[English] 日本語
Yorodumi
- PDB-4wq2: Human calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacry... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wq2
TitleHuman calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacrylic acid bound
ComponentsCalpain small subunit 1
KeywordsHYDROLASE / Calpain / Domain VI / PEF(S) / Human / Calcium Binding / Protease / EF-Hand
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-3SU / Calpain small subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsAdams, S.E. / Rizkallah, P.J. / Miller, D.J. / Hallett, M.B. / Allemann, R.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0701192 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
DepositionOct 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 30, 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 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,19816
Polymers40,0332
Non-polymers1,16514
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-106 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.720, 78.430, 56.300
Angle α, β, γ (deg.)90.000, 91.120, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Calpain small subunit 1 / / CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent ...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: Protease domain, UNP residues 92-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPNS1, CAPN4, CAPNS / Plasmid: pET21d / Production host: Escherichia Coli BL21(DE3) (bacteria) / References: UniProt: P04632
#2: Chemical ChemComp-3SU / (2Z)-3-(6-bromo-1H-indol-3-yl)-2-sulfanylprop-2-enoic acid


Mass: 298.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8BrNO2S
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3 UL PROTEIN (10 MG/ML PEF(S), 5 MM SODIUM CACODYLATE, 2 MM EDTA, 5 MM BME, 1 MM CALCIUM CHLORIDE, PH 7.0) + 3 UL PRECIPITANT (50 MM SODIUM CACODYLATE, 12.5% PEG6000, 20 MM CALCIUM CHLORIDE, PH 7.0) + 1 UL WATER

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.64→41.99 Å / Num. all: 51550 / Num. obs: 51550 / % possible obs: 97.5 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Net I/σ(I): 16.1 / Num. measured all: 190491
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
1.64-1.683.60.9011.71358337490.6660.54796.5
7.33-41.993.40.03340.219345620.9890.02289.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.2.12data scaling
Coot0.6.2model building
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4phj

4phj


Resolution: 1.64→41.99 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2032 / WRfactor Rwork: 0.1735 / FOM work R set: 0.8594 / SU B: 3.918 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0853 / SU Rfree: 0.0848 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 2620 5.1 %RANDOM
Rwork0.1699 48906 --
obs0.1713 48906 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.85 Å2 / Biso mean: 34.082 Å2 / Biso min: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.38 Å2
2--1.07 Å20 Å2
3----0.91 Å2
Refinement stepCycle: final / Resolution: 1.64→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 56 157 3019
Biso mean--53.53 41.46 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193113
X-RAY DIFFRACTIONr_bond_other_d0.0020.022863
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.9534215
X-RAY DIFFRACTIONr_angle_other_deg1.0043.0016591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42424.268157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97915556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2461522
X-RAY DIFFRACTIONr_chiral_restr0.1420.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023656
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02774
X-RAY DIFFRACTIONr_mcbond_it2.2032.161506
X-RAY DIFFRACTIONr_mcbond_other2.2032.161505
X-RAY DIFFRACTIONr_mcangle_it3.0583.2281914
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 202 -
Rwork0.27 3542 -
all-3744 -
obs--96.4 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.10760.0346-0.21320.9144-0.56460.50610.0022-0.05120.07930.09090.07580.0477-0.0778-0.0825-0.0780.02830.0015-0.00050.06040.00020.05920.32410.089527.7861
21.1902-0.3880.3820.21820.12491.3270.14690.0598-0.0163-0.0455-0.0622-0.04910.1891-0.1138-0.08470.0759-0.0335-0.00030.09460.02580.067935.60870.007912.685
318.5742-15.58391.791217.13982.48534.0858-0.0264-0.1324-0.0715-0.3164-0.14150.2357-0.3356-0.25780.16790.1372-0.00080.00240.10490.01570.148.89876.943933.1037
429.5398-3.6482-16.47891.7328-0.573717.8330.6359-0.31180.6305-0.1295-0.0398-0.1564-0.23910.6097-0.5960.1641-0.0165-0.01950.1863-0.02430.16136.9509-11.40436.7792
51.93251.0384-1.65261.4115-0.74271.43810.0422-0.0064-0.01730.0909-0.0735-0.0272-0.0011-0.01040.03130.09-0.0157-0.03980.083-0.01250.08519.22113.882428.3406
62.32811.2654-0.0521.64930.85050.80460.06040.0467-0.01470.0988-0.14190.08240.0642-0.15730.08150.1773-0.05020.0050.13110.02010.035230.4349-3.412911.8867
70.5543-0.1841-1.74340.57210.05286.11680.08460.03030.0237-0.0184-0.0759-0.0462-0.2582-0.0581-0.00870.0213-0.0117-0.00230.03770.01680.033224.21174.684120.912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A96 - 268
2X-RAY DIFFRACTION2B96 - 268
3X-RAY DIFFRACTION3A270
4X-RAY DIFFRACTION4B270
5X-RAY DIFFRACTION5A301 - 304
6X-RAY DIFFRACTION6B301 - 304
7X-RAY DIFFRACTION7E1 - 4

+
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