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- PDB-5d69: Human calpain PEF(S) with (2Z,2Z')-2,2'-disulfanediylbis(3-(6-iod... -

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Basic information

Entry
Database: PDB / ID: 5d69
TitleHuman calpain PEF(S) with (2Z,2Z')-2,2'-disulfanediylbis(3-(6-iodoindol-3-yl)acrylic acid) bound
ComponentsCalpain small subunit 1
KeywordsHYDROLASE / PEF(S) / domain VI / calcium binding domain / cysteine protease / mercaptoacrylic acid
Function / homology
Function and homology information


calpain complex / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome ...calpain complex / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
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
Chem-57T / Calpain small subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsAdams, S.E. / Robinson, E.J. / Rizkallah, P.J. / Miller, D.J. / Hallett, M.B. / Allemann, R.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
EPSRC and MRCG0701192 United Kingdom
CitationJournal: Chem Sci / Year: 2015
Title: Conformationally restricted calpain inhibitors.
Authors: Adams, S.E. / Robinson, E.J. / Miller, D.J. / Rizkallah, P.J. / Hallett, M.B. / Allemann, R.K.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain small subunit 1
B: Calpain small subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,67013
Polymers40,0332
Non-polymers1,63711
Water2,072115
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-116 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.030, 79.650, 57.160
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 96 - 268 / Label seq-ID: 1 - 173

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Calpain small subunit 1 / / Penta EF Short / CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / ...Penta EF Short / CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent protease small subunit / CDPS / Calcium-dependent protease small subunit 1 / Calpain regulatory subunit


Mass: 20016.607 Da / Num. of mol.: 2 / Fragment: UNP residues 96-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPNS1, CAPN4, CAPNS / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / References: UniProt: P04632
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-57T / (2E,2'Z)-2,2'-disulfanediylbis[3-(4-iodophenyl)prop-2-enoic acid]


Mass: 610.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H12I2O4S2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12% PEG6000, 20 MM CACL2, 50 MM CACODYLATE BUFFER, PH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.97→34.47 Å / Num. obs: 31256 / % possible obs: 98.4 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.043 / Net I/σ(I): 9.5 / Num. measured all: 113627
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.97-2.023.80.8861.4876823250.7160.51999
8.81-34.473.50.03925.912643620.9970.02296.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.97 Å34.47 Å
Translation1.97 Å34.47 Å

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHASER2.5.6phasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→34.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.418 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 1482 4.7 %RANDOM
Rwork0.1989 ---
obs0.2006 29754 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.92 Å2 / Biso mean: 49.919 Å2 / Biso min: 29.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0.85 Å2
2---0 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 1.97→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 117 115 3038
Biso mean--71.11 50.21 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192993
X-RAY DIFFRACTIONr_bond_other_d0.0070.022716
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9414030
X-RAY DIFFRACTIONr_angle_other_deg1.4532.9876215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.68624.065155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16215518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0071523
X-RAY DIFFRACTIONr_chiral_restr0.1380.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023439
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02764
X-RAY DIFFRACTIONr_mcbond_it1.2021.7881392
X-RAY DIFFRACTIONr_mcbond_other1.21.7871391
X-RAY DIFFRACTIONr_mcangle_it1.9382.671740
Refine LS restraints NCS

Ens-ID: 1 / Number: 19780 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 121 -
Rwork0.321 2192 -
all-2313 -
obs--98.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.09420.31050.31561.8925-0.5491.4440.1163-0.201-0.18820.1692-0.04630.16210.1828-0.0678-0.070.409-0.03260.01190.3714-0.03740.148313.9202-0.130215.4117
23.0167-0.4461-0.20112.15170.86641.034-0.00040.08550.1243-0.16080.083-0.1025-0.15540.0389-0.08260.3437-0.0395-0.02220.23480.04940.120629.03879.88550.2022
300000000000000-00.5371-0.0786-0.10310.61010.04840.103128.26250.07628.2962
400000000000000-00.6536-0.01910.04970.4950.00690.003921.55958.37825.9153
500000000000000-00.6892-0.0496-0.09740.3671-0.11090.39497.0611-14.68814.3559
600000000000000-00.55520.012-0.03740.4713-0.05490.095319.6981-8.0276.7068
70.21870.87830.17585.44450.2530.26590.12280.0294-0.03960.4273-0.08470.07620.12830.157-0.03820.49910.00660.02910.57020.01030.500114.5527-11.750924.068
800000000000000-00.4222-0.0382-0.19810.5138-0.05260.102723.9198-3.727-12.3207
900000000000000-00.5175-0.0042-0.1040.42490.04010.071818.50085.683-10.1827
1000000000000000-00.39090.0277-0.06350.5411-0.13480.185944.539210.565111.9007
1100000000000000-00.4685-0.03740.00680.26030.01220.066733.75721.6679.2847
1211.20234.18358.274111.448116.753825.0876-0.74280.27050.4411-0.30120.8032-0.1843-0.53940.9981-0.06040.4836-0.0137-0.02030.496-0.02570.473439.92314.846-7.7468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A96 - 268
2X-RAY DIFFRACTION2B96 - 268
3X-RAY DIFFRACTION3A301
4X-RAY DIFFRACTION4A302
5X-RAY DIFFRACTION5A303
6X-RAY DIFFRACTION6A304
7X-RAY DIFFRACTION7A401
8X-RAY DIFFRACTION8B301
9X-RAY DIFFRACTION9B302
10X-RAY DIFFRACTION10B303
11X-RAY DIFFRACTION11B304
12X-RAY DIFFRACTION12B401

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