[English] 日本語
Yorodumi
- PDB-6oww: Crystal structure of a Human Cardiac Calsequestrin Filament Compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oww
TitleCrystal structure of a Human Cardiac Calsequestrin Filament Complexed with Ytterbium
ComponentsCalsequestrin-2
KeywordsMETAL BINDING PROTEIN / Calsequestrin / Calcium-Binding Proteins / Sarcoplasmic Reticulum Proteins
Function / homology
Function and homology information


calcium ion sequestering activity / negative regulation of potassium ion transmembrane transporter activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / sequestering of calcium ion / Purkinje myocyte to ventricular cardiac muscle cell signaling / sarcoplasmic reticulum lumen / regulation of membrane repolarization / cellular response to caffeine / negative regulation of ryanodine-sensitive calcium-release channel activity ...calcium ion sequestering activity / negative regulation of potassium ion transmembrane transporter activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / sequestering of calcium ion / Purkinje myocyte to ventricular cardiac muscle cell signaling / sarcoplasmic reticulum lumen / regulation of membrane repolarization / cellular response to caffeine / negative regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of potassium ion transport / detection of calcium ion / protein polymerization / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cardiac muscle contraction / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / calcium channel complex / sarcoplasmic reticulum membrane / regulation of heart rate / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / intracellular calcium ion homeostasis / calcium-dependent protein binding / calcium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin ...Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
YTTERBIUM (III) ION / Calsequestrin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 Å
AuthorsTitus, E.W. / Deiter, F.H. / Shi, C. / Jura, N. / Deo, R.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F30HL137329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007618 United States
American Heart Association17IRG33460152 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)DP2HL123228 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: The structure of a calsequestrin filament reveals mechanisms of familial arrhythmia.
Authors: Titus, E.W. / Deiter, F.H. / Shi, C. / Wojciak, J. / Scheinman, M. / Jura, N. / Deo, R.C.
History
DepositionMay 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calsequestrin-2
B: Calsequestrin-2
C: Calsequestrin-2
D: Calsequestrin-2
E: Calsequestrin-2
F: Calsequestrin-2
G: Calsequestrin-2
H: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,13176
Polymers359,7498
Non-polymers11,38268
Water00
1
A: Calsequestrin-2
hetero molecules

F: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,89820
Polymers89,9372
Non-polymers2,96118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
2
B: Calsequestrin-2
E: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,80219
Polymers89,9372
Non-polymers2,86517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calsequestrin-2
H: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,62918
Polymers89,9372
Non-polymers2,69216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Calsequestrin-2
G: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,80219
Polymers89,9372
Non-polymers2,86517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.832, 86.015, 214.340
Angle α, β, γ (deg.)90.000, 89.910, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Calsequestrin-2 / Calsequestrin / cardiac muscle isoform


Mass: 44968.637 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASQ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O14958
#2: Chemical...
ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 63 / Source method: obtained synthetically / Formula: Yb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, lithium sulfate / Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.3857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3857 Å / Relative weight: 1
ReflectionResolution: 3.84→214.34 Å / Num. obs: 29912 / % possible obs: 98.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 59.129 Å2 / Rpim(I) all: 0.162 / Rrim(I) all: 0.548 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
3.84-3.9111.60.81733214990.993.40297.8
10.42-214.6710.519.21661615750.0380.12699.1

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Blu-Icedata collection
ELVESdata processing
DIALSdata reduction
DIALSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OWV

6owv


Resolution: 3.84→214.34 Å / SU ML: 0.67 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 37.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3401 2799 4.86 %
Rwork0.2898 54798 -
obs0.2922 29777 98.39 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 347.97 Å2 / Biso mean: 98.7266 Å2 / Biso min: 41.16 Å2
Refinement stepCycle: final / Resolution: 3.84→214.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21720 0 88 0 21808
Biso mean--141.39 --
Num. residues----2632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.84-3.90580.42461200.3644278997
3.9058-3.97690.42011700.3559259497
3.9769-4.05340.50711500.3619280798
4.0534-4.13610.42881140.3457266998
4.1361-4.22610.3321200.3223279098
4.2261-4.32440.42931500.2968277799
4.3244-4.43250.3182840.2862275198
4.4325-4.55240.388820.2915283498
4.5524-4.68630.3531210.2957271899
4.6863-4.83760.32981820.305270899
4.8376-5.01050.30931240.2768275298
5.0105-5.21120.34921240.2977271698
5.2112-5.44830.33931580.2891273798
5.4483-5.73560.37321600.2983277698
5.7356-6.0950.37261560.2999272499
6.095-6.56560.33871120.2848274999
6.5656-7.22640.32772150.2885271299
7.2264-8.27210.32061370.2558275499
8.2721-10.4220.28711650.1954273399
10.422-214.340.24951550.2722270898

+
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