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- PDB-4nkg: Crystal structure of SspH1 LRR domain in complex PKN1 HR1b domain -

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Basic information

Entry
Database: PDB / ID: 4nkg
TitleCrystal structure of SspH1 LRR domain in complex PKN1 HR1b domain
Components
  • E3 ubiquitin-protein ligase sspH1
  • Serine/threonine-protein kinase N1
KeywordsLigase/Transferase / LEUCINE-RICH REPEAT / COILED-COIL / E3 ligase substrate interaction / Ligase-Transferase complex
Function / homology
Function and homology information


epithelial cell migration / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / renal system process / protein secretion by the type III secretion system / regulation of cell motility / histone H3T11 kinase activity / B cell apoptotic process / regulation of germinal center formation / regulation of immunoglobulin production ...epithelial cell migration / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / renal system process / protein secretion by the type III secretion system / regulation of cell motility / histone H3T11 kinase activity / B cell apoptotic process / regulation of germinal center formation / regulation of immunoglobulin production / regulation of androgen receptor signaling pathway / hyperosmotic response / nuclear androgen receptor binding / RHOB GTPase cycle / negative regulation of B cell proliferation / RHOC GTPase cycle / B cell homeostasis / cleavage furrow / RHOA GTPase cycle / spleen development / RHO GTPases activate PKNs / RAC1 GTPase cycle / post-translational protein modification / protein kinase C binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RING-type E3 ubiquitin transferase / small GTPase binding / histone deacetylase binding / ubiquitin-protein transferase activity / midbody / histone binding / host cell cytoplasm / transcription coactivator activity / protein phosphorylation / protein kinase activity / endosome / intracellular signal transduction / protein ubiquitination / protein serine kinase activity / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / host cell nucleus / signal transduction / protein-containing complex / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase N1, second HR1 domain / HR1 repeat / Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting ...Serine/threonine-protein kinase N1, second HR1 domain / HR1 repeat / Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / : / HR1 rho-binding domain / REM-1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / Alpha-Beta Horseshoe / C2 domain / C2 domain profile. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Leucine-rich repeat profile. / C2 domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Helix Hairpins / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HEXANE-1,6-DIOL / E3 ubiquitin-protein ligase SspH1 / Serine/threonine-protein kinase N1
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKeszei, A.F.A. / Xiaojing, T. / Mccormick, C. / Zeqiraj, E. / Rohde, J.R. / Tyers, M. / Sicheri, F.
CitationJournal: Mol.Cell.Biol. / Year: 2014
Title: Structure of an SspH1-PKN1 Complex Reveals the Basis for Host Substrate Recognition and Mechanism of Activation for a Bacterial E3 Ubiquitin Ligase.
Authors: Keszei, A.F. / Tang, X. / McCormick, C. / Zeqiraj, E. / Rohde, J.R. / Tyers, M. / Sicheri, F.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase sspH1
B: Serine/threonine-protein kinase N1
C: E3 ubiquitin-protein ligase sspH1
D: Serine/threonine-protein kinase N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5296
Polymers71,2934
Non-polymers2362
Water543
1
A: E3 ubiquitin-protein ligase sspH1
B: Serine/threonine-protein kinase N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7653
Polymers35,6472
Non-polymers1181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase sspH1
D: Serine/threonine-protein kinase N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7653
Polymers35,6472
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.623, 167.623, 89.143
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThere are two heterodimers in the asymmetric unit. The biological heterodimer belongs to the pairs: (i) Chain A and Chain B, and (ii) Chain C and Chain D.

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Components

#1: Protein E3 ubiquitin-protein ligase sspH1 / Salmonella secreted protein H1 / Secreted effector protein sspH1


Mass: 26580.072 Da / Num. of mol.: 2 / Fragment: LRR domains, UNP residues 161-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028S / Gene: sspH1, STM14_1483 / Plasmid: pProEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3) RIL
References: UniProt: D0ZVG2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Serine/threonine-protein kinase N1 / Protease-activated kinase 1 / PAK-1 / Protein kinase C-like 1 / Protein kinase C-like PKN / Protein ...Protease-activated kinase 1 / PAK-1 / Protein kinase C-like 1 / Protein kinase C-like PKN / Protein kinase PKN-alpha / Protein-kinase C-related kinase 1 / Serine-threonine protein kinase N


