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- PDB-7tzk: EPS8 SH3 Domain with NleH1 PxxDY Motif -

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Basic information

Entry
Database: PDB / ID: 7tzk
TitleEPS8 SH3 Domain with NleH1 PxxDY Motif
Components
  • Epidermal growth factor receptor kinase substrate 8
  • T3SS secreted effector NleH homolog
KeywordsPROTEIN BINDING / NleH kinase / protein-protein interaction / SH3 domain
Function / homology
Function and homology information


regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / behavioral response to ethanol / stereocilium / regulation of Rho protein signal transduction / barbed-end actin filament capping / Sensory processing of sound by outer hair cells of the cochlea ...regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / behavioral response to ethanol / stereocilium / regulation of Rho protein signal transduction / barbed-end actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of ruffle assembly / NMDA selective glutamate receptor complex / Sensory processing of sound by inner hair cells of the cochlea / exit from mitosis / Rac protein signal transduction / regulation of postsynaptic membrane neurotransmitter receptor levels / brush border / actin filament bundle assembly / Rho protein signal transduction / adult locomotory behavior / cellular response to leukemia inhibitory factor / small GTPase binding / ruffle membrane / actin binding / cell cortex / regulation of cell shape / growth cone / vesicle / postsynaptic density / glutamatergic synapse / extracellular exosome / plasma membrane
Similarity search - Function
Epidermal growth factor receptor kinase substrate, phosphotyrosine-binding domain / Eps8, SH3 domain / Epidermal growth factor receptor kinase substrate 8-like / SAM domain / SAM domain (Sterile alpha motif) / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Sterile alpha motif/pointed domain superfamily ...Epidermal growth factor receptor kinase substrate, phosphotyrosine-binding domain / Eps8, SH3 domain / Epidermal growth factor receptor kinase substrate 8-like / SAM domain / SAM domain (Sterile alpha motif) / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
T3SS secreted effector NleH homolog / Epidermal growth factor receptor kinase substrate 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli O127:H6 str. E2348/69 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å
AuthorsGrishin, A.M. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)GSP-48370 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Targeting of microvillus protein Eps8 by the NleH effector kinases from enteropathogenic E. coli
Authors: Pollock, G.L. / Grishin, A.M. / Giogha, C. / Gan, J. / Oates, C.V. / McMillan, P.J. / Gaeta, I. / Tyska, M.J. / Pearson, J.S. / Scott, N.E. / Cygler, M. / Hartland, E.L.
History
DepositionFeb 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epidermal growth factor receptor kinase substrate 8
B: Epidermal growth factor receptor kinase substrate 8
C: T3SS secreted effector NleH homolog
D: T3SS secreted effector NleH homolog


Theoretical massNumber of molelcules
Total (without water)17,4054
Polymers17,4054
Non-polymers00
Water5,423301
1
A: Epidermal growth factor receptor kinase substrate 8
C: T3SS secreted effector NleH homolog


Theoretical massNumber of molelcules
Total (without water)8,7032
Polymers8,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-5 kcal/mol
Surface area5390 Å2
MethodPISA
2
B: Epidermal growth factor receptor kinase substrate 8
D: T3SS secreted effector NleH homolog


Theoretical massNumber of molelcules
Total (without water)8,7032
Polymers8,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-6 kcal/mol
Surface area5380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.681, 35.280, 53.647
Angle α, β, γ (deg.)90.000, 105.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Epidermal growth factor receptor kinase substrate 8


Mass: 7372.294 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPS8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12929
#2: Protein/peptide T3SS secreted effector NleH homolog


Mass: 1330.440 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Escherichia coli O127:H6 str. E2348/69 (bacteria)
References: UniProt: B7ULW4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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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: 1.82 Å3/Da / Density % sol: 32.28 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 35% PEG 8,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18064 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18064 Å / Relative weight: 1
ReflectionResolution: 1.43→35.28 Å / Num. obs: 23092 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.037 / Rrim(I) all: 0.067 / Net I/σ(I): 10.3 / Num. measured all: 72959
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.43-1.453.21.042369611660.3460.6811.25199.5
7.83-35.2830.034911620.9980.020.03625.898.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.20_4459refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I0C

