding / LEGIONELLA PNEUMOPHILA / STRUCTURAL GENOMICS / APC108076 / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PSI-BIOLOGY
Function / homology
Function and homology information


regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Interleukin-2 signaling / Signaling by LTK / Shc-EGFR complex / epidermal growth factor receptor binding ...regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Interleukin-2 signaling / Signaling by LTK / Shc-EGFR complex / epidermal growth factor receptor binding / epidermal growth factor binding / Signaling by ALK / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / Signalling to RAS / Signal attenuation / SHC-related events triggered by IGF1R / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by CSF3 (G-CSF) / Tie2 Signaling / insulin-like growth factor receptor binding / ephrin receptor binding / phosphotyrosine residue binding / SHC1 events in EGFR signaling / Integrin signaling / FCERI mediated Ca+2 mobilization / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / Constitutive Signaling by Overexpressed ERBB2 / negative regulation of angiogenesis / insulin receptor binding / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / cell-cell adhesion / Signaling by ERBB2 ECD mutants / receptor tyrosine kinase binding / Signaling by ERBB2 KD Mutants / phospholipid binding / cellular response to growth factor stimulus / Signaling by CSF1 (M-CSF) in myeloid cells / epidermal growth factor receptor signaling pathway / Signaling by ALK fusions and activated point mutants / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / insulin receptor signaling pathway / GPER1 signaling / DAP12 signaling / heart development / actin cytoskeleton organization / RAF/MAP kinase cascade / angiogenesis / Extra-nuclear estrogen signaling / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / intracellular signal transduction / defense response to bacterium / mitochondrial matrix / focal adhesion / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / plasma membrane / cytosol
Similarity search - Function
Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
SHC-transforming protein 1 / Uncharacterized protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Kaneko, T. / Li, S. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074942 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: Crystal structure of the SH2 domain from RavO (Lpg1129) from Legionella pneumophila in complex with Homo sapiens Shc1 phospho-Tyr317 peptide
Authors: Kaneko, T.
History
DepositionJun 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RavO
E: Shc1 phospho-Tyr317 peptide
B: RavO
C: RavO
G: Shc1 phospho-Tyr317 peptide
D: RavO
H: Shc1 phospho-Tyr317 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,29613
Polymers57,7207
Non-polymers5766
Water7,963442
1
A: RavO
E: Shc1 phospho-Tyr317 peptide
B: RavO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8017
Polymers28,4173
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-62 kcal/mol
Surface area13700 Å2
2
C: RavO
G: Shc1 phospho-Tyr317 peptide
D: RavO
H: Shc1 phospho-Tyr317 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4956
Polymers29,3034
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-51 kcal/mol
Surface area13700 Å2
Unit cell
Length a, b, c (Å)44.454, 45.035, 74.748
Angle α, β, γ (deg.)72.60, 90.14, 77.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
RavO


Mass: 13765.521 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1129 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5ZWF6
#2: Protein/peptide Shc1 phospho-Tyr317 peptide


Mass: 885.854 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P29353*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 mM pTyr317 Shc1 peptide, 0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 5K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 41529 / % possible obs: 96.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.036 / Rrim(I) all: 0.062 / Net I/σ(I): 33.19
