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- PDB-2nqa: Catalytic Domain of Human Calpain 8 -

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Basic information

Entry
Database: PDB / ID: 2nqa
TitleCatalytic Domain of Human Calpain 8
Components
  • Calpain-8
  • Leupeptin Inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CALPAIN / CALCIUM-DEPENDENT CYTOPLASMIC CYSTEINE PROTEINASES / PAPAIN-LIKE / EF-HAND / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


calpain-2 / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion / cortical actin cytoskeleton / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models ...calpain-2 / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion / cortical actin cytoskeleton / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of cardiac muscle cell apoptotic process / behavioral response to pain / regulation of cytoskeleton organization / pseudopodium / blastocyst development / protein autoprocessing / cellular response to interferon-beta / response to mechanical stimulus / cysteine-type peptidase activity / digestion / cytoskeletal protein binding / Degradation of the extracellular matrix / proteolysis involved in protein catabolic process / female pregnancy / cellular response to amino acid stimulus / response to hydrogen peroxide / cellular response to lipopolysaccharide / lysosome / hydrolase activity / response to hypoxia / membrane raft / external side of plasma membrane / focal adhesion / neuronal cell body / calcium ion binding / dendrite / protein-containing complex binding / chromatin / Golgi apparatus / enzyme binding / endoplasmic reticulum / proteolysis / extracellular exosome / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Calpain-8 / CAPN2, penta-EF hand, calcium binding motif / Calpain subdomain III / Peptidase C2, calpain, domain III / calpain_III / Peptidase C2, calpain, large subunit, domain III / Peptidase C2, calpain family / Calpain large subunit, domain III superfamily / Calpain large subunit, domain III / Peptidase C2, calpain, catalytic domain ...Calpain-8 / CAPN2, penta-EF hand, calcium binding motif / Calpain subdomain III / Peptidase C2, calpain, domain III / calpain_III / Peptidase C2, calpain, large subunit, domain III / Peptidase C2, calpain family / Calpain large subunit, domain III superfamily / Calpain large subunit, domain III / Peptidase C2, calpain, catalytic domain / Calpain family cysteine protease / Cysteine proteinase, calpain-type, catalytic domain profile. / Calpain-like thiol protease family. / EF-hand domain pair / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
LEUPEPTIN / Calpain-8 / Calpain-2 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Actinomycetes Streptomyces roseus MA 839-A1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDavis, T.L. / Paramanathan, R. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of Human Calpain 8
Authors: Davis, T.L. / Paramanathan, R. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionOct 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_mod_residue.details / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_name
Revision 1.6Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain-8
B: Calpain-8
D: Leupeptin Inhibitor
E: Leupeptin Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4209
Polymers74,2194
Non-polymers2005
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-81 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.794, 91.794, 194.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe biological assembly is a monomer

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Components

#1: Protein Calpain-8 / E.C.3.4.22.52 / New calpain 2 / nCL-2 / Stomach-specific M-type calpain


Mass: 36680.020 Da / Num. of mol.: 2 / Fragment: Residues 23-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPN8, NCL2 / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A6NHC0, UniProt: P17655*PLUS, calpain-2
#2: Protein/peptide Leupeptin Inhibitor


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 429.578 Da / Num. of mol.: 2 / Fragment: Leupeptin Inhibitor / Source method: obtained synthetically / Details: Commercially available from Sigma L2884
Source: (synth.) Actinomycetes Streptomyces roseus MA 839-A1 (bacteria)
References: LEUPEPTIN
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LEUPEPTIN IS COVALENTLY CONNECTED TO ACTIVE_SITE CYS 105 OF THE ENZYME TO FORM A HEMITHIOACETAL.
Sequence detailsELECTRON DENSITY SHOWS CLEARLY TYR AT THIS POSITION 225. THERE IS A DISCREPANCY IN THE NORINE AND ...ELECTRON DENSITY SHOWS CLEARLY TYR AT THIS POSITION 225. THERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ONE RESIDUE. SO THE DBREF WILL REPORT 4 PDB RESIDUES MATCHING NORINE 3 RESIDUE

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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: 3.19 Å3/Da / Density % sol: 61.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2M NH4PO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 4, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 7.1 / Number: 214956 / Rmerge(I) obs: 0.119 / Χ2: 1.08 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 45317 / % possible obs: 96.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745090.810.0550.7515
3.764.7493.310.0570.814.9
3.293.7695.110.0780.9094.8
2.993.2996.510.1311.0714.8
2.772.999710.2041.134.7
2.612.7797.410.31.24.7
2.482.6197.910.3961.2334.7
2.372.4898.210.5211.2444.6
2.282.3798.410.6671.2254.6
2.22.2898.610.8121.2464.5
ReflectionResolution: 2.2→50 Å / Num. all: 47063 / Num. obs: 45317 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.812 / % possible all: 98.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å38.94 Å
Translation2.5 Å38.94 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ARY

