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- PDB-4upu: Crystal structure of IP3 3-K calmodulin binding region in complex... -

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Basic information

Entry
Database: PDB / ID: 4upu
TitleCrystal structure of IP3 3-K calmodulin binding region in complex with Calmodulin
Components
  • CALMODULIN
  • INOSITOL-TRISPHOSPHATE 3-KINASE A
KeywordsTRANSFERASE
Function / homology
Function and homology information


inositol-trisphosphate 3-kinase / inositol-1,4,5-trisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / modification of postsynaptic actin cytoskeleton / inositol metabolic process / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of ryanodine-sensitive calcium-release channel activity ...inositol-trisphosphate 3-kinase / inositol-1,4,5-trisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / modification of postsynaptic actin cytoskeleton / inositol metabolic process / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / : / positive regulation of protein autophosphorylation / positive regulation of dendritic spine morphogenesis / negative regulation of peptidyl-threonine phosphorylation / postsynaptic actin cytoskeleton / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / calcium/calmodulin-dependent protein kinase activity / dendritic spine maintenance / CaM pathway / Cam-PDE 1 activation / positive regulation of peptidyl-threonine phosphorylation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / 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 / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / 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 / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / Phase 0 - rapid depolarisation / phosphatidylinositol phosphate biosynthetic process / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / adenylate cyclase binding / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / positive regulation of protein serine/threonine kinase activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / 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 / activation of adenylate cyclase activity / cellular response to interferon-beta / Protein methylation / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of nitric-oxide synthase activity / eNOS activation / enzyme regulator activity / titin binding / sperm midpiece / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / cellular response to calcium ion / FCGR3A-mediated IL10 synthesis / calyx of Held / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to amphetamine / adenylate cyclase activator activity / sarcomere
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / : / 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
Similarity search - Domain/homology
Calmodulin-1 / Inositol-trisphosphate 3-kinase A / Calmodulin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsFranco-Echevarria, E. / Banos-Sanz, J.I. / Monterroso, B. / Round, A. / Sanz-Aparicio, J. / Gonzalez, B.
CitationJournal: Biochem.J. / Year: 2014
Title: A New Calmodulin Binding Motif for Inositol 1,4,5-Trisphosphate 3-Kinase Regulation.
Authors: Franco-Echevarria, E. / Banos-Sanz, J.I. / Monterroso, B. / Round, A. / Sanz-Aparicio, J. / Gonzalez, B.
History
DepositionJun 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Other / Structure summary
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: CALMODULIN
B: INOSITOL-TRISPHOSPHATE 3-KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0418
Polymers19,7492
Non-polymers2926
Water1,45981
1
A: CALMODULIN
B: INOSITOL-TRISPHOSPHATE 3-KINASE A
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)480,992192
Polymers473,97348
Non-polymers7,020144
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_564-x,z+1,y-11
crystal symmetry operation7_564-z,-x+1,y-11
crystal symmetry operation20_564x,-z+1,y-11
crystal symmetry operation8_566-z,x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation17_566x,z+1,-y+11
crystal symmetry operation22_575z,-y+2,x1
crystal symmetry operation19_566-x,-z+1,-y+11
crystal symmetry operation10_665-y+1,z+1,-x1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation13_465y-1,x+1,-z1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation15_465y-1,-x+1,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation9_465y-1,z+1,x1
crystal symmetry operation11_465y-1,-z+1,-x1
crystal symmetry operation24_575-z,-y+2,-x1
crystal symmetry operation14_665-y+1,-x+1,-z1
crystal symmetry operation16_665-y+1,x+1,z1
Buried area119950 Å2
ΔGint-2468.9 kcal/mol
Surface area165820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.480, 159.480, 159.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-1153-

CA

21A-2018-

HOH

31A-2019-

HOH

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Components

#1: Protein CALMODULIN / CAM


Mass: 16721.350 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide INOSITOL-TRISPHOSPHATE 3-KINASE A / INOSITOL 1\ / 4\ / 5-TRISPHOSPHATE 3-KINASE A / IP3 3-KINASE A / IP3K A / INSP 3-KINASE A


Mass: 3027.520 Da / Num. of mol.: 1 / Fragment: CALMODULIN BINDING REGION, RESIDUES 158-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PKLSLT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: P23677, inositol-trisphosphate 3-kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 4 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 4
Details: 29% W/V POLYETHYLENE GLYCOL 4000, 0.2 M (NH4)2SO4, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.0 AND 10 MM SPERMIDINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2012 / Details: KB FOCUSING MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.34→79.74 Å / Num. obs: 14994 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.91
Reflection shellResolution: 2.34→2.46 Å / Redundancy: 12.66 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.06 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VAY

2vay


Resolution: 2.34→79.65 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.581 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21041 752 5 %RANDOM
Rwork0.18805 ---
obs0.18916 14144 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.465 Å2
Baniso -1Baniso -2Baniso -3
1-5.77 Å2-1.8 Å2-18.88 Å2
2---11.33 Å2-2.03 Å2
3---5.56 Å2
Refinement stepCycle: LAST / Resolution: 2.34→79.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 11 81 1397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191342
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.961806
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23926.21674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03815251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.743157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021024
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.1043.285661
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2864.903825
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4783.663680
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 54 -
Rwork0.223 1031 -
obs--100 %

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