Mass: 9066.469 Da / Num. of mol.: 2 / Fragment: HR1b domain, REM 2 domain, UNP residues 122-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1, PKN, PKN1, PRK1, PRKCL1 / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3) RIL / References: UniProt: Q16512, protein kinase C
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 5.07 Å3/Da / Density % sol: 75.74 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 26% PEG3350, 0.18M tri-Ammonium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 16, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 32240 / % possible obs: 100 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→2.98 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.35 Å / SU ML: 0.68 / σ(F): 1.35 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1615 5.05 %
Rwork0.209 --
obs0.21 32008 99.3 %
all-32008 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.45 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5617 Å20 Å20 Å2
2---2.5617 Å2-0 Å2
3---5.1234 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 16 3 4507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034668
X-RAY DIFFRACTIONf_angle_d0.6896350
X-RAY DIFFRACTIONf_dihedral_angle_d11.6021794
X-RAY DIFFRACTIONf_chiral_restr0.048744
X-RAY DIFFRACTIONf_plane_restr0.003830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9009-2.98620.3841330.32172513X-RAY DIFFRACTION99
2.9862-3.08250.30311500.28712496X-RAY DIFFRACTION100
3.0825-3.19270.3351260.27192523X-RAY DIFFRACTION100
3.1927-3.32040.31981470.27052500X-RAY DIFFRACTION100
3.3204-3.47150.31081520.25642495X-RAY DIFFRACTION100
3.4715-3.65440.2591340.22462542X-RAY DIFFRACTION100
3.6544-3.88310.22111270.20522527X-RAY DIFFRACTION99
3.8831-4.18270.21991240.18082530X-RAY DIFFRACTION100
4.1827-4.6030.21021270.17372551X-RAY DIFFRACTION99
4.603-5.26770.21311250.18092553X-RAY DIFFRACTION99
5.2677-6.63160.2291360.20362540X-RAY DIFFRACTION99
6.6316-39.35630.21671340.19782615X-RAY DIFFRACTION98
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)
16.3179-0.67362.98315.96281.55774.6952-0.0091-0.87380.15030.6711-0.0597-0.21330.1258-1.52560.06270.5719-0.07660.04370.5759-0.02250.630765.1743-26.936366.6404
24.52820.9560.41977.07390.71557.65280.3032-0.3337-0.61790.2002-0.0962-0.88720.4431-0.5284-0.13370.296-0.0832-0.12910.15740.01490.676366.418-30.224255.5435
33.65681.72841.07484.7425-0.99257.3981-0.46670.4935-0.3141-0.67560.2845-0.1066-0.2593-0.27340.30160.5254-0.0882-0.02980.246-0.06850.812967.7714-25.568333.452
44.6335-1.1665-4.58289.1142.04874.62350.29240.1241-1.0636-0.9292-0.34840.78780.0004-0.5141-0.4691.3196-0.1582-0.49110.88630.21631.156760.8802-18.909213.0579
54.94263.06045.92756.17152.40539.0529-0.26850.31741.3193-1.1708-0.31920.1539-0.5364-0.36490.68071.0370.115-0.16360.39590.0331.059367.018-5.310633.2536
63.71062.44370.95135.92892.05092.70580.5377-0.3661-0.15340.77730.16840.1730.502-0.1288-0.58360.93110.0739-0.08280.26290.16060.90268.7163-9.205141.6699
79.1172.92070.77487.65854.99213.57440.29510.7951-0.7145-0.3609-0.1387-1.2494-0.4653-0.3509-0.33440.3934-0.07450.02410.6779-0.09540.523362.2299-55.341119.4341
88.47575.84291.4585.72423.65426.0139-0.17751.1281.2197-1.1757-0.29612.458-1.413-0.74190.37260.52320.0198-0.14850.67610.13490.731355.2963-49.059222.0322
92.98490.6221-0.67192.92211.40985.26960.3130.2713-0.0585-0.5370.0075-0.0458-0.4436-0.3614-0.46180.2983-0.12080.03730.4872-0.03960.730758.0188-51.048830.2773
102.0108-0.3958-0.87644.9065-1.24944.52980.0922-0.05090.11630.8652-0.0258-1.0471-0.3208-0.09340.00180.3754-0.2646-0.10710.4083-0.07440.829659.8566-56.437146.2292
116.960.6810.02322.37832.35488.5516-0.0353-0.53940.03251.880.0165-0.6591-0.7201-0.2208-0.02251.3752-0.3744-0.09710.6634-0.02630.605754.9551-58.133261.4696
127.2221-3.7615-0.45352.44171.76224.85340.1065-0.85510.56770.11660.2148-1.09610.3379-0.4097-0.39691.453-0.29650.17210.6139-0.1250.803151.6692-61.303165.2547
135.2016-2.50983.21012.6487-0.23583.58280.3692-1.78710.06041.0657-0.26250.45371.0501-1.6937-0.43631.5516-0.61740.3011.3638-0.11710.904747.305-59.449272.1301
141.8118-0.46980.75367.30372.53162.1024-0.0599-0.1726-0.48030.47010.1661-0.03520.3832-0.1821-0.18940.6393-0.41020.16750.68410.06191.070142.1294-72.542554.59
151.60341.99372.30595.56735.77636.16130.37521.27520.1028-0.06190.3641-1.53480.51312.1797-1.38521.3274-0.2420.20192.0947-0.32441.907158.1782-86.001241.1448
166.39580.0697-3.09071.6218-0.91716.2333-0.23430.5817-0.2588-0.63190.32990.1183-0.3354-0.0783-0.22040.5516-0.29670.18540.5716-0.04020.842545.5799-68.922847.489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 162:211)
2X-RAY DIFFRACTION2chain 'A' and (resseq 212:244)
3X-RAY DIFFRACTION3chain 'A' and (resseq 245:373)
4X-RAY DIFFRACTION4chain 'A' and (resseq 374:394)
5X-RAY DIFFRACTION5chain 'B' and (resseq 125:151)
6X-RAY DIFFRACTION6chain 'B' and (resseq 152:190)
7X-RAY DIFFRACTION7chain 'C' and (resseq 160:178)
8X-RAY DIFFRACTION8chain 'C' and (resseq 179:195)
9X-RAY DIFFRACTION9chain 'C' and (resseq 196:223)
10X-RAY DIFFRACTION10chain 'C' and (resseq 224:318)
11X-RAY DIFFRACTION11chain 'C' and (resseq 319:338)
12X-RAY DIFFRACTION12chain 'C' and (resseq 339:353)
13X-RAY DIFFRACTION13chain 'C' and (resseq 354:394)
14X-RAY DIFFRACTION14chain 'D' and (resseq 125:151)
15X-RAY DIFFRACTION15chain 'D' and (resseq 152:156)
16X-RAY DIFFRACTION16chain 'D' and (resseq 157:189)

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