[English] 日本語
Yorodumi
- PDB-1qiw: Calmodulin complexed with N-(3,3,-diphenylpropyl)-N'-[1-R-(3,4-bi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qiw
TitleCalmodulin complexed with N-(3,3,-diphenylpropyl)-N'-[1-R-(3,4-bis-butoxyphenyl)-ethyl]-propylenediamine (DPD)
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 / negative regulation of high voltage-gated calcium channel activity / nitric-oxide synthase binding / positive regulation of DNA binding / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / calcineurin-mediated signaling / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of synaptic vesicle endocytosis / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / regulation of cardiac muscle contraction / calcium channel regulator activity / detection of calcium ion / 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 complex / potassium ion transmembrane transport / nitric-oxide synthase regulator activity / response to amphetamine / adenylate cyclase activator activity / regulation of heart rate / sarcomere / positive regulation of nitric-oxide synthase activity / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / calcium-mediated signaling / spindle pole / response to calcium ion / 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: 2.3 Å
AuthorsHarmat, V. / Bocskei, Z.S. / Vertessy, B.G. / Ovadi, J. / Naray-Szabo, G.
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: 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.
#2: 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.
#3: 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 / software / 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 / _software.name / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CALMODULIN
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,31413
Polymers33,4432
Non-polymers1,87111
Water00
1
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9157
Polymers16,7211
Non-polymers1,1946
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3986
Polymers16,7211
Non-polymers6775
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.960, 56.200, 35.270
Angle α, β, γ (deg.)99.52, 114.47, 96.86
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.638671, 0.193606, -0.744725), (0.194159, -0.895966, -0.399434), (-0.744581, -0.399702, 0.534637)
Vector: 25.519, 72.2145, 31.1185)

-
Components

#1: Protein CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 2 / 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.: 8 / 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.: 3 / Source method: obtained synthetically / Formula: C34H48N2O2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.185 Å3/Da / Density % sol: 44 %
Description: THE TWO DOMAINS OF 1LIN WERE USED SEPARATEDLY AS MODELS
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP TECHNIQUE. 50 MM PH=6.0 SODIUM CACODYLATE/HCL BUFFER, 10 MM MGCL2, 10 MM CACL2, 2MM DPD AND 30% PEG 8000 THE CRYSTAL COULD NOT BE REPRODUCED., pH 6.00
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

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 15, 1996 / 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: 2.3→54.23 Å / Num. obs: 8711 / % possible obs: 69.2 % / Observed criterion σ(I): 3 / Redundancy: 1.7 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.093 / Net I/σ(I): 2.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.513 / % possible all: 25.3

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
bioteXdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIN

1lin


Resolution: 2.3→54.23 Å / Rfactor Rfree error: 0.014 / 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 A2, A7, A47, A78, A79, A86, A114, A123, B6, B13, B69, B77, B82, B84, B123, B127 AND 146 AS WELL AS TRIMETHYL-LYSINES A115, B115 ARE NOT PRESENT IN THE ...Details: DISORDERED SIDE CHAIN ATOMS OF RESIDUES A2, A7, A47, A78, A79, A86, A114, A123, B6, B13, B69, B77, B82, B84, B123, B127 AND 146 AS WELL AS TRIMETHYL-LYSINES A115, B115 ARE NOT PRESENT IN THE STRUCTURE TEMPERATURE FACTORS FOR THE ATOMS IN THE CENTRAL REGIONS (A73-A80, B75- B82),ATOMS AT THE ENDS OF THE POLIPEPTIDE CHAINS (A144-A146, B4-B7, B144) AS WELL AS FOR SOME SURFACE RESIDUES (A45, A84, A107, A112, B107, B119, B126) ARE UNUSUALLY HIGH, INDICATING FLEXIBILITY IN THESE PARTS OF THE STRUCTURE. THE C-TERMINAL RESIDUES FOR BOTH CHAINS A AND B WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.317 483 5.5 %RANDOM
Rwork0.232 ---
obs0.232 8711 69.24 %-
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.008 Å2-0.196 Å2-1.001 Å2
2---12.279 Å2-2.453 Å2
3----14.919 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.423 Å0.263 Å
Luzzati d res low-2.7 Å
Luzzati sigma a0.41 Å0.0962 Å
Refinement stepCycle: LAST / Resolution: 2.3→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 112 0 2324
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.232
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.506
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
Refine LS restraints NCSRms dev Biso : 5.019 Å2 / Rms dev position: 0.078 Å / Weight Biso : 10 / Weight position: 50
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.28 13 3.39 %
Rwork0.105 370 -
obs--24.39 %
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_deg25.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.506
LS refinement shell
*PLUS
Rfactor Rfree: 0.28

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more