2ary


Resolution: 2.2→38.954 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.221
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 2229 5.09 %RANDOM
Rwork0.2048 ---
all0.2048 ---
obs0.2048 43796 93.282 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.005 Å20 Å2
2--0.01 Å20 Å2
3----0.014 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5073 0 5 308 5386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225207
X-RAY DIFFRACTIONr_bond_other_d0.0010.023557
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9517049
X-RAY DIFFRACTIONr_angle_other_deg1.06638630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg23.8195.309647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93224.595259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69415839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8091527
X-RAY DIFFRACTIONr_chiral_restr0.1240.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021088
X-RAY DIFFRACTIONr_nbd_refined0.2070.2963
X-RAY DIFFRACTIONr_nbd_other0.1890.23486
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22357
X-RAY DIFFRACTIONr_nbtor_other0.0840.22491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2194
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.25
X-RAY DIFFRACTIONr_mcbond_it0.7111.53323
X-RAY DIFFRACTIONr_mcbond_other0.1371.51292
X-RAY DIFFRACTIONr_mcangle_it1.10425025
X-RAY DIFFRACTIONr_mcangle_other0.52824211
X-RAY DIFFRACTIONr_scbond_it1.54832322
X-RAY DIFFRACTIONr_scbond_other0.50733319
X-RAY DIFFRACTIONr_scangle_it2.3094.52024
X-RAY DIFFRACTIONr_scangle_other1.1244.54419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2570.3951650.2893000346591.342
2.257-2.3190.3211550.2682928335491.92
2.319-2.3860.3111640.2582882328492.753
2.386-2.4590.3371550.252833319493.55
2.459-2.5390.3481470.242760309194.047
2.539-2.6280.3011330.2392698299494.556
2.628-2.7270.3041350.2312592287494.885
2.727-2.8370.2891420.2242473275195.056
2.837-2.9630.2921300.2142431268995.24
2.963-3.1070.2861140.2142299252995.413
3.107-3.2740.2821130.2022203243695.074
3.274-3.4710.2551050.1952050227494.767
3.471-3.7080.2371100.1821928217693.658
3.708-4.0020.223820.1741802200494.012
4.002-4.380.199820.1551619185591.698
4.38-4.8890.203780.1591447166791.482
4.889-5.630.25700.1781291148091.959
5.63-6.860.257640.2171086126391.053
6.86-9.5540.261630.280798588.325
9.554-38.9540.276220.22743858578.632
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)
11.02150.68650.62691.83160.18561.73570.01140.0381-0.0162-0.0149-0.03940.1432-0.0447-0.1620.02790.1739-0.00520.00430.16010.01790.146342.39660.764214.8416
20.67130.57230.11021.1240.08820.8517-0.05090.0674-0.4179-0.05320.0212-0.20120.40050.19730.02960.13420.0032-0.00390.14440.00580.131943.296511.13440.0415
31.62360.39080.11981.1605-0.09580.97710.00460.0404-0.1201-0.0321-0.00540.09380.1029-0.09230.00070.11810.00610.00250.10290.0020.090542.28358.17189.4642
40.37740.03540.00190.59480.02360.93480.0029-0.10070.07950.0740.0052-0.0859-0.05870.1064-0.0080.1413-0.0075-0.00440.13510.00010.146144.845930.3579-0.0397
50.98230.1914-0.12951.1625-0.06841.815-0.00540.18010.0451-0.15520.0068-0.0157-0.02820.0296-0.00150.09980.00780.00390.0987-0.00370.124335.703128.7853-11.1148
61.4757-0.17720.09811.63530.94691.91950.0229-0.1497-0.11330.1654-0.044-0.01450.0605-0.01130.02110.12490.0059-0.00580.2032-0.00840.183639.333940.034626.6277
71.13-0.16090.02611.06120.63921.43630.06160.01630.4284-0.0332-0.00980.0532-0.4519-0.0921-0.05170.1391-0.0009-0.00350.15150.0090.145657.132938.181527.7944
81.1295-0.0497-0.16250.94430.06161.72620.0033-0.11630.0720.1258-0.00290.0093-0.0956-0.0397-0.00030.0860.0003-0.0040.0949-0.00050.114147.909536.766926.5312
90.92220.1860.14870.65220.09990.3895-0.020.1268-0.0414-0.13720.01840.03140.0729-0.05780.00160.15020.00660.00310.1467-0.00860.137864.880720.740819.7573
102.05990.28950.03321.03960.20630.97560.0008-0.01190.03860.0219-0.0014-0.1608-0.04230.18630.00070.13770.00520.0050.10580.00750.117373.66322.550931.1351
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA23 - 603 - 40
22AA70 - 11250 - 92
33AA113 - 17793 - 157
44AA178 - 239158 - 219
55AA240 - 323220 - 303
66BB23 - 663 - 46
77BB68 - 11248 - 92
88BB113 - 17793 - 157
99BB178 - 239158 - 219
1010BB240 - 323220 - 303

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