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- PDB-5i4r: Contact-dependent inhibition system from Escherichia coli NC101 -... -

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Basic information

Entry
Database: PDB / ID: 5i4r
TitleContact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified)
Components
  • (Elongation factor Tu) x 2
  • Contact-dependent inhibitor A
  • Contact-dependent inhibitor I
KeywordsTOXIN/ANTITOXIN / toxin / antitoxin / elongation factor / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / response to antibiotic / GTPase activity ...guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / response to antibiotic / GTPase activity / GTP binding / magnesium ion binding / RNA binding / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Family of unknown function (DUF6862) / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain ...: / : / Family of unknown function (DUF6862) / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Pectin lyase fold / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Pectin lyase fold/virulence factor / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu 1 / Elongation factor Tu 1 / Elongation factor Tu 2 / tRNA nuclease CdiA / Immunity protein CdiI
Similarity search - Component
Biological speciesEscherichia coli NC101 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMichalska, K. / Stols, L. / Eschenfeldt, W. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102318 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs.
Authors: Michalska, K. / Gucinski, G.C. / Garza-Sanchez, F. / Johnson, P.M. / Stols, L.M. / Eschenfeldt, W.H. / Babnigg, G. / Low, D.A. / Goulding, C.W. / Joachimiak, A. / Hayes, C.S.
History
DepositionFeb 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 25, 2017Group: 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.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contact-dependent inhibitor A
C: Elongation factor Tu
D: Elongation factor Tu
B: Contact-dependent inhibitor I
E: Contact-dependent inhibitor A
G: Elongation factor Tu
H: Elongation factor Tu
F: Contact-dependent inhibitor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,83610
Polymers132,9508
Non-polymers8862
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.395, 128.354, 100.358
Angle α, β, γ (deg.)90.00, 109.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12C
22G
32D
42H
13B
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILELYSLYSAA169 - 2536 - 90
21ILEILELYSLYSEE169 - 2536 - 90
12LYSLYSGLYGLYCB10 - 4210 - 42
22LYSLYSGLYGLYGF10 - 4210 - 42
32GLYGLYLEULEUDC60 - 3931 - 334
42GLYGLYLEULEUHG60 - 3931 - 334
13ASPASPGLUGLUBD2 - 1062 - 106
23ASPASPGLUGLUFH2 - 1062 - 106

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Contact-dependent inhibitor A / CdiA


Mass: 10476.635 Da / Num. of mol.: 2 / Fragment: toxin domain
Source method: isolated from a genetically manipulated source
Details: The cloned fragment corresponds to Val3035-Lys3289 of the full-length protein (CdiA-CT). The final purified ternary complex was treated with trypsin that cleaved CdiA-CT after Lys3196.
Source: (gene. exp.) Escherichia coli NC101 (bacteria) / Strain: NC101 / Plasmid: pMCSG58 / Details (production host): dual expression vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: P0DSI1*PLUS
#2: Protein/peptide Elongation factor Tu / EF-Tu


Mass: 4804.528 Da / Num. of mol.: 2 / Fragment: N-terminal / Source method: isolated from a natural source
Details: Short trypsin treatment prior to crystallization cleaved EF-Tu after Arg45 and after Arg59. The sample is a mixture of tufA and tufB gene products (GI 947838, 948482).
Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3) / References: UniProt: A7ZSL4, UniProt: P0CE48*PLUS
#3: Protein Elongation factor Tu / EF-Tu


Mass: 36966.277 Da / Num. of mol.: 2 / Fragment: C-terminal / Source method: isolated from a natural source
Details: Short trypsin treatment prior to crystallization cleaved EF-Tu after Arg45 and after Arg59. The sample is a mixture of tufA and tufB gene products (GI 947838, 948482).
Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3) / References: UniProt: A7ZSL4, UniProt: P0CE47*PLUS
#4: Protein Contact-dependent inhibitor I / CdiI


Mass: 14227.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli NC101 (bacteria) / Strain: NC101 / Plasmid: pMCSG58 / Details (production host): dual expression vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: P0DSM8*PLUS
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
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: 3.41 Å3/Da / Density % sol: 63.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05 M KCl 0.1 M HEPES pH=7.0, 1.0 M ammonium sulfate, cryo 3.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2014 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 26374 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 10.6
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I4Q,1ERC

