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- PDB-3v6m: Inhibition of caspase-6 activity by single mutation outside the a... -

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Basic information

Entry
Database: PDB / ID: 3v6m
TitleInhibition of caspase-6 activity by single mutation outside the active site
ComponentsCaspase-6
KeywordsHYDROLASE / caspase domain
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / Apoptotic cleavage of cellular proteins ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / protein autoprocessing / intrinsic apoptotic signaling pathway by p53 class mediator / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / epithelial cell differentiation / activation of innate immune response / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain ...Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.692 Å
AuthorsCao, Q. / Wang, X.J. / Liu, D.F. / Li, L.F. / Su, X.D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Inhibitory mechanism of caspase-6 phosphorylation revealed by crystal structures, molecular dynamics simulations, and biochemical assays
Authors: Cao, Q. / Wang, X.J. / Liu, C.W. / Liu, D.F. / Li, L.F. / Gao, Y.Q. / Su, X.D.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references / Structure summary
Revision 1.2Nov 8, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-6
B: Caspase-6
C: Caspase-6
D: Caspase-6
F: Caspase-6
G: Caspase-6
I: Caspase-6
J: Caspase-6


Theoretical massNumber of molelcules
Total (without water)257,8238
Polymers257,8238
Non-polymers00
Water1,17165
1
A: Caspase-6
B: Caspase-6


Theoretical massNumber of molelcules
Total (without water)64,4562
Polymers64,4562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-18 kcal/mol
Surface area17180 Å2
MethodPISA
2
C: Caspase-6
D: Caspase-6


Theoretical massNumber of molelcules
Total (without water)64,4562
Polymers64,4562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-19 kcal/mol
Surface area17110 Å2
MethodPISA
3
F: Caspase-6
G: Caspase-6


Theoretical massNumber of molelcules
Total (without water)64,4562
Polymers64,4562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-18 kcal/mol
Surface area17170 Å2
MethodPISA
4
I: Caspase-6
J: Caspase-6


Theoretical massNumber of molelcules
Total (without water)64,4562
Polymers64,4562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-22 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.146, 162.630, 89.150
Angle α, β, γ (deg.)90.00, 95.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51F
61G
71I
81J

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHECYSCYSchain A and (resseq 31:163 or resseq 199:212 or resseq 222:260 or resseq 274:292 )AA31 - 1639 - 141
12THRTHRVALVALchain A and (resseq 31:163 or resseq 199:212 or resseq 222:260 or resseq 274:292 )AA199 - 212177 - 190
13THRTHRARGARGchain A and (resseq 31:163 or resseq 199:212 or resseq 222:260 or resseq 274:292 )AA222 - 260200 - 238
14GLNGLNSERSERchain A and (resseq 31:163 or resseq 199:212 or resseq 222:260 or resseq 274:292 )AA274 - 292252 - 270
21PHEPHECYSCYSchain B and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )BB31 - 1639 - 141
22TYRTYRVALVALchain B and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )BB198 - 212176 - 190
23THRTHRARGARGchain B and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )BB222 - 259200 - 237
24VALVALSERSERchain B and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )BB275 - 292253 - 270
31PHEPHECYSCYSchain C and (resseq 31:163 or resseq 198:212 or resseq 222:260 or resseq 275:292 )CC31 - 1639 - 141
32TYRTYRVALVALchain C and (resseq 31:163 or resseq 198:212 or resseq 222:260 or resseq 275:292 )CC198 - 212176 - 190
33THRTHRARGARGchain C and (resseq 31:163 or resseq 198:212 or resseq 222:260 or resseq 275:292 )CC222 - 260200 - 238
34VALVALSERSERchain C and (resseq 31:163 or resseq 198:212 or resseq 222:260 or resseq 275:292 )CC275 - 292253 - 270
41PHEPHECYSCYSchain D and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )DD31 - 1639 - 141
42TYRTYRVALVALchain D and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )DD198 - 212176 - 190
43THRTHRARGARGchain D and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )DD222 - 259200 - 237
44VALVALSERSERchain D and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )DD275 - 292253 - 270
51ASPASPCYSCYSchain F and (resseq 32:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )FE32 - 16310 - 141
52TYRTYRVALVALchain F and (resseq 32:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )FE198 - 212176 - 190
53THRTHRARGARGchain F and (resseq 32:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )FE222 - 259200 - 237
54VALVALSERSERchain F and (resseq 32:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )FE275 - 292253 - 270
61PHEPHECYSCYSchain G and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )GF31 - 1639 - 141
62TYRTYRVALVALchain G and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )GF198 - 212176 - 190
63THRTHRARGARGchain G and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )GF222 - 259200 - 237
64VALVALSERSERchain G and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )GF275 - 292253 - 270
71PHEPHECYSCYSchain I and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )IG31 - 1639 - 141
72TYRTYRVALVALchain I and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )IG198 - 212176 - 190
73THRTHRARGARGchain I and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )IG222 - 259200 - 237
74VALVALSERSERchain I and (resseq 31:163 or resseq 198:212 or resseq 222:259 or resseq 275:292 )IG275 - 292253 - 270
81PHEPHECYSCYSchain J and (resseq 31:163 or resseq 198:212 or resseq 222:261 or resseq 275:292 )JH31 - 1639 - 141
82TYRTYRVALVALchain J and (resseq 31:163 or resseq 198:212 or resseq 222:261 or resseq 275:292 )JH198 - 212176 - 190
83THRTHRVALVALchain J and (resseq 31:163 or resseq 198:212 or resseq 222:261 or resseq 275:292 )JH222 - 261200 - 239
84VALVALSERSERchain J and (resseq 31:163 or resseq 198:212 or resseq 222:261 or resseq 275:292 )JH275 - 292253 - 270

