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- PDB-1qiv: CALMODULIN COMPLEXED WITH N-(3,3,-DIPHENYLPROPYL)-N'-[1-R-(3,4-BI... -

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Basic information

Entry
Database: PDB / ID: 1qiv
TitleCALMODULIN COMPLEXED WITH N-(3,3,-DIPHENYLPROPYL)-N'-[1-R-(3,4-BIS-BUTOXYPHENYL)-ETHYL]-PROPYLENEDIAMINE (DPD), 1:2 COMPLEX
ComponentsCALMODULIN
KeywordsCALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / : / regulation of high voltage-gated calcium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : ...regulation of store-operated calcium channel activity / : / regulation of high voltage-gated calcium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / positive regulation of DNA binding / negative regulation of high voltage-gated calcium channel activity / 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 / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / calcineurin-mediated signaling / regulation of synaptic vesicle endocytosis / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / voltage-gated potassium channel complex / calcium channel regulator activity / potassium ion transmembrane transport / calcium channel complex / nitric-oxide synthase regulator activity / response to amphetamine / positive regulation of nitric-oxide synthase activity / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / spindle microtubule / calcium-mediated signaling / response to calcium ion / spindle pole / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / disordered domain specific binding / myelin sheath / growth cone / protein autophosphorylation / vesicle / transmembrane transporter binding / neuron projection / positive regulation of apoptotic process / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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
Chem-DPD / Calmodulin-1 / Calmodulin
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsHarmat, V. / Bocskei, Z.S. / Vertessy, B.G. / Naray-Szabo, G. / Ovadi, J.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: A New Potent Calmodulin Antagonist with Arylalkylamine Structure: Crystallographic, Spectroscopic and Functional Studies
Authors: Harmat, V. / Bocskei, Z.S. / Naray-Szabo, G. / Bata, I. / Csutor, A.S. / Hermecz, I. / Aranyi, P. / Szabo, B. / Liliom, K. / Vertessy, B.G. / Ovadi, J.
#1: Journal: Biochemistry / Year: 1998
Title: Simultaneous Binding of Drugs with Different Chemical Structures to Ca 2+ Calmodulin: Crystallographic and Spectroscopic Studies
Authors: Vertessy, B.G. / Harmat, V. / Bocskei, Z.S. / Naray-Szabo, G. / Orosz, F. / Ovadi, J.
#2: Journal: Proteins: Struct.,Funct., Genet. / Year: 1997
Title: Crystallization and Preliminary Diffraction Analysis of Ca(2+)-Calmodulin-Drug and Apocalmodulin-Drug Complexes.
Authors: Vertessy, B.G. / Bocskei, Z.S. / Harmath, V. / Naray-Szabo, G. / Ovadi, J.
#3: Journal: Nat.Struct.Biol. / Year: 1994
Title: Trifluoperazine-Induced Conformational Change in Ca (2+)-Calmodulin
Authors: Vandonselaar, M. / Hickie, R.A. / Quail, J.W. / Delbaere, L.T.J.
#4: Journal: Biochemistry / Year: 1994
Title: Drug Binding by Calmodulin: Crystal Structure of a Calmodulin-Trifluoperazine Complex
Authors: Cook, W.J. / Walter, L.J. / Walter, M.R.
History
DepositionJun 17, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9157
Polymers16,7211
Non-polymers1,1946
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.125, 40.125, 173.814
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Cellular location: CYTOPLASM / Organ: BRAIN / References: UniProt: P02593, UniProt: P62157*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DPD / N-(3,3,-DIPHENYLPROPYL)-N'-[1-R-(2 3,4-BIS-BUTOXYPHENYL)-ETHYL]-PROPYLENEDIAMINE


Mass: 516.757 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H48N2O2

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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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP TECHNIQUE AT ROOM TEMPERATURE FROM 50 MM PH=5.0 SODIUM CACODYLATE/HCL BUFFER, 10 MM MGCL2, 10 MM CACL2, 2MM DPD AND 28% PEG 8000. CRYSTAL GROWTH TOOK 2-3 WEEKS., pH 5.00
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21 mMHEPES1drop
35 mM1dropCaCl2
42 mMAAA1drop
550 mMsodium cacodylate1reservoir
610 mM1reservoirCaCl2
710 mM1reservoirMgCl2
825-30 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: NORMAL FOCUS
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.63→24.58 Å / Num. obs: 4969 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.6
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 9 / % possible all: 76.2
Reflection
*PLUS
Num. measured all: 107694

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIN

1lin


Resolution: 2.64→24.58 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED SIDE CHAIN ATOMS OF RESIDUES ARG 74 - THR 79 AND SER 81 OF THE CENTRAL REGION, GLU 6, GLU 83, TRIMETHYL-LYSINE 115, GLU 123 AND GLU 127 ARE NOT SEEN IN THE CRYSTAL STRUCTURE, AS ...Details: DISORDERED SIDE CHAIN ATOMS OF RESIDUES ARG 74 - THR 79 AND SER 81 OF THE CENTRAL REGION, GLU 6, GLU 83, TRIMETHYL-LYSINE 115, GLU 123 AND GLU 127 ARE NOT SEEN IN THE CRYSTAL STRUCTURE, AS WELL AS THE N-TERMINAL ALA 1, ASP 2 AND C-TERMINAL ALA 147, LYS 148 RESIDUES. TEMPERATURE FACTORS FOR THE ATOMS IN RESIDUES 75 - 81 ARE UNUSUALLY HIGH, INDICATING FLEXIBILITY IN THIS REGION. THE C-TERMINAL RESIDUES WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.301 259 5.1 %RANDOM
Rwork0.207 ---
obs0.207 4965 94.3 %-
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--0.676 Å2-1.466 Å20 Å2
2---0.676 Å20 Å2
3----2.985 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.431 Å0.29 Å
Luzzati d res low-2.74 Å
Luzzati sigma a0.526 Å0.246 Å
Refinement stepCycle: LAST / Resolution: 2.64→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1096 0 80 0 1176
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.358
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.234
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.566
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.64→2.76 Å / Rfactor Rfree error: 0.085 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.445 30 5.2 %
Rwork0.228 473 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2CA.PARCA.TOP
X-RAY DIFFRACTION3AAA.PARAAA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.566

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