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- PDB-4ejf: Allosteric peptides that bind to a caspase zymogen and mediate ca... -

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Basic information

Entry
Database: PDB / ID: 4ejf
TitleAllosteric peptides that bind to a caspase zymogen and mediate caspase tetramerization
Components
  • Caspase-6
  • phage-derived peptide 419
KeywordsHYDROLASE / Caspase-6 / zymogen / C163A / Caspase / protease
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / cellular response to staurosporine / positive regulation of necroptotic process / Apoptotic cleavage of cellular proteins / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / pyroptotic inflammatory response / protein autoprocessing ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / cellular response to staurosporine / positive regulation of necroptotic process / Apoptotic cleavage of cellular proteins / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / pyroptotic inflammatory response / protein autoprocessing / intrinsic apoptotic signaling pathway by p53 class mediator / Caspase-mediated cleavage of cytoskeletal proteins / epithelial cell differentiation / cysteine-type peptidase activity / 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 / cytoplasm / cytosol
Similarity search - Function
Rossmann fold - #1460 / Peptidase C14 family / 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 ...Rossmann fold - #1460 / Peptidase C14 family / 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
PHOSPHATE ION / Caspase-6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6465 Å
AuthorsMurray, J.M.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Allosteric peptides bind a caspase zymogen and mediate caspase tetramerization.
Authors: Stanger, K. / Steffek, M. / Zhou, L. / Pozniak, C.D. / Quan, C. / Franke, Y. / Tom, J. / Tam, C. / Elliott, J.M. / Lewcock, J.W. / Zhang, Y. / Murray, J. / Hannoush, R.N.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Derived calculations
Revision 1.2Sep 5, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: phage-derived peptide 419
F: phage-derived peptide 419
G: phage-derived peptide 419
H: phage-derived peptide 419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,34310
Polymers137,1538
Non-polymers1902
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-116 kcal/mol
Surface area39330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.299, 105.692, 91.924
Angle α, β, γ (deg.)90.000, 106.610, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.181619, -0.007389, 0.983341), (-0.005804, -0.999946, -0.008586), (0.983352, -0.007267, 0.181566)7.62406, -73.454498, -8.27234
2given(-0.999997, 0.0012, 0.001894), (0.001271, 0.999279, 0.037935), (-0.001847, 0.037937, -0.999278)51.153, -1.91358, 45.631199
3given(-0.956126, -0.292951, 0.001682), (-0.2929, 0.955817, -0.024969), (0.005707, -0.024366, -0.999687)46.112301, 7.81898, 44.403198
4given(-0.190634, 0.069836, 0.979174), (-0.000554, -0.997474, 0.071033), (0.981661, 0.012999, 0.190191)13.9373, -75.587097, -5.83303
5given(0.122646, 0.218388, -0.968124), (-0.005248, -0.975332, -0.220679), (-0.992437, 0.032146, -0.118475)56.855099, -68.173103, 52.1763

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Components

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


Mass: 32055.627 Da / Num. of mol.: 4 / Mutation: C163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6, MCH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P55212, caspase-6
#2: Protein/peptide
phage-derived peptide 419


Mass: 2232.581 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 20% (w/v) PEG3350, 0.2 M NaThiocyanate pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.64→80.148 Å / Num. all: 34281 / Num. obs: 34281 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 35.28 Å2 / Rsym value: 0.086 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.64-2.793.80.4561.71878549930.45699.8
2.79-2.963.80.2982.61779347320.29899.8
2.96-3.163.70.23.91651044100.299.8
3.16-3.423.70.1246.21555341550.12499.8
3.42-3.743.70.07510.11408537800.07599.8
3.74-4.183.70.05713.21285334690.05799.9
4.18-4.833.70.04317.31116830470.04399.6
4.83-5.923.60.04516.4930225720.04599.5
5.92-8.373.70.03918.6752120060.03999.8
8.37-80.1483.60.02126.6405211170.02199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIXdev_713refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NR2