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Components

#1: Protein
Caspase-6 / CASP-6 / Apoptotic protease Mch-2 / Caspase-6 subunit p18 / Caspase-6 subunit p11


Mass: 32227.865 Da / Num. of mol.: 8 / Fragment: UNP residues 24-293 / Mutation: S257E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6 / Production host: Escherichia coli (E. coli) / References: UniProt: P55212, caspase-6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTAGENESIS. SUPPRESSION OF CASPASE-6 ACTIVATION.

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mM HEPES, 2.0M sodium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.692→50 Å / Num. all: 59504 / Num. obs: 59504 / % possible obs: 93.7 % / Biso Wilson estimate: 46.65 Å2
Reflection shellResolution: 2.692→2.75 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NR2

3nr2


Resolution: 2.692→19.991 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7795 / SU ML: 0.86 / σ(F): 1.35 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 2976 5.04 %RANDOM
Rwork0.2146 ---
obs0.2169 59021 92.87 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.287 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 164.12 Å2 / Biso mean: 53.691 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1-11.2689 Å2-0 Å211.0933 Å2
2---6.2732 Å20 Å2
3----4.9957 Å2
Refinement stepCycle: LAST / Resolution: 2.692→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12718 0 0 65 12783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513009
X-RAY DIFFRACTIONf_angle_d1.38517519
X-RAY DIFFRACTIONf_chiral_restr0.0951940
X-RAY DIFFRACTIONf_plane_restr0.0052218
X-RAY DIFFRACTIONf_dihedral_angle_d15.5174615
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1560X-RAY DIFFRACTIONPOSITIONAL0.148
12B1560X-RAY DIFFRACTIONPOSITIONAL0.148
13C1518X-RAY DIFFRACTIONPOSITIONAL0.142
14D1557X-RAY DIFFRACTIONPOSITIONAL0.12
15F1542X-RAY DIFFRACTIONPOSITIONAL0.139
16G1560X-RAY DIFFRACTIONPOSITIONAL0.146
17I1547X-RAY DIFFRACTIONPOSITIONAL0.143
18J1565X-RAY DIFFRACTIONPOSITIONAL0.143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6916-2.73570.44961410.37162544268589
2.7357-2.78270.40811560.31212828298499
2.7827-2.83320.34881590.29282821298099
2.8332-2.88750.35991510.27022876302799
2.8875-2.94630.33461480.26122833298199
2.9463-3.01010.30731680.247528262994100
3.0101-3.07990.31061620.235428533015100
3.0799-3.15660.29391380.231928542992100
3.1566-3.24160.31791640.23372850301499
3.2416-3.33660.28591700.22022788295899
3.3366-3.44380.28971380.22652800293897
3.4438-3.56620.29281290.22482726285593
3.5662-3.70810.27811040.22981993209769
3.7081-3.87570.2559540.22721363141748
3.8757-4.07840.2283950.211902199767
4.0784-4.33150.21451470.173128823029100
4.3315-4.6620.20021490.16992860300999
4.662-5.1240.1881400.17042842298299
5.124-5.84920.22631590.19862851301099
5.8492-7.3090.23811490.209129013050100
7.309-19.99170.21221550.19442852300798
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)
10.0729-0.187-0.00920.55790.00590.1997-0.0765-0.0194-0.22390.1245-0.08670.54030.23450.0289-0.32340.28870.03910.15770.07360.16090.7296-1.9241-17.620612.7396
20.0926-0.15840.06830.3156-0.09420.23970.30.2404-0.2188-0.4642-0.1590.25680.43550.16250.56820.68280.3576-0.24010.1676-0.20320.47753.5975-15.514-21.9935
