[English] 日本語
Yorodumi
- PDB-5mra: human SCBD (sorcin calcium binding domain) in complex with doxorubicin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mra
Titlehuman SCBD (sorcin calcium binding domain) in complex with doxorubicin
ComponentsSorcinSRI (gene)
KeywordsMETAL BINDING PROTEIN / Sorcin (soluble resistance-related calcium binding protein)
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 / regulation of striated muscle contraction / negative regulation of cardiac muscle contraction / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / muscle organ development / regulation of heart contraction / Reduction of cytosolic Ca++ levels ...regulation of relaxation of muscle / regulation of high voltage-gated calcium channel activity / regulation of cell communication by electrical coupling / regulation of striated muscle contraction / negative regulation of cardiac muscle contraction / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / muscle organ development / regulation of heart contraction / Reduction of cytosolic Ca++ levels / negative regulation of heart rate / action potential / regulation of cell communication by electrical coupling involved in cardiac conduction / intracellular sequestering of iron ion / positive regulation of insulin secretion involved in cellular response to glucose stimulus / calcium channel regulator activity / regulation of calcium ion transport / Ion transport by P-type ATPases / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / sarcoplasmic reticulum membrane / T-tubule / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / calcium ion transport / heart development / DNA-binding transcription factor binding / protease binding / transmembrane transporter binding / protein heterodimerization activity / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / membrane / identical protein binding / 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
DOXORUBICIN / Sorcin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.74 Å
AuthorsIlari, A. / Fiorillo, A. / Colotti, G. / Genovese, I.
CitationJournal: Cell Death Dis / Year: 2017
Title: Binding of doxorubicin to Sorcin impairs cell death and increases drug resistance in cancer cells.
Authors: Genovese, I. / Fiorillo, A. / Ilari, A. / Masciarelli, S. / Fazi, F. / Colotti, G.
History
DepositionDec 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sorcin
B: Sorcin
C: Sorcin
D: Sorcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,25816
Polymers75,3934
Non-polymers86512
Water181
1
A: Sorcin
B: Sorcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4409
Polymers37,6972
Non-polymers7437
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-55 kcal/mol
Surface area15960 Å2
MethodPISA
2
C: Sorcin
D: Sorcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8187
Polymers37,6972
Non-polymers1225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-61 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.229, 104.831, 113.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Sorcin / SRI (gene) / 22 kDa protein / CP-22 / CP22 / V19


Mass: 18848.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRI / Production host: Escherichia coli (E. coli) / References: UniProt: P30626
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN / Doxorubicin


Mass: 543.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO11 / Comment: medication, chemotherapy*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M MgCl2, 0.1 M Tris pH=7, NaCl 2.5 M

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.74→76.94 Å / Num. obs: 11800 / % possible obs: 99 % / Redundancy: 6.53 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.81
Reflection shellResolution: 3.74→3.96 Å / Redundancy: 6.47 % / Mean I/σ(I) obs: 1.45 / CC1/2: 0.561 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UPG

4upg


Resolution: 3.74→76.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU ML: 0.6 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28501 569 4.8 %RANDOM
Rwork0.19185 ---
obs0.19623 11193 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 177.223 Å2
Baniso -1Baniso -2Baniso -3
1--7.39 Å2-0 Å2-0 Å2
2---1.22 Å20 Å2
3---8.61 Å2
Refinement stepCycle: 1 / Resolution: 3.74→76.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 53 1 5280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025376
X-RAY DIFFRACTIONr_bond_other_d0.0020.024910
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9547277
X-RAY DIFFRACTIONr_angle_other_deg1.001311241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9885664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.36223.955268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.69915872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0641541
X-RAY DIFFRACTIONr_chiral_restr0.0670.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021327
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_it9.83717.7752668
X-RAY DIFFRACTIONr_mcbond_other9.83417.7742667
X-RAY DIFFRACTIONr_mcangle_it15.74626.6283328
X-RAY DIFFRACTIONr_mcangle_other15.74326.6293329
X-RAY DIFFRACTIONr_scbond_it8.50118.2492708
X-RAY DIFFRACTIONr_scbond_other8.518.2522709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.18427.2073950
X-RAY DIFFRACTIONr_long_range_B_refined21.046492
X-RAY DIFFRACTIONr_long_range_B_other21.0386493
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.74→3.833 Å
RfactorNum. reflection% reflection
Rfree0.37 46 -
Rwork0.35 765 -
obs--94.52 %

+
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