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- PDB-6k4k: Crystal structure of SidJ-CaM binary complex at 2.71 A -

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Basic information

Entry
Database: PDB / ID: 6k4k
TitleCrystal structure of SidJ-CaM binary complex at 2.71 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 / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / regulation of ryanodine-sensitive calcium-release channel activity / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / cellular response to interferon-beta / Protein methylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / Ion homeostasis / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / cysteine-type peptidase activity / FCERI mediated Ca+2 mobilization / calcium channel complex / substantia nigra development / regulation of heart rate / FCGR3A-mediated IL10 synthesis / Ras activation upon Ca2+ influx through NMDA receptor / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / adenylate cyclase activator activity / sarcomere / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / regulation of cytokinesis / VEGFR2 mediated vascular permeability / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / RAF activation / Transcriptional activation of mitochondrial biogenesis / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Stimuli-sensing channels / spindle pole / Signaling by RAF1 mutants / calcium-dependent protein binding / RAS processing / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / long-term synaptic potentiation / Platelet degranulation / sperm midpiece / myelin sheath / synaptic vesicle membrane / Inactivation, recovery and regulation of the phototransduction cascade / transferase activity / RAF/MAP kinase cascade / Ca2+ pathway
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 / MOLECULAR REPLACEMENT / Resolution: 2.715 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
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)234,4626
Polymers234,3824
Non-polymers802
Water362
1
A: SidJ
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2313
Polymers117,1912
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-23 kcal/mol
Surface area37950 Å2
MethodPISA
2
B: SidJ
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2313
Polymers117,1912
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-11 kcal/mol
Surface area36990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.955, 159.533, 135.611
Angle α, β, γ (deg.)90.000, 101.890, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 100 through 105 or resid 107...
21(chain B and (resid 100 through 105 or resid 107...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 100 through 105 or resid 107...A100 - 105
121(chain A and (resid 100 through 105 or resid 107...A107 - 165
131(chain A and (resid 100 through 105 or resid 107...A167 - 204
141(chain A and (resid 100 through 105 or resid 107...A206 - 258
151(chain A and (resid 100 through 105 or resid 107...A324 - 342
161(chain A and (resid 100 through 105 or resid 107...A346 - 353
171(chain A and (resid 100 through 105 or resid 107...A371 - 379
181(chain A and (resid 100 through 105 or resid 107...A361 - 369
191(chain A and (resid 100 through 105 or resid 107...A374
1101(chain A and (resid 100 through 105 or resid 107...A381 - 402
1111(chain A and (resid 100 through 105 or resid 107...A404 - 415
1121(chain A and (resid 100 through 105 or resid 107...A404 - 415
1131(chain A and (resid 100 through 105 or resid 107...A424 - 432
1141(chain A and (resid 100 through 105 or resid 107...A432 - 430
1151(chain A and (resid 100 through 105 or resid 107...A448 - 483
1161(chain A and (resid 100 through 105 or resid 107...A438 - 446
1171(chain A and (resid 100 through 105 or resid 107...A490 - 518
1181(chain A and (resid 100 through 105 or resid 107...A517
1191(chain A and (resid 100 through 105 or resid 107...A526 - 560
1201(chain A and (resid 100 through 105 or resid 107...A562 - 577
1211(chain A and (resid 100 through 105 or resid 107...A562 - 577
1221(chain A and (resid 100 through 105 or resid 107...A631 - 679
1231(chain A and (resid 100 through 105 or resid 107...A673 - 681
1241(chain A and (resid 100 through 105 or resid 107...A704 - 757
1251(chain A and (resid 100 through 105 or resid 107...A689 - 702
1261(chain A and (resid 100 through 105 or resid 107...A761 - 829
1271(chain A and (resid 100 through 105 or resid 107...A827 - 845
1281(chain A and (resid 100 through 105 or resid 107...A827 - 843
1291(chain A and (resid 100 through 105 or resid 107...A846 - 848
211(chain B and (resid 100 through 105 or resid 107...B100 - 105
221(chain B and (resid 100 through 105 or resid 107...B107 - 165
231(chain B and (resid 100 through 105 or resid 107...B167 - 204
241(chain B and (resid 100 through 105 or resid 107...B206 - 258
251(chain B and (resid 100 through 105 or resid 107...B260 - 294
261(chain B and (resid 100 through 105 or resid 107...B296 - 322
271(chain B and (resid 100 through 105 or resid 107...B324 - 343
281(chain B and (resid 100 through 105 or resid 107...B346 - 359
291(chain B and (resid 100 through 105 or resid 107...B361 - 369
2101(chain B and (resid 100 through 105 or resid 107...B371 - 372
2111(chain B and (resid 100 through 105 or resid 107...B374
2121(chain B and (resid 100 through 105 or resid 107...B376 - 379
2131(chain B and (resid 100 through 105 or resid 107...B381 - 402
2141(chain B and (resid 100 through 105 or resid 107...B417 - 419
2151(chain B and (resid 100 through 105 or resid 107...B421 - 42
2161(chain B and (resid 100 through 105 or resid 107...B424
2171(chain B and (resid 100 through 105 or resid 107...B430
2181(chain B and (resid 100 through 105 or resid 107...B432 - 433
2191(chain B and (resid 100 through 105 or resid 107...B448 - 4456
2201(chain B and (resid 100 through 105 or resid 107...B99 - 846
2211(chain B and (resid 100 through 105 or resid 107...B99 - 846
2221(chain B and (resid 100 through 105 or resid 107...B99 - 846
2231(chain B and (resid 100 through 105 or resid 107...B99 - 846
2241(chain B and (resid 100 through 105 or resid 107...B99 - 846

