[English] 日本語
Yorodumi
- PDB-6aki: Calcium release-activated calcium channel protein 1, P288L mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aki
TitleCalcium release-activated calcium channel protein 1, P288L mutant
ComponentsCalcium release-activated calcium channel protein 1
KeywordsMEMBRANE PROTEIN / Calcium Channel
Function / homology
Function and homology information


store-operated calcium entry / store-operated calcium channel activity / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of calcium ion transport / calcium channel regulator activity / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / nervous system development / membrane ...store-operated calcium entry / store-operated calcium channel activity / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of calcium ion transport / calcium channel regulator activity / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / nervous system development / membrane / identical protein binding / plasma membrane
Similarity search - Function
Calcium release-activated calcium channel protein / Orai superfamily / Mediator of CRAC channel activity
Similarity search - Domain/homology
Calcium release-activated calcium channel protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.496 Å
AuthorsLiu, X. / Wu, G. / Yang, X. / Shen, Y.
CitationJournal: To Be Published
Title: Calcium release-activated calcium channel protein 1, P288L mutant
Authors: Liu, X. / Wu, G. / Yang, X. / Shen, Y.
History
DepositionSep 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
A: Calcium release-activated calcium channel protein 1
B: Calcium release-activated calcium channel protein 1
C: Calcium release-activated calcium channel protein 1
D: Calcium release-activated calcium channel protein 1
E: Calcium release-activated calcium channel protein 1
F: Calcium release-activated calcium channel protein 1
O: Calcium release-activated calcium channel protein 1
P: Calcium release-activated calcium channel protein 1
Q: Calcium release-activated calcium channel protein 1
R: Calcium release-activated calcium channel protein 1
S: Calcium release-activated calcium channel protein 1
T: Calcium release-activated calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,00716
Polymers284,86612
Non-polymers1424
Water0
1
A: Calcium release-activated calcium channel protein 1
B: Calcium release-activated calcium channel protein 1
C: Calcium release-activated calcium channel protein 1
D: Calcium release-activated calcium channel protein 1
E: Calcium release-activated calcium channel protein 1
F: Calcium release-activated calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5048
Polymers142,4336
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19210 Å2
ΔGint-270 kcal/mol
Surface area44600 Å2
MethodPISA
2
O: Calcium release-activated calcium channel protein 1
P: Calcium release-activated calcium channel protein 1
Q: Calcium release-activated calcium channel protein 1
R: Calcium release-activated calcium channel protein 1
S: Calcium release-activated calcium channel protein 1
T: Calcium release-activated calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5048
Polymers142,4336
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19610 Å2
ΔGint-274 kcal/mol
Surface area44910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.107, 90.659, 178.721
Angle α, β, γ (deg.)90.00, 106.31, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Calcium release-activated calcium channel protein 1 / Protein orai / dOrai


Mass: 23738.793 Da / Num. of mol.: 12 / Fragment: UNP residues 132-341 / Mutation: P288L, C283T, C224S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell line (production host): HEK293S-GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q9U6B8
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.05M NaCl,0.02M MgCl2, 0.1M Sodium citrate pH 6.5, 16-20% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.49→50 Å / Num. obs: 17659 / % possible obs: 80.7 % / Redundancy: 3.5 % / Net I/σ(I): 7.94
Reflection shellResolution: 4.49→4.66 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.496→26.475 Å / SU ML: 1.02 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 47.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3862 2958 10.09 %
Rwork0.3246 --
obs0.3306 17659 69.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.496→26.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12372 0 4 0 12376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412540
X-RAY DIFFRACTIONf_angle_d0.92817124
X-RAY DIFFRACTIONf_dihedral_angle_d2.9247356
X-RAY DIFFRACTIONf_chiral_restr0.0472340
X-RAY DIFFRACTIONf_plane_restr0.0062016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4964-4.56970.389410.3374362X-RAY DIFFRACTION20
4.5697-4.64810.355460.3332369X-RAY DIFFRACTION21
4.6481-4.73220.3553550.3352431X-RAY DIFFRACTION24
4.7322-4.82260.4007610.3073457X-RAY DIFFRACTION26
4.8226-4.92050.4504570.2953598X-RAY DIFFRACTION32
4.9205-5.02670.4146820.2639716X-RAY DIFFRACTION40
5.0267-5.14290.4643970.2931873X-RAY DIFFRACTION48
5.1429-5.27050.5321190.32961054X-RAY DIFFRACTION59
5.2705-5.41180.45761440.3671318X-RAY DIFFRACTION74
5.4118-5.56960.44111800.40981607X-RAY DIFFRACTION90
5.5696-5.74760.45211770.41021687X-RAY DIFFRACTION92
5.7476-5.95080.41931890.43061692X-RAY DIFFRACTION94
5.9508-6.18620.43811960.42231661X-RAY DIFFRACTION93
6.1862-6.46380.38981800.39881712X-RAY DIFFRACTION94
6.4638-6.79920.47741920.40441630X-RAY DIFFRACTION92
6.7992-7.2170.45941740.38621656X-RAY DIFFRACTION92
7.217-7.76120.41821900.34371777X-RAY DIFFRACTION97
7.7612-8.51860.32721980.26551722X-RAY DIFFRACTION98
8.5186-9.69780.2882070.23861759X-RAY DIFFRACTION97
9.6978-12.02460.30411830.25781664X-RAY DIFFRACTION92
12.0246-26.47510.38681900.35161609X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 105.4684 Å / Origin y: -80.5324 Å / Origin z: 43.3799 Å
111213212223313233
T0.7409 Å20.21 Å2-0.4297 Å2-1.4671 Å2-0.0568 Å2--0.8579 Å2
L2.3964 °20.8889 °22.2316 °2-0.3474 °20.7191 °2--2.3416 °2
S0.0194 Å °0.3643 Å °0.0405 Å °-0.1877 Å °0.089 Å °0.1461 Å °0.0886 Å °0.1999 Å °0.038 Å °
Refinement TLS groupSelection details: all

+
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