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- PDB-6siu: Crystal structure of IbpAFic2 covalently tethered to Cdc42 -

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Basic information

Entry
Database: PDB / ID: 6siu
TitleCrystal structure of IbpAFic2 covalently tethered to Cdc42
Components
  • Cell division control protein 42 homolog
  • Protein adenylyltransferase and cysteine protease IbpA
KeywordsTRANSFERASE / FIC DOMAIN / ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE / PROXIMITY ENABLED COUPLING
Function / homology
Function and homology information


GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of epithelial cell proliferation involved in lung morphogenesis / positive regulation of pinocytosis / AMPylase activity / modification of synaptic structure / protein adenylylation / Cdc42 protein signal transduction ...GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of epithelial cell proliferation involved in lung morphogenesis / positive regulation of pinocytosis / AMPylase activity / modification of synaptic structure / protein adenylylation / Cdc42 protein signal transduction / positive regulation of synapse structural plasticity / protein adenylyltransferase / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / apolipoprotein A-I receptor binding / neuron fate determination / GTP-dependent protein binding / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / cardiac conduction system development / Inactivation of CDC42 and RAC1 / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / positive regulation of intracellular protein transport / neuropilin signaling pathway / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / regulation of modification of postsynaptic structure / regulation of stress fiber assembly / thioesterase binding / embryonic heart tube development / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / adherens junction organization / DCC mediated attractive signaling / sprouting angiogenesis / CD28 dependent Vav1 pathway / negative regulation of GTPase activity / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / RHOV GTPase cycle / phagocytosis, engulfment / establishment or maintenance of cell polarity / heart contraction / positive regulation of cytokinesis / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of substrate adhesion-dependent cell spreading / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / substantia nigra development / RAC1 GTPase cycle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / secretory granule / positive regulation of DNA replication / filopodium / actin filament organization / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / FCGR3A-mediated phagocytosis / cell outer membrane / positive regulation of JNK cascade / EGFR downregulation / protein modification process / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / G protein activity / cellular response to type II interferon / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation / G beta:gamma signalling through CDC42
Similarity search - Function
Peptidase C58, Yersinia/Haemophilus virulence surface antigen / Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / Fido domain-containing protein / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain ...Peptidase C58, Yersinia/Haemophilus virulence surface antigen / Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / Fido domain-containing protein / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain / Extended Signal Peptide of Type V secretion system / Fido-like domain / Cdc42 / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Small GTPase Rho / small GTPase Rho family profile. / Pectin lyase fold / Pectin lyase fold/virulence factor / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Papain-like cysteine peptidase superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Chem-LJN / Cell division control protein 42 homolog / Protein adenylyltransferase and cysteine protease IbpA
Similarity search - Component
Biological speciesHistophilus somni (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsGulen, B. / Roselin, M. / Albers, M. / Hedberg, C. / Itzen, A. / Pogenberg, V.
Funding support Sweden, Germany, 3items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
German Research FoundationSFB1035 B05 Germany
Alexander von Humboldt Foundation3.1 - USA - 1187240 - HFST-P Germany
CitationJournal: Nat.Chem. / Year: 2020
Title: Identification of targets of AMPylating Fic enzymes by co-substrate-mediated covalent capture.
Authors: Gulen, B. / Rosselin, M. / Fauser, J. / Albers, M.F. / Pett, C. / Krisp, C. / Pogenberg, V. / Schluter, H. / Hedberg, C. / Itzen, A.
History
DepositionAug 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 5, 2020Group: 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
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein adenylyltransferase and cysteine protease IbpA
B: Protein adenylyltransferase and cysteine protease IbpA
C: Cell division control protein 42 homolog
D: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,40320
Polymers113,6674
Non-polymers2,73616
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-201 kcal/mol
Surface area41320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.241, 102.213, 129.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Protein adenylyltransferase and cysteine protease IbpA / HMW IgBP / p120