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Components

#1: Protein SidJ


Mass: 100338.469 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-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 3350, 0.2M NaI / PH range: 6.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.71→132.7 Å / Num. obs: 66303 / % possible obs: 97 % / Redundancy: 12.9 % / Biso Wilson estimate: 61.36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.061 / Net I/σ(I): 2
Reflection shellResolution: 2.71→2.86 Å / Rmerge(I) obs: 1.401 / Num. unique obs: 857415 / CC1/2: 0.607

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.715→55.87 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.35
RfactorNum. reflection% reflection
Rfree0.2426 1994 3.01 %
Rwork0.2049 --
obs0.2061 66244 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 204.6 Å2 / Biso mean: 68.1487 Å2 / Biso min: 31.86 Å2
Refinement stepCycle: final / Resolution: 2.715→55.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13089 0 2 2 13093
Biso mean--128.39 57.77 -
Num. residues----1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113369
X-RAY DIFFRACTIONf_angle_d0.91918135
X-RAY DIFFRACTIONf_chiral_restr0.0532072
X-RAY DIFFRACTIONf_plane_restr0.0062334
X-RAY DIFFRACTIONf_dihedral_angle_d5.1198014
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6296X-RAY DIFFRACTION9.451TORSIONAL
12B6296X-RAY DIFFRACTION9.451TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.715-2.78280.3026142456497
2.7828-2.8580.2961444.930.265462398
2.858-2.94210.34411470.2833467899
2.9421-3.03710.32581480.2674467799
3.0371-3.14560.30951420.2481464099
3.1456-3.27160.29891450.2299470499
3.2716-3.42040.28761450.2296470399
3.4204-3.60070.26221510.2236471499
3.6007-3.82630.2414970.1996322768
3.8263-4.12160.2291410.1859470399
4.1216-4.53620.19281460.16844713100
4.5362-5.19220.20731460.17144753100
5.1922-6.54010.26081560.21154738100
6.5401-55.870.19241440.18394813100
Refinement TLS params.Method: refined / Origin x: -3.2778 Å / Origin y: -32.727 Å / Origin z: -21.2012 Å
111213212223313233
T0.3334 Å2-0.003 Å2-0.044 Å2-0.3807 Å2-0.0062 Å2--0.463 Å2
L0.3701 °2-0.0035 °2-0.2557 °2-0.3 °20.0537 °2--1.0239 °2
S0.0164 Å °0.0253 Å °-0.0565 Å °0.0249 Å °-0.0348 Å °0.0227 Å °-0.0417 Å °-0.0409 Å °0.0169 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA99 - 848
2X-RAY DIFFRACTION1allB99 - 846
3X-RAY DIFFRACTION1allC3 - 142
4X-RAY DIFFRACTION1allD4 - 121
5X-RAY DIFFRACTION1allF1 - 2
6X-RAY DIFFRACTION1allE1 - 2

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