[English] 日本語
Yorodumi
- PDB-1aj5: CALPAIN DOMAIN VI APO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aj5
TitleCALPAIN DOMAIN VI APO
ComponentsCALPAIN
KeywordsCALCIUM-BINDING PROTEIN / CALCIUM-DEPENDENT PROTEASE / APO FORM / SMALL SUBUNIT
Function / homology
Function and homology information


Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Degradation of the extracellular matrix / calpain complex / calcium-dependent cysteine-type endopeptidase activity / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein catabolic process / calcium ion binding / protein-containing complex binding / proteolysis / membrane ...Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Degradation of the extracellular matrix / calpain complex / calcium-dependent cysteine-type endopeptidase activity / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein catabolic process / calcium ion binding / protein-containing complex binding / proteolysis / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
EF-hand domain pair / EF-hand / Recoverin; domain 1 / 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
Calpain small subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.3 Å
AuthorsCygler, M. / Grochulski, P. / Blanchard, H.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of a calpain Ca(2+)-binding domain reveals a novel EF-hand and Ca(2+)-induced conformational changes.
Authors: Blanchard, H. / Grochulski, P. / Li, Y. / Arthur, J.S. / Davies, P.L. / Elce, J.S. / Cygler, M.
#1: Journal: Protein Sci. / Year: 1996
Title: Ca(2+)-Binding Domain Vi of Rat Calpain is a Homodimer in Solution: Hydrodynamic, Crystallization and Preliminary X-Ray Diffraction Studies
Authors: Blanchard, H. / Li, Y. / Cygler, M. / Kay, C.M. / Arthur, J.S. / Davies, P.L. / Elce, J.S.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Active Recombinant Rat Calpain II. Bacterially Produced Large and Small Subunits Associate Both in Vivo and in Vitro
Authors: Graham-Siegenthaler, K. / Gauthier, S. / Davies, P.L. / Elce, J.S.
History
DepositionMay 15, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Feb 7, 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: CALPAIN
B: CALPAIN


Theoretical massNumber of molelcules
Total (without water)40,0552
Polymers40,0552
Non-polymers00
Water2,162120
1
A: CALPAIN

A: CALPAIN


Theoretical massNumber of molelcules
Total (without water)40,0552
Polymers40,0552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4140 Å2
ΔGint-21 kcal/mol
Surface area15940 Å2
MethodPISA, PQS
2
B: CALPAIN

B: CALPAIN


Theoretical massNumber of molelcules
Total (without water)40,0552
Polymers40,0552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3940 Å2
ΔGint-26 kcal/mol
Surface area16320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.500, 73.000, 156.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.055906, -0.998257, -0.018923), (0.995796, 0.057125, -0.071606), (0.072562, -0.01484, 0.997253)
Vector: 69.2975, -34.1384, -40.8175)
DetailsTHERE ARE TWO INDEPENDENT "PHYSIOLOGICAL" DIMERS OF THE SAME TYPE: AA' AND BB'. A AND A' ARE RELATED BY CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY ALONG THE X AXIS. B AND B' ARE RELATED BY CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY ALONG Y AXIS AND TRANSLATED BY VECTOR (1.0,0.0,0.5). THE DIMERS ARE RELATED BY THE NCS SYMMETRY.

-
Components

#1: Protein CALPAIN


Mass: 20027.633 Da / Num. of mol.: 2
Fragment: SMALL REGULATORY SUBUNIT, DOMAIN VI, MET 87 - SER 270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: BL21 (DE3) / Cell line: BL21 / Gene: CAPN4 / Organ: LIVER / Plasmid: PT7-7F-21K / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q64537
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.8
Details: 38%SATURATED AMMONIUM SULFATE AND 25MM PIPES BUFFER, PH 6.8
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1ammonium sulfate11
21
31
41

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 24, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 17172 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.19 / % possible all: 94
Reflection
*PLUS
Num. measured all: 80668
Reflection shell
*PLUS
% possible obs: 94.2 %

-
Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: NCS USED ONLY AT THE EARLY STAGE OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1636 9.9 %RANDOM
Rwork0.22 ---
obs0.22 16470 96.5 %-
Displacement parametersBiso mean: 33.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 0 120 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.081.5
X-RAY DIFFRACTIONx_mcangle_it4.532
X-RAY DIFFRACTIONx_scbond_it3.612
X-RAY DIFFRACTIONx_scangle_it5.042.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 258 9.9 %
Rwork0.28 2340 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23
LS refinement shell
*PLUS
Rfactor obs: 0.28

+
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