Mass: 35492.918 Da / Num. of mol.: 2 / Mutation: I3755C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Histophilus somni (strain 2336) (bacteria)
Strain: 2336 / Gene: ibpA, p76, HSM_1489 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2
References: UniProt: Q06277, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 21340.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The ligand is the product of a bifunctional linker (TReND-1), exhibiting one chemically as well as one enzymatically reactive moiety. The chemical moiety was a thiol-reactive chloroacetamide ...Details: The ligand is the product of a bifunctional linker (TReND-1), exhibiting one chemically as well as one enzymatically reactive moiety. The chemical moiety was a thiol-reactive chloroacetamide that couple to Cys3755 (IbpA). The enzymatically reactive moiety was a tri-phosphate that transferred to the natural Tyr32 (Cdc42). This reaction resulted in the cross-linking of the two proteins. Therefore it should be covalently bonded to the S atom of Cys3755 (IbpA).
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P60953, small monomeric GTPase

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Non-polymers , 5 types, 125 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-LJN / [(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 352.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N4O8P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 1.6 M ammonium sulfate and 0.1 M citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.979124 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2019 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979124 Å / Relative weight: 1
ReflectionResolution: 2.49→80.2 Å / Num. obs: 43472 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 50.4 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.077 / Net I/σ(I): 5.2
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.626 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4472 / CC1/2: 0.576 / Rpim(I) all: 0.762 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
DIALSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ITR

