[English] 日本語
Yorodumi
- PDB-1qx5: Crystal structure of apoCalmodulin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qx5
TitleCrystal structure of apoCalmodulin
ComponentsCalmodulin
KeywordsSIGNALING PROTEIN / apoCalmodulin / domain swap / dimer / EF hands / calcium 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 / presynaptic endocytosis / 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 / postsynaptic cytosol / 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 / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / 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 / sperm midpiece / calcium channel complex / calyx of Held / 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 / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / calcium-mediated signaling / Schaffer collateral - CA1 synapse / cellular response to type II interferon / 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
Calmodulin-1 / Calmodulin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.54 Å
AuthorsSchumacher, M.A. / Crum, M. / Miller, M.C.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex.
Authors: Schumacher, M.A. / Crum, M. / Miller, M.C.
History
DepositionSep 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Calmodulin
I: Calmodulin
B: Calmodulin
J: Calmodulin
K: Calmodulin
T: Calmodulin
R: Calmodulin
Y: Calmodulin


Theoretical massNumber of molelcules
Total (without water)133,7718
Polymers133,7718
Non-polymers00
Water3,153175
1
D: Calmodulin
Y: Calmodulin


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,4432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-37 kcal/mol
Surface area14400 Å2
MethodPISA
2
I: Calmodulin
R: Calmodulin


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,4432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-38 kcal/mol
Surface area14510 Å2
MethodPISA
3
J: Calmodulin
T: Calmodulin


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,4432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-37 kcal/mol
Surface area14460 Å2
MethodPISA
4
B: Calmodulin
K: Calmodulin


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,4432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-38 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.000, 146.000, 78.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsapoCaM forms a domain swapped dimer: there are four, essentially identical dimers in the ASU

-
Components

#1: Protein
Calmodulin


Mass: 16721.350 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: CALM1, CAM1, CALM, CAM, CALM2, CAM2, CAMB, CALM3, CAM3, CAMC
Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Citrate, 150 mM NaCl, Hepes , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.54→66.4 Å / Num. all: 61810 / Num. obs: 61810 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 75.4 Å2 / Rsym value: 0.047 / Net I/σ(I): 10.2
Reflection shellResolution: 2.54→2.7 Å / % possible all: 98.6

-
Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.54→66.39 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3041 5 %RANDOM
Rwork0.227 ---
all0.229 60402 --
obs0.227 60402 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.8149 Å2 / ksol: 0.374381 e/Å3
Displacement parametersBiso mean: 71.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å29.51 Å20 Å2
2---0.81 Å20 Å2
3---1.61 Å2
Refine analyzeLuzzati coordinate error free: 0.48 Å / Luzzati sigma a free: 0.51 Å
Refinement stepCycle: LAST / Resolution: 2.54→66.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9158 0 0 175 9333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shellResolution: 2.54→2.7 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.493 511 5.1 %
Rwork0.4 9531 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

+
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