5i4q

1erc


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.897 / SU B: 65.902 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R Free: 0.545 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26778 1008 3.9 %RANDOM
Rwork0.24299 ---
obs0.24399 24766 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 115.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å23.4 Å2
2--4.69 Å20 Å2
3----5.95 Å2
Refinement stepCycle: 1 / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8885 0 56 0 8941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199141
X-RAY DIFFRACTIONr_bond_other_d0.0040.028728
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.96912376
X-RAY DIFFRACTIONr_angle_other_deg1.0892.99820138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76551115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11823.81420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.271151551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1331564
X-RAY DIFFRACTIONr_chiral_restr0.0810.21346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110325
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022023
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9828.7844484
X-RAY DIFFRACTIONr_mcbond_other1.9818.7844483
X-RAY DIFFRACTIONr_mcangle_it3.39213.1775591
X-RAY DIFFRACTIONr_mcangle_other3.39213.1775592
X-RAY DIFFRACTIONr_scbond_it2.3369.0464657
X-RAY DIFFRACTIONr_scbond_other2.3369.0464657
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.95613.4776786
X-RAY DIFFRACTIONr_long_range_B_refined7.85783.19336622
X-RAY DIFFRACTIONr_long_range_B_other7.85783.19536623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A97120.07
12E97120.07
21C441420.09
22G441420.09
23D441420.09
24H441420.09
31B123280.09
32F123280.09
LS refinement shellResolution: 3.304→3.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 65 -
Rwork0.369 1725 -
obs--90.96 %
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)
18.5304-8.58960.812910.23951.70698.85710.3250.31150.012-1.06910.1253-0.2462-0.2770.0413-0.45020.71-0.10330.35260.47110.23970.3869103.15590.267310.6754
20.50360.62040.3733.3704-0.09282.8654-0.0287-0.16920.0663-0.4405-0.07260.1795-0.16190.10520.10130.554-0.01960.00770.10440.03040.134691.52535.144819.3133
34.28796.61952.846312.62641.56225.25360.53430.147-0.58611.01290.1618-0.62730.16720.2493-0.6960.15540.0665-0.02550.1938-0.01320.358284.2402-23.311343.5391
40.78632.7347-0.13819.73660.40773.93620.02960.00090.0682-0.0223-0.03910.3157-0.5487-0.2690.00950.42020.0102-0.02270.13010.04410.239491.46116.54838.6709
53.1719-0.4715-1.0311.32020.03411.4216-0.0473-0.216-0.1515-0.1675-0.19890.07460.1890.26050.24630.51450.060.02260.1059-0.00710.1174120.458-46.636414.4306
62.23180.1039-2.62324.02611.1583.55680.21390.0555-0.1056-0.4132-0.2770.0349-0.2716-0.15630.06320.52210.1144-0.01360.10890.0540.141892.371-17.392814.3018
71.9096-0.92450.16721.5004-1.0533.2722-0.1205-0.0236-0.0565-0.0748-0.02650.14740.1739-0.09320.14690.4678-0.0474-0.01120.0682-0.02990.196796.161-39.900629.9853
86.57143.991-0.96683.9573-0.82119.10680.176-0.2532-0.4025-0.0820.0912-0.1409-0.0128-0.2816-0.26720.0994-0.0343-0.02340.29950.12940.23463.585-29.302160.199
92.34322.1214-1.81097.35941.72355.60880.36760.0359-0.0907-0.2652-0.22250.005-0.1991-0.3196-0.14510.20990.0447-0.0980.43010.04560.316753.9371-21.934451.0632
108.56086.77282.73538.49873.82062.09520.21420.1868-0.51680.3307-0.0144-0.75830.40580.1333-0.19980.31630.05840.01190.2048-0.01340.315891.449-16.339837.7153
116.47432.62060.48073.10483.09274.19910.01450.29470.0237-0.2553-0.10890.0554-0.2761-0.39970.09440.2239-0.069-0.08230.2228-0.02310.299764.4463-30.638735.5521
121.10720.376-0.46540.9406-0.97082.1082-0.1216-0.07270.09330.1927-0.09370.01570.09040.36810.21530.41620.033-0.08130.23240.0070.1385106.1507-33.310983.966
133.06651.66470.14811.8257-0.71634.13660.0052-0.07040.1130.19940.1378-0.1544-0.1501-0.3017-0.1430.12080.0414-0.0280.36650.07240.17876.2281-15.307964.3986
145.7218-0.25411.12713.3913-1.1931.79910.2175-0.07760.3699-0.0311-0.20570.1089-0.15120.1539-0.01180.1197-0.0629-0.03930.25530.01230.2438103.2366-17.501959.1694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A168 - 186
2X-RAY DIFFRACTION2A187 - 254
3X-RAY DIFFRACTION3B2 - 23
4X-RAY DIFFRACTION4B24 - 108
5X-RAY DIFFRACTION5C9 - 42
6X-RAY DIFFRACTION5D60 - 204
7X-RAY DIFFRACTION6D205 - 299
8X-RAY DIFFRACTION7D300 - 394
9X-RAY DIFFRACTION8E169 - 205
10X-RAY DIFFRACTION9E206 - 254
11X-RAY DIFFRACTION10F2 - 24
12X-RAY DIFFRACTION11F25 - 107
13X-RAY DIFFRACTION12G10 - 42
14X-RAY DIFFRACTION12H60 - 204
15X-RAY DIFFRACTION13H205 - 302
16X-RAY DIFFRACTION14H303 - 394

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