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- PDB-6k4l: Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A -

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Basic information

Entry
Database: PDB / ID: 6k4l
TitleCrystal structure of Se-labelled SidJ complex with CaM at 2.95 A
Components
  • Calmodulin-1
  • SidJ
KeywordsTRANSFERASE/CELL CYCLE / effect factor / TOXIN / TRANSFERASE-CELL CYCLE complex
Function / homology
Function and homology information


protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Ligases / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...protein-glutamic acid ligase activity, initiating / protein-glutamic acid ligase activity, elongating / Ligases / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / cysteine-type peptidase activity / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / RAS processing / spindle pole / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade / Platelet degranulation / myelin sheath / transferase activity / Ca2+ pathway / RAF/MAP kinase cascade / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells
Similarity search - Function
EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-dependent glutamylase SidJ
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.949 Å
AuthorsOuyang, S.Y.
CitationJournal: Nature / Year: 2019
Title: Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase.
Authors: Gan, N. / Zhen, X. / Liu, Y. / Xu, X. / He, C. / Qiu, J. / Liu, Y. / Fujimoto, G.M. / Nakayasu, E.S. / Zhou, B. / Zhao, L. / Puvar, K. / Das, C. / Ouyang, S. / Luo, Z.Q.
History
DepositionMay 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Oct 16, 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 / _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: SidJ
B: SidJ
C: Calmodulin-1
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,91710
Polymers235,6954
Non-polymers2226
Water28816
1
A: SidJ
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9595
Polymers117,8482
Non-polymers1113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-53 kcal/mol
Surface area35890 Å2
MethodPISA
2
B: SidJ
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9595
Polymers117,8482
Non-polymers1113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-34 kcal/mol
Surface area34640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.060, 159.246, 135.809
Angle α, β, γ (deg.)90.00, 101.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SidJ


Mass: 100995.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg2155 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZTK6
#2: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 3350, 0.2M NaI / PH range: 6.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97981 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
ReflectionResolution: 2.949→133 Å / Num. obs: 53504 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 2
Reflection shellResolution: 2.95→3.11 Å / Num. unique obs: 54886 / CC1/2: 0.607
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.949→68.316 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.74 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2686 2575 4.82 %
Rwork0.2427 --
obs0.2439 53446 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.949→68.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12576 0 6 16 12598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412866
X-RAY DIFFRACTIONf_angle_d0.87217496
X-RAY DIFFRACTIONf_dihedral_angle_d5.437695
X-RAY DIFFRACTIONf_chiral_restr0.0492021
X-RAY DIFFRACTIONf_plane_restr0.0052250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9493-3.0060.39421450.35832808X-RAY DIFFRACTION100
3.006-3.06740.35521380.32612823X-RAY DIFFRACTION100
3.0674-3.13410.34531490.31562804X-RAY DIFFRACTION100
3.1341-3.2070.35291180.31022867X-RAY DIFFRACTION100
3.207-3.28720.32841220.29662818X-RAY DIFFRACTION100
3.2872-3.37610.30921360.28942849X-RAY DIFFRACTION100
3.3761-3.47540.33881530.28222788X-RAY DIFFRACTION100
3.4754-3.58760.31131350.27422835X-RAY DIFFRACTION100
3.5876-3.71580.27221550.24542808X-RAY DIFFRACTION100
3.7158-3.86460.25591720.23842788X-RAY DIFFRACTION100
3.8646-4.04040.2821690.22152811X-RAY DIFFRACTION100
4.0404-4.25340.25921450.21692806X-RAY DIFFRACTION100
4.2534-4.51980.27051580.20032791X-RAY DIFFRACTION100
4.5198-4.86870.22481590.19962836X-RAY DIFFRACTION100
4.8687-5.35850.21681320.21442825X-RAY DIFFRACTION100
5.3585-6.13350.24191260.23762887X-RAY DIFFRACTION100
6.1335-7.72580.25211320.24722860X-RAY DIFFRACTION100
7.7258-68.33430.21631310.22112867X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 34.0432 Å / Origin y: 50.9321 Å / Origin z: 20.8439 Å
111213212223313233
T0.0751 Å20.0019 Å2-0.0191 Å2-0.1083 Å20.0183 Å2--0.1315 Å2
L0.1137 °2-0.0039 °2-0.139 °2-0.2047 °2-0.1455 °2--0.5843 °2
S0.0102 Å °-0.0455 Å °-0.0385 Å °-0.0223 Å °-0.0466 Å °-0.0405 Å °-0.072 Å °0.0561 Å °-0.0047 Å °
Refinement TLS groupSelection details: all

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