4itr


Resolution: 2.49→80.2 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.54
Details: Ellipsoidal anisotropic corrections were applied to the merged data using STARANISO and explain the poor completeness in the high-resolution shells.
RfactorNum. reflection% reflection
Rfree0.239 1504 4.76 %
Rwork0.19 --
obs0.1926 31612 72.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.85 Å2 / Biso mean: 52.475 Å2 / Biso min: 13.91 Å2
Refinement stepCycle: final / Resolution: 2.49→80.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7521 0 118 109 7748
Biso mean--63.61 38.11 -
Num. residues----962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4924-2.57280.2866170.2542687
2.5728-2.66480.266230.228448713
2.6648-2.77150.2636580.2577108229
2.7715-2.89760.2821150.2575223460
2.8976-3.05040.30521580.2544331989
3.0504-3.24150.2961890.2382369199
3.2415-3.49180.25321780.20293729100
3.4918-3.84320.22121800.18213770100
3.8432-4.39930.2292130.15913750100
4.3993-5.54240.20611880.1663802100
5.5424-80.20.22731850.17833976100
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)
11.71280.1164-0.02240.3722-0.80153.7524-0.1045-0.69020.37120.37550.2973-0.0823-0.3671-0.19960.05330.73710.3867-0.02670.6355-0.0291-0.107710.949310.6841-11.4638
27.79874.17042.63776.54045.64445.0568-0.6310.4024-0.94970.46090.9255-0.88840.59740.5115-0.40640.63330.157-0.17390.72840.00240.339132.5035-3.6889-12.9477
33.0211-3.4039-1.03744.72332.99924.7376-0.7062-1.02390.59890.53091.0187-0.7102-0.07360.8877-0.160.57380.0207-0.19780.7339-0.00140.278727.08198.0616-6.5362
45.1862-1.6069-0.79051.9351-0.17722.0395-0.4014-0.9502-0.06320.11270.20620.09510.67760.60560.14990.68760.0765-0.0220.51350.08710.268816.6120.7038-8.0527
56.43021.09064.32896.3255-5.27598.796-0.4077-0.61750.34150.8716-0.1960.010.2851-0.39530.02090.79160.01160.05490.56820.22310.09335.90971.7547-6.7239
66.6729-3.4582-2.32942.90511.65363.1450.46780.22390.4476-0.3536-0.2618-0.3949-0.2890.3566-0.18470.3545-0.0126-0.0120.20770.03350.189118.07557.9874-44.4432
78.0533-0.1008-1.31372.1476-0.43942.23540.1073-0.4277-1.13720.0405-0.3038-0.37430.17680.57130.10490.33560.1004-0.04390.35660.07070.367928.2775-12.1974-44.7289
80.7965-0.40740.72092.6056-2.17227.0793-0.07910.1518-0.043-0.3647-0.109-0.09780.2974-0.27320.11030.25850.0032-0.00040.1953-0.05530.1828-2.2978-14.1727-53.826
92.7484-0.06121.96882.8947-0.47155.2871-0.09450.04710.2087-0.24850.02260.3029-0.364-0.55760.02030.2520.0613-0.00450.23190.01220.2097-9.11756.306-61.6865
103.8359-0.5049-0.4224.0427-1.14733.3335-0.0093-0.23880.08550.5870.19160.1904-0.56990.0145-0.15610.39310.01170.16850.31170.0380.3838-17.234-7.1669-30.011
115.17051.419-0.83741.7058-2.27633.32560.31370.57490.52370.2259-0.00950.1464-0.4316-0.1008-0.26390.54770.09840.07210.3839-0.04490.4189-14.57231.9575-42.3473
125.4671-2.2173-4.05066.87144.71764.77410.1264-1.02370.37630.0390.2116-0.1583-1.4011.1977-0.45130.3459-0.02180.10480.4618-0.09880.3636-14.4841-6.8276-22.5728
137.8548-2.83330.54514.3738-0.21375.2835-0.047-0.0004-0.53050.36130.44390.55440.5149-0.3998-0.41470.332-0.04890.11420.25340.06750.3564-20.1511-18.3038-34.865
149.04853.96866.37445.79892.49294.6629-0.50810.2710.372-0.65910.14590.3323-1.1678-0.72010.41060.33380.13840.10880.64750.11680.5888-34.9747-2.957-45.3849
153.1046-1.04621.67592.8698-0.84471.24310.2899-0.1890.30280.52530.04720.7583-0.4003-0.808-0.28250.46790.1260.30890.6860.10950.6177-30.7026-10.5918-29.8158
164.80312.03641.9033.7481-0.1221.0635-1.1308-1.2589-0.10840.2503-0.33991.38191.1507-0.11450.99640.8560.14110.14960.5952-0.06860.4575-10.1871-27.3333-30.046
172.3426-1.8976-0.3836.61191.74955.4415-0.016-0.1091-0.72280.3756-0.24740.93340.4335-0.35950.21080.49070.05850.03010.39870.1110.18549.09830.0396-17.7154
183.7113-2.5175-1.89632.90612.61465.37360.3494-0.4835-0.4528-0.2145-0.15310.30230.51530.8254-0.10120.54790.0455-0.01780.50340.1270.318217.3561-8.4685-28.0993
194.91750.4577-3.1665.2957-2.35789.03120.0955-0.8441-0.4520.9507-0.74620.91411.0475-0.38170.65270.7824-0.2530.21580.5550.00320.48222.0342-0.9495-15.5362
207.6443-1.00273.56483.45120.42344.0751-0.4636-0.27680.39070.37220.2802-0.131-0.26330.42480.22040.4808-0.0149-0.02660.2654-0.0070.162515.253811.3937-19.5845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 105 through 115 )D105 - 115
2X-RAY DIFFRACTION2chain 'D' and (resid 116 through 131 )D116 - 131
3X-RAY DIFFRACTION3chain 'D' and (resid 132 through 148 )D132 - 148
4X-RAY DIFFRACTION4chain 'D' and (resid 149 through 164 )D149 - 164
5X-RAY DIFFRACTION5chain 'D' and (resid 165 through 179 )D165 - 179
6X-RAY DIFFRACTION6chain 'A' and (resid 3487 through 3568 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 3569 through 3781 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 3488 through 3568 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 3569 through 3784 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 25 )C1 - 25
11X-RAY DIFFRACTION11chain 'C' and (resid 26 through 39 )C26 - 39
12X-RAY DIFFRACTION12chain 'C' and (resid 40 through 61 )C40 - 61
13X-RAY DIFFRACTION13chain 'C' and (resid 62 through 115 )C62 - 115
14X-RAY DIFFRACTION14chain 'C' and (resid 116 through 132 )C116 - 132
15X-RAY DIFFRACTION15chain 'C' and (resid 133 through 177 )C133 - 177
16X-RAY DIFFRACTION16chain 'C' and (resid 178 through 191 )C178 - 191
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 25 )D1 - 25
18X-RAY DIFFRACTION18chain 'D' and (resid 26 through 39 )D26 - 39
19X-RAY DIFFRACTION19chain 'D' and (resid 40 through 61 )D40 - 61
20X-RAY DIFFRACTION20chain 'D' and (resid 62 through 104 )D62 - 104

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