[English] 日本語
Yorodumi
- PDB-4upg: X-ray structure of calcium-free human sorcin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4upg
TitleX-ray structure of calcium-free human sorcin
ComponentsSORCIN
KeywordsMETAL BINDING PROTEIN / CA-BINDING PROTEIN / PENTA-EF HAND / APOPTOSIS REGULATION
Function / homology
Function and homology information


regulation of relaxation of muscle / regulation of high voltage-gated calcium channel activity / regulation of cell communication by electrical coupling / negative regulation of cardiac muscle contraction / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / negative regulation of heart rate / regulation of cell communication by electrical coupling involved in cardiac conduction ...regulation of relaxation of muscle / regulation of high voltage-gated calcium channel activity / regulation of cell communication by electrical coupling / negative regulation of cardiac muscle contraction / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / negative regulation of heart rate / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of ryanodine-sensitive calcium-release channel activity / Ion transport by P-type ATPases / regulation of calcium ion transport / transcription regulator inhibitor activity / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / sarcoplasmic reticulum membrane / calcium channel regulator activity / T-tubule / protein sequestering activity / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / calcium ion transport / protease binding / DNA-binding transcription factor binding / transmembrane transporter binding / protein heterodimerization activity / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
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 / 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
DI(HYDROXYETHYL)ETHER / Sorcin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIlari, A. / Fiorillo, A. / Colotti, G.
CitationJournal: Sci.Rep. / Year: 2015
Title: Structural Basis of Sorcin-Mediated Calcium-Dependent Signal Transduction.
Authors: Ilari, A. / Fiorillo, A. / Poser, E. / Lalioti, V.S. / Sundell, G.N. / Ivarsson, Y. / Genovese, I. / Colotti, G.
History
DepositionJun 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / 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 / _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: SORCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7678
Polymers19,0741
Non-polymers6937
Water1,31573
1
A: SORCIN
hetero molecules

A: SORCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,53416
Polymers38,1492
Non-polymers1,38514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_444-y-1/2,-x-1/2,-z-1/21
Buried area6540 Å2
ΔGint-129.3 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.450, 106.450, 77.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1200-

SO4

21A-1200-

SO4

-
Components

#1: Protein SORCIN / 22 KDA PROTEIN / CP-22 / CP22 / V19


Mass: 19074.498 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30626
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.58 Å3/Da / Density % sol: 43.9 % / Description: NONE
Crystal growDetails: 20% PEG4000, 0.3 M AMMONIUM SULFATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 197835 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.82
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.61 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JUO

1juo


Resolution: 2.1→40.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.939 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21974 673 5.1 %RANDOM
Rwork0.18144 ---
obs0.18324 12641 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.342 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 39 73 1448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021451
X-RAY DIFFRACTIONr_bond_other_d0.0040.021327
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9621969
X-RAY DIFFRACTIONr_angle_other_deg0.84633050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8525184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28324.21176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70815243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0371512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021688
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02362
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 48 -
Rwork0.234 922 -
obs--99.9 %

+
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