3nr2


Resolution: 2.6465→58.933 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.72 / σ(F): 1.35 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 1718 5.02 %
Rwork0.1882 --
obs0.1907 34192 99.43 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.754 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 202.79 Å2 / Biso mean: 44.3314 Å2 / Biso min: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1--9.5681 Å2-0 Å26.5607 Å2
2---2.8825 Å2-0 Å2
3---12.4506 Å2
Refinement stepCycle: LAST / Resolution: 2.6465→58.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8196 0 10 279 8485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038359
X-RAY DIFFRACTIONf_angle_d0.72611259
X-RAY DIFFRACTIONf_chiral_restr0.0491223
X-RAY DIFFRACTIONf_plane_restr0.0031428
X-RAY DIFFRACTIONf_dihedral_angle_d14.3433044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6465-2.72440.31041530.256426752828100
2.7244-2.81230.33881320.251127342866100
2.8123-2.91280.31510.234126662817100
2.9128-3.02950.28771450.22262689283499
3.0295-3.16730.26451280.210327152843100
3.1673-3.33430.26341300.200427172847100
3.3343-3.54320.26441520.1926992851100
3.5432-3.81670.23441620.170726882850100
3.8167-4.20070.2191420.151627272869100
4.2007-4.80830.16691330.13862712284599
4.8083-6.0570.18931330.17852735286899
6.057-58.94710.23111570.20252717287498
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)
12.52920.4548-0.08182.91080.05332.13690.3052-0.14280.26480.03410.07180.0539-0.3748-0.037-0.22330.15980.01310.03720.35360.0180.29895.2128-21.24836.9841
23.1286-0.9833-1.48451.39220.88954.43740.72750.40061.5457-0.03820.25111.624-0.8935-0.0888-0.08570.09870.089-0.45160.58080.3042-0.3623-1.7404-19.532124.8695
31.91220.1129-0.39721.562-0.44031.79720.0979-0.11640.4807-0.1069-0.0557-0.0785-0.4219-0.0372-0.0290.20390.02040.01980.336-0.00720.28288.68-15.486134.6382
41.6863-0.4444-1.04731.6777-0.05523.9248-0.03710.0470.0058-0.1024-0.1293-0.44150.33370.54690.18850.2315-00.07980.3707-0.00030.348815.5191-23.080333.8508
53.34990.28470.5562.32711.07212.58950.07840.53980.1098-0.47250.04730.16440.11030.010.04760.2687-0.0015-0.02680.34330.01340.32875.9253-29.710925.3829
62.38660.62880.61171.9356-0.12372.39620.10150.2069-0.1502-0.10480.19360.28020.1846-0.3104-0.23750.1934-0.0039-0.03160.38190.05180.272-3.3835-31.439730.5529
71.82990.3443-1.70354.63940.78182.58840.27261.2101-0.6215-1.0244-0.02930.80731.0224-0.9722-0.13670.5162-0.1896-0.21070.8157-0.11130.3697-4.789-37.668719.4716
85.05040.25040.99172.6034-1.54563.6344-0.0791-0.6931-0.0979-0.17820.41140.15370.0924-0.7672-0.06220.3371-0.05980.08320.3371-0.07480.159-0.8892-27.285247.8214
93.4411-3.0372-0.60257.0307-1.1311.93970.02550.4316-0.5866-0.33940.23230.6797-0.0794-0.4032-0.13140.2398-0.00130.03070.49370.04940.4206-10.4011-49.339438.7954
108.1010.7033-1.20941.66850.06862.2717-0.0940.5009-0.5964-0.43270.4479-0.8399-0.06390.7392-0.06230.18270.1422-0.01230.29880.20920.527722.6584-58.20737.7347
116.87471.2583-0.25082.0763-0.24461.7168-0.06-0.6622-0.45790.41580.0839-0.30150.02840.2321-0.01670.3482-0.0054-0.07810.3690.08190.282117.0131-55.865247.769
121.8332-1.0184-0.82031.1530.60541.2741-0.0141-0.1893-0.3131-0.22340.0059-0.02460.0937-0.0558-0.05410.2295-0.0458-0.0480.25220.0960.27212.4646-58.351534.7917
132.04811.495-0.88843.1211-0.49391.6803-0.28811.32930.5189-0.86480.47620.39680.2441-0.0162-0.11390.36480.0137-0.0330.44880.09790.29927.7006-53.185926.8241
142.54150.69680.31331.73850.35181.5228-0.17990.0540.3528-0.0028-0.0002-0.41050.12620.28080.14750.21140.0173-0.01480.30160.11250.324615.6814-46.373939.1345