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.22 / Num. unique obs: 2095 / CC1/2: 0.864 / Rpim(I) all: 0.392 / Rrim(I) all: 0.696 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→14.815 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 1977 4.82 %RANDOM
Rwork0.1825 ---
obs0.1847 41046 96.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 30 442 4485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044158
X-RAY DIFFRACTIONf_angle_d0.6165618
X-RAY DIFFRACTIONf_dihedral_angle_d20.5641555
X-RAY DIFFRACTIONf_chiral_restr0.051620
X-RAY DIFFRACTIONf_plane_restr0.003708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94740.33971470.27112763X-RAY DIFFRACTION96
1.9474-20.26961440.24442784X-RAY DIFFRACTION97
2-2.05870.24741370.22522785X-RAY DIFFRACTION96
2.0587-2.12490.28271290.21662806X-RAY DIFFRACTION97
2.1249-2.20070.26641490.21292780X-RAY DIFFRACTION97
2.2007-2.28850.2611360.21022819X-RAY DIFFRACTION97
2.2885-2.39220.25071390.19982789X-RAY DIFFRACTION97
2.3922-2.51770.29371370.20992842X-RAY DIFFRACTION98
2.5177-2.67460.26631430.21242817X-RAY DIFFRACTION98
2.6746-2.87970.25141500.19942797X-RAY DIFFRACTION98
2.8797-3.1670.23371400.19122856X-RAY DIFFRACTION98
3.167-3.61940.23671450.17252792X-RAY DIFFRACTION98
3.6194-4.53820.17991450.14352815X-RAY DIFFRACTION98
4.5382-14.8150.20021360.16262624X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.67310.01793.23486.8369-2.98883.6047-0.4959-2.0394-0.21831.03090.3554-0.0271-0.2193-0.22660.07730.40380.22870.00070.82570.0820.3626-20.866725.3806-48.325
24.5181-0.0004-3.83574.52381.74227.9255-0.05250.05190.1446-0.41980.15670.30640.222-0.5301-0.10.26260.0555-0.09580.35040.02930.3027-21.529926.5171-69.4737
38.47080.9026-2.19044.7449-3.84985.3763-0.31950.2719-0.3114-1.13940.67280.26231.1259-0.0957-0.42330.42990.0231-0.10130.3531-0.02280.2697-18.743422.2354-64.875
45.48365.47125.3335.46655.33025.2645-0.21780.9575-5.0721-0.8990.32620.63572.48550.81460.01851.20340.0570.0361.0117-0.15271.89-20.96867.8996-53.2084
54.7469-0.834-0.44055.1431-2.416.99190.01550.1203-0.1646-0.38460.0745-0.05461.00920.6724-0.01780.30390.1421-0.06160.4166-0.04750.3025-13.211819.6858-63.9521
66.4224-0.5612-0.86176.051.20834.9256-0.2701-1.1134-0.75140.8505-0.0359-0.07530.82210.31830.23370.58490.241-0.08620.79670.06510.4278-13.104417.1693-50.0415
74.17280.04310.86298.57762.15415.46030.2679-0.5723-0.48310.22920.2842-1.21441.04130.963-0.5590.44230.2357-0.02080.7421-0.00310.3731-7.939118.1238-54.682
86.8882-4.1172-6.78059.22396.4979.16710.52270.21640.7876-0.6034-0.0698-0.6169-0.45620.3438-0.38970.25650.117-0.04350.5999-0.04480.3658-4.892326.5231-63.7874
96.26256.9108-2.95989.7123-3.16841.41550.47220.9794-1.2707-0.4627-0.415-0.81810.53931.1573-0.00320.96250.1485-0.07440.7846-0.06210.5328-7.917714.9499-67.1267
106.80970.328-0.78788.9827-1.75812.48010.07610.1907-2.0135-0.7321-0.0332-0.49451.59690.0060.01550.5608-0.0343-0.0410.35230.01530.6911-29.188721.1075-52.919
115.26392.97041.10987.23013.58547.16610.1572-0.02380.4579-0.22330.0568-0.2374-1.30440.5651-0.17860.3937-0.08690.06290.26840.0130.3239-28.384741.7457-48.8773
127.0575-1.00771.03242.9893-3.91775.7237-0.3547-0.00390.13730.9264-0.0167-0.3626-1.1361-0.00590.46010.4009-0.0382-0.03340.2331-0.02410.2681-31.282836.1488-45.6667
131.60660.57031.49364.00883.92144.42650.5354-2.5109-2.2351.9344-0.4902-1.04471.4673-0.1921-0.28671.0294-0.0539-0.17310.88840.23930.5961-31.249720.1181-36.7066
144.7857-0.44810.97188.08850.4177.33820.1459-0.0990.2791-0.1705-0.28070.2271-0.6164-0.96310.1180.22150.0476-0.00080.3617-0.01880.2127-37.375636.6136-43.9379
155.37440.2075-0.06373.98822.59747.7870.2604-0.137-0.60460.6106-0.40710.04581.1205-0.91340.14260.4032-0.1849-0.00290.3968-0.01830.3301-40.366223.4716-45.0661
168.8332-0.11890.01265.55671.04977.3545-0.0384-0.21140.2285-0.1292-0.32130.7628-0.9293-1.09980.32210.31620.1076-0.04680.6278-0.06340.3286-45.325736.8568-50.1645
176.7648-0.02840.07114.0259-4.83395.81390.09021.0309-0.6703-1.92780.18390.8306-0.0949-0.6255-0.24991.00890.1884-0.16520.4837-0.0460.4133-30.322536.9576-92.2565