1i0c


Resolution: 1.43→32.28 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2016 8.74 %
Rwork0.195 21051 -
obs0.1984 23067 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.62 Å2 / Biso mean: 26.1973 Å2 / Biso min: 9.88 Å2
Refinement stepCycle: final / Resolution: 1.43→32.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 0 301 1506
Biso mean---33.29 -
Num. residues----152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.470.40641480.39211492164099
1.47-1.510.35321470.35341489163699
1.51-1.550.38221410.29911489163099
1.55-1.60.29881470.258615011648100
1.6-1.660.27881380.24631510164899
1.66-1.720.30321420.25161495163799
1.72-1.80.30191430.241482162599
1.8-1.90.27771460.2031516166299
1.9-2.020.24311330.18261485161898
2.02-2.170.23021420.17411511165399
2.17-2.390.19051460.1751486163298
2.39-2.740.23731490.19461508165798
2.74-3.450.1941410.16361516165798
3.45-32.280.20021530.17321571172499
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)
10.9135-0.212-1.65921.27531.40594.0279-0.0320.1342-0.0778-0.0496-0.0245-0.02960.2062-0.1716-0.04280.16490.0111-0.01660.1548-0.00530.16734.139-1.17318.508
21.55190.0942-0.26091.22820.35651.18760.0130.0347-0.07020.0269-0.04270.0594-0.00990.02940.03640.13670.0086-0.00880.1328-0.00420.13525.231-4.28226.13
31.6191-0.91561.75942.2335-0.39552.44390.04670.43970.0353-0.2808-0.1373-0.08440.03890.12730.14620.13220.01110.00260.17680.01530.16180.39-2.3721.025
40.230.3338-0.49741.0305-1.7474.7677-0.03110.13130.0239-0.1839-0.0801-0.07070.01530.12640.19940.23740.0133-0.00780.17250.00980.1575-8.242-7.027-3.625
51.33120.12320.41291.2547-0.12151.2061-0.0241-0.04370.0828-0.0429-0.04090.009-0.0489-0.02720.07090.20670.0059-0.00180.1457-0.00420.1223-13.285-4.4492.95
63.8856-0.1653-0.50693.0877-0.04111.65040.00660.41560.0575-0.3313-0.1065-0.3409-0.07070.16430.0590.236-0.00150.02750.20580.01320.1507-6.559-6.3351.182
71.27980.08271.26214.0446-1.23083.2497-0.4059-0.1552-0.13380.2680.15240.2884-0.13620.06930.18830.21540.00440.0490.18840.04810.2058-2.465-8.43333.224
84.2435-1.20720.36933.5453-0.89583.7617-0.0679-0.2673-0.10480.0851-0.05460.055-0.0458-0.12810.07480.1978-0.0109-0.01710.1525-0.01950.1484-10.823-0.21613.094
90.1307-0.09070.11750.0562-0.07560.09770.0158-0.0032-0.0141-0.05360.01390.01120.0103-0.017200.19210.0009-0.00080.1881-0.00350.1809-4.417-4.30113.332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -2:543 )A-2 - 543
2X-RAY DIFFRACTION2( CHAIN A AND RESID 544:576 )A544 - 576
3X-RAY DIFFRACTION3( CHAIN A AND RESID 577:591 )A577 - 591
4X-RAY DIFFRACTION4( CHAIN B AND RESID -2:543 )B-2 - 543
5X-RAY DIFFRACTION5( CHAIN B AND RESID 544:576 )B544 - 576
6X-RAY DIFFRACTION6( CHAIN B AND RESID 577:591 )B577 - 591
7X-RAY DIFFRACTION7( CHAIN C AND RESID 121:132 )C121 - 132
8X-RAY DIFFRACTION8( CHAIN D AND RESID 121:132 )D121 - 132
9X-RAY DIFFRACTION9( CHAIN A AND RESID 601:723 ) OR ( CHAIN B AND RESID 601:729 ) OR ( CHAIN C AND RESID 201:225 ) OR ( CHAIN D AND RESID 201:224 )A601 - 723
10X-RAY DIFFRACTION9( CHAIN A AND RESID 601:723 ) OR ( CHAIN B AND RESID 601:729 ) OR ( CHAIN C AND RESID 201:225 ) OR ( CHAIN D AND RESID 201:224 )B601 - 729
11X-RAY DIFFRACTION9( CHAIN A AND RESID 601:723 ) OR ( CHAIN B AND RESID 601:729 ) OR ( CHAIN C AND RESID 201:225 ) OR ( CHAIN D AND RESID 201:224 )C201 - 225
12X-RAY DIFFRACTION9( CHAIN A AND RESID 601:723 ) OR ( CHAIN B AND RESID 601:729 ) OR ( CHAIN C AND RESID 201:225 ) OR ( CHAIN D AND RESID 201:224 )D201 - 224

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