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Basic information

Entry
Database: PDB / ID: 5dow
TitleSolution of the Variably-Twinned Structure of a Novel Calmodulin-Peptide Complex in a Novel Configuration
Components
  • Calmodulin
  • Chloride anion exchanger
KeywordsCALCIUM BINDING PROTEIN / Calmodulin-Peptide Complex
Function / homology
Function and homology information


Multifunctional anion exchangers / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / chloride:bicarbonate antiporter activity / establishment of protein localization to mitochondrial membrane / negative regulation of peptidyl-threonine phosphorylation ...Multifunctional anion exchangers / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / chloride:bicarbonate antiporter activity / establishment of protein localization to mitochondrial membrane / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / bicarbonate transmembrane transporter activity / membrane hyperpolarization / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / chloride transmembrane transporter activity / 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 / positive regulation of DNA binding / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / sperm capacitation / 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 / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / adenylate cyclase binding / 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 / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / 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 / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / cellular response to cAMP / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / FCERI mediated Ca+2 mobilization / response to amphetamine / positive regulation of nitric-oxide synthase activity / Ras activation upon Ca2+ influx through NMDA receptor / 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
Similarity search - Function
Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / : ...Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / : / 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 / Calmodulin-3 / Chloride anion exchanger
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsKeller, J.P.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Solution of the structure of a calmodulin-peptide complex in a novel configuration from a variably twinned data set.
Authors: Keller, J.P.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Oct 9, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_reflns_twin / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_reflns_twin.operator / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Chloride anion exchanger
C: Calmodulin
D: Chloride anion exchanger
E: Calmodulin
F: Chloride anion exchanger
G: Calmodulin
H: Chloride anion exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,65342
Polymers77,3158
Non-polymers1,33834
Water19,7081094
1
A: Calmodulin
B: Chloride anion exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6449
Polymers19,3292
Non-polymers3157
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-91 kcal/mol
Surface area8970 Å2
MethodPISA
2
C: Calmodulin
D: Chloride anion exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,66412
Polymers19,3292
Non-polymers33610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-108 kcal/mol
Surface area9380 Å2
MethodPISA
3
E: Calmodulin
F: Chloride anion exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,66611
Polymers19,3292
Non-polymers3389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-116 kcal/mol
Surface area9080 Å2
MethodPISA
4
G: Calmodulin
H: Chloride anion exchanger
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,67910
Polymers19,3292
Non-polymers3508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-104 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.874, 98.874, 128.583
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21G-457-

HOH

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ACEGBDFH

#1: Protein
Calmodulin / CaM


Mass: 16769.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide
Chloride anion exchanger / slc26a3 transporter / Down-regulated in adenoma / Protein DRA / Solute carrier family 26 member 3


Mass: 2559.262 Da / Num. of mol.: 4 / Fragment: peptide (UNP residues 563-583) / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9WVC8

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Non-polymers , 5 types, 1128 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1094 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: ammonium sulfate, lithium sulfate, Tris/HEPES / PH range: 7.0 - 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 27, 2015 / Details: Varimax CuHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.42
11-h,-k,l20.58
ReflectionResolution: 1.7→22.81 Å / Num. obs: 76360 / % possible obs: 96.5 % / Redundancy: 21.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.021 / Net I/σ(I): 22.1 / Num. measured all: 1645262 / Scaling rejects: 2402
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.733.10.3332.9167.6
8.99-22.8126.90.0735.8193.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å22.82 Å
Translation1.7 Å22.82 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimless0.5.12data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→22.81 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.932 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14078 3697 4.8 %RANDOM
Rwork0.09711 ---
obs0.09928 72624 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.167 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å2-0 Å2
2---0.82 Å2-0 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 0 42 1094 6449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195883
X-RAY DIFFRACTIONr_bond_other_d0.0010.025506
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9717853
X-RAY DIFFRACTIONr_angle_other_deg0.808312746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7095747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53125.763321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3481544
X-RAY DIFFRACTIONr_chiral_restr0.0730.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021267
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_it1.5711.7672910
X-RAY DIFFRACTIONr_mcbond_other1.571.7672908
X-RAY DIFFRACTIONr_mcangle_it1.9692.6483671
X-RAY DIFFRACTIONr_mcangle_other1.9682.6483672
X-RAY DIFFRACTIONr_scbond_it1.8122.1292973
X-RAY DIFFRACTIONr_scbond_other1.7932.1222966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2853.5714171
X-RAY DIFFRACTIONr_long_range_B_refined4.49416.2286567
X-RAY DIFFRACTIONr_long_range_B_other3.4714.4375843
X-RAY DIFFRACTIONr_rigid_bond_restr6.113311380
X-RAY DIFFRACTIONr_sphericity_free29.2925227
X-RAY DIFFRACTIONr_sphericity_bonded9.592512140
LS refinement shellResolution: 1.699→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 187 -
Rwork0.193 3942 -
obs--70.73 %

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