186.5672-0.7495-4.44246.02850.90083.35860.1065-0.1746-0.0586-0.2746-0.03150.06960.0227-0.1703-0.05130.32520.016-0.05030.28220.05180.2002-27.887737.3722-71.1903
197.8618-0.72961.80926.3996-0.75778.43680.0123-0.05280.0678-0.0766-0.00820.7588-0.1487-1.09640.03750.37730.09550.01580.34830.05560.3572-36.772943.0333-78.3492
207.10750.9823-0.81822.2462-1.76296.15950.14440.18150.5115-0.55340.23250.5667-0.5849-0.9371-0.4260.76440.1698-0.06560.37130.05390.3982-35.368749.3222-87.9055
217.2716-4.2403-5.54538.23696.84887.55020.1029-0.31120.5773-0.24110.2695-0.629-0.93570.2844-0.27810.6030.07710.03610.26160.04010.3165-25.453952.3199-77.314
225.77811.99715.73161.84151.99485.6796-0.3838-0.14361.11980.96470.2141-0.1451-1.3482-0.07290.19830.97960.0885-0.00690.7821-0.08820.7475-36.598250.8439-72.2247
232.25431.8857-0.1967.49022.0062.75920.1366-0.48350.2178-0.3571-0.29911.277-0.2806-1.33080.17560.51440.0687-0.11120.588-0.05350.5484-36.142929.6532-87.4896
243.9846-0.783-2.79944.38272.54047.147-0.02760.08560.2502-0.40840.5427-1.3014-0.52961.3522-0.47860.4028-0.07170.03640.5195-0.1090.5675-16.575526.0194-92.664
259.37921.030.17864.17420.38298.83060.04250.16440.2901-0.189-0.0062-0.4259-0.0290.6033-0.0130.379-0.02250.00660.2849-0.06360.3079-22.465224.2268-95.3732
266.8186-0.6287-4.55520.06040.46573.387-0.25032.33740.7688-2.0692-0.35740.7246-2.0909-0.49030.35281.44890.2643-0.24321.0890.20270.7011-37.818129.3517-104.7804
279.7886-1.80060.69635.08542.02628.3471-0.13730.0954-0.4087-0.04280.1436-0.26950.4160.53080.02340.34910.0146-0.02410.22330.01420.2315-25.20819.098-97.0186
282.8875-0.4019-0.47342.98231.59783.4752-0.1835-0.0634-0.170.3942-0.29770.30760.541-1.42220.44250.3434-0.05340.01160.3737-0.05050.2361-36.665618.0479-95.3781
295.1177-0.9189-0.88785.4020.08366.8648-0.2534-0.2552-0.66380.3580.097-0.16361.49130.69650.09480.63860.0819-0.05040.30340.03870.3009-25.233210.8996-90.1505
303.1585-3.81861.9854.9651-3.46335.63990.03260.3535-0.7253-0.2051-0.1319-0.04351.39430.09270.22560.78940.0978-0.04070.5453-0.11640.424-24.312913.3716-101.7459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 226 through 237 )
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 258 )
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 273 )
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 278 )
5X-RAY DIFFRACTION5chain 'A' and (resid 279 through 300 )
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 308 )
7X-RAY DIFFRACTION7chain 'A' and (resid 309 through 324 )
8X-RAY DIFFRACTION8chain 'A' and (resid 325 through 344 )
9X-RAY DIFFRACTION9chain 'E' and (resid 902 through 908 )
10X-RAY DIFFRACTION10chain 'B' and (resid 226 through 237 )
11X-RAY DIFFRACTION11chain 'B' and (resid 238 through 258 )
12X-RAY DIFFRACTION12chain 'B' and (resid 259 through 273 )
13X-RAY DIFFRACTION13chain 'B' and (resid 274 through 279 )
14X-RAY DIFFRACTION14chain 'B' and (resid 280 through 299 )
15X-RAY DIFFRACTION15chain 'B' and (resid 300 through 324 )
16X-RAY DIFFRACTION16chain 'B' and (resid 325 through 344 )
17X-RAY DIFFRACTION17chain 'C' and (resid 226 through 237 )
18X-RAY DIFFRACTION18chain 'C' and (resid 238 through 263 )
19X-RAY DIFFRACTION19chain 'C' and (resid 264 through 299 )
20X-RAY DIFFRACTION20chain 'C' and (resid 300 through 324 )
21X-RAY DIFFRACTION21chain 'C' and (resid 325 through 344 )
22X-RAY DIFFRACTION22chain 'G' and (resid 902 through 907 )
23X-RAY DIFFRACTION23chain 'D' and (resid 226 through 237 )
24X-RAY DIFFRACTION24chain 'D' and (resid 238 through 258 )
25X-RAY DIFFRACTION25chain 'D' and (resid 259 through 273 )
26X-RAY DIFFRACTION26chain 'D' and (resid 274 through 278 )
27X-RAY DIFFRACTION27chain 'D' and (resid 279 through 300 )
28X-RAY DIFFRACTION28chain 'D' and (resid 301 through 324 )
29X-RAY DIFFRACTION29chain 'D' and (resid 325 through 344 )
30X-RAY DIFFRACTION30chain 'H' and (resid 902 through 908 )

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