30.33020.0311-0.09690.2225-0.21150.4420.2599-0.1748-0.04650.0648-0.1519-0.1154-0.16940.42310.77290.0444-0.1087-0.0420.35270.00170.13484.362320.0985-20.4171
40.2082-0.0427-0.0830.16360.08130.1006-0.07850.1191-0.00780.0916-0.09090.105-0.2426-0.0358-0.15680.187-0.03340.01640.1482-0.01510.06891.292517.953714.8084
50.0805-0.0738-0.01550.24450.1380.0919-0.1039-0.0465-0.03380.20920.04690.21720.08920.0316-0.28720.24920.07460.26210.08190.29410.36723.3506-8.456323.1669
60.3921-0.2351-0.0890.15430.07680.095-0.05760.0169-0.15950.0963-0.01610.1614-0.0148-0.0607-0.12770.25030.10370.20270.11870.04060.2696-6.06627.770922.7803
70.4718-0.17010.06390.3667-0.08190.17310.08280.0878-0.1473-0.3873-0.1190.31310.23620.0517-0.27410.55880.2748-0.21960.2643-0.13930.3162-0.9533-4.5443-31.2641
80.0039-0.0106-0.00240.0218-0.0770.21870.0581-0.0015-0.0368-0.0931-0.096-0.08340.10330.26360.05810.02110.33580.01870.31010.03810.025210.56339.9319-29.3658
90.3045-0.19830.13310.29870.02750.14550.11050.31560.3176-0.1768-0.0756-0.1654-0.0570.0687-0.11220.24440.06020.43230.43640.44380.646144.6768-44.849321.8316
100.0954-0.13460.1180.1989-0.18690.2234-0.00390.13470.2037-0.035-0.0786-0.1457-0.08840.0407-0.55060.21340.14070.24850.22130.24130.391329.2376-34.428420.5112
110.29560.2087-0.06180.46980.01510.3926-0.0336-0.28080.25480.1413-0.0028-0.1413-0.04520.18970.30750.27340.1355-0.3420.3992-0.16430.439638.0965-37.254975.5154
120.49410.4005-0.09130.44270.01870.1038-0.1179-0.1271-0.1220.13090.0767-0.19970.09170.0154-0.1550.34930.1451-0.03510.1875-0.05370.165422.8511-47.785372.9007
130.45410.04520.08330.00310.01330.028-0.05220.32310.595-0.137-0.0432-0.2991-0.09170.193-0.1515-0.0439-0.01640.46680.37030.3381.04453.8536-39.947532.9272
140.128-0.02480.03150.185-0.10160.12480.02080.10410.1337-0.0312-0.1064-0.2204-0.02290.0191-0.03850.18980.10630.01660.11560.1330.212818.0591-40.620228.2173
150.1058-0.0491-0.10270.11860.22970.4367-0.1712-0.44390.29290.20760.1784-0.2818-0.05580.5190.11640.31110.1124-0.15750.6872-0.15460.745548.996-42.788667.3025
160.2886-0.09-0.02790.22490.0120.2828-0.1421-0.04720.01720.04560.1604-0.0182-0.0424-0.06730.11580.20110.01960.01850.07960.01180.086413.7901-40.901863.0396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 31:163)A31 - 163
2X-RAY DIFFRACTION2chain C and (resseq 31:163)C31 - 163
3X-RAY DIFFRACTION3chain D and (resseq 31:163)D31 - 163
4X-RAY DIFFRACTION4chain B and (resseq 31:163)B31 - 163
5X-RAY DIFFRACTION5chain A and (resseq 199:292)A199 - 292
6X-RAY DIFFRACTION6chain B and (resseq 198:292)B198 - 292
7X-RAY DIFFRACTION7chain C and (resseq 198:292)C198 - 292
8X-RAY DIFFRACTION8chain D and (resseq 198:292)D198 - 292
9X-RAY DIFFRACTION9chain F and (resseq 198:292)F198 - 292
10X-RAY DIFFRACTION10chain G and (resseq 198:292)G198 - 292
11X-RAY DIFFRACTION11chain I and (resseq 198:292)I198 - 292
12X-RAY DIFFRACTION12chain J and (resseq 198:292)J198 - 292
13X-RAY DIFFRACTION13chain F and (resseq 32:163)F32 - 163
14X-RAY DIFFRACTION14chain G and (resseq 31:163)G31 - 163
15X-RAY DIFFRACTION15chain I and (resseq 31:163)I31 - 163
16X-RAY DIFFRACTION16chain J and (resseq 31:163)J31 - 163

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