152.0347-0.12650.29631.14620.37071.4286-0.0719-0.30430.17650.06480.1130.0718-0.06480.1106-0.01130.2745-0.0521-0.03590.42070.09190.211.3502-43.745448.3052
163.46180.2486-0.70723.95370.21962.08650.1801-0.81540.33470.46680.0378-0.1689-0.12560.7311-0.12740.2267-0.0767-0.03990.6596-0.00490.061712.049-41.136847.375
172.7329-1.2439-0.93857.91322.6963.57680.13220.538-0.0231-0.7386-0.1115-0.1721-0.1236-0.0248-0.15080.363-0.02890.0860.3212-0.04960.260149.4655-24.401-9.2901
183.66930.3609-3.04782.4494-2.32758.19680.7393-0.23790.77011.15650.3637-0.119-0.0994-0.2854-0.1720.192-0.07170.11460.3532-0.22430.457842.365-15.680922.8073
192.60880.5839-1.81391.3716-0.4855.6210.4101-0.17340.87860.69290.6082-0.8025-0.89970.4707-0.24690.29880.0148-0.11630.4837-0.25890.550153.077-17.830519.3567
200.9013-0.3493-0.05241.08531.5271.7290.1613-0.17470.3730.0798-0.0827-0.1047-0.25560.0923-0.07360.2798-0.0097-0.00290.2399-0.0690.383641.2906-15.513112.4642
212.54981.1361-2.02683.1615-1.03154.7182-0.33220.3270.1612-0.35990.42650.2780.6009-1.20820.03750.2553-0.02910.0030.2614-0.04210.283734.3805-20.79036.3408
222.1234-0.30520.46351.9391-1.07244.27630.0265-0.4117-0.02930.3550.0739-0.250.13810.1573-0.080.2566-0.0129-0.03920.2426-0.1150.244945.5737-27.141116.8537
231.4182-0.3490.34621.5995-0.56363.0116-0.0314-0.28870.01680.060.0276-0.36560.21450.4336-0.00370.22040.0311-0.01150.3892-0.12080.310454.5581-29.911113.5963
242.8848-0.1912-1.42514.1849-1.21711.15340.7301-1.0934-0.62341.10720.0151-0.64871.23071.0965-0.0820.48330.2218-0.22671.0085-0.01170.406655.4127-36.010624.1201
256.1810.21470.06542.20681.2183.23660.21710.1081-0.0072-1.0515-0.2401-0.616-0.34280.5273-0.08010.31970.03370.06120.3133-0.02450.325251.9907-25.4679-3.672
263.72220.8037-1.09625.1796-0.33431.7632-0.6221-0.6295-0.7161-0.4877-0.0958-0.6656-1.15630.56580.0012-0.12930.110.20060.2688-0.12310.57261.3496-47.74334.9989
275.9309-0.7438-1.36832.0826-0.71372.5587-0.36020.3336-0.3409-0.22760.18540.29720.1329-0.34730.14480.2623-0.0181-0.00910.1888-0.0360.242731.6455-55.11470.1148
282.04281.04060.06020.9604-0.30150.7735-0.1792-0.3726-0.19480.17570.048-0.14850.1534-0.06290.14890.29310.04060.01920.2478-0.00640.267738.6405-56.8598.5929
296.299-1.3109-0.97352.76610.54640.8116-0.1076-1.73770.27610.47140.2659-0.0972-0.28340.08760.130.35590.12960.03120.52480.02420.338943.4129-51.874516.7852
301.9338-0.9174-0.29631.8436-0.33431.9388-0.0327-0.16960.4778-0.1743-0.07420.1501-0.065-0.370.09180.23920.029-0.02930.1711-0.04630.289435.3903-44.71624.7032
313.09810.41270.07291.8419-0.96291.8213-0.25330.18540.2553-0.2950.187-0.0517-0.1594-0.08580.040.29140.02210.00690.1847-0.04690.215939.7342-41.8103-4.3877
322.9209-0.4839-0.68693.82330.63772.26990.06630.32310.491-0.397-0.06830.31910.0073-0.6932-0.05050.2636-0.02070.02670.34620.06270.180638.9281-39.1743-3.3458
333.13330.7809-0.8193.75241.11625.17170.108-0.00930.56240.31410.06480.16420.13150.046-0.00640.28220.03840.01910.4785-0.04750.279724.8824-15.535524.5506
342.9587-0.3286-0.30523.07360.27154.1886-0.0860.00240.3303-0.0926-0.4271-0.6095-0.12380.00680.06420.34060.0238-0.03010.38010.02120.226427.1961-15.148422.3052
351.63150.8029-0.87483.68140.34322.75110.5819-0.54680.20190.1802-0.331-0.5308-0.04070.4226-0.12720.30290.01410.02640.4917-0.03690.450528.8115-58.896822.2528
363.4789-1.1478-0.85364.89960.05373.397-0.0412-0.31350.18110.38280.0944-0.6030.388-0.5811-0.09240.2963-0.06670.00950.33810.030.172822.9922-58.944422.3789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 31:59)A31 - 59
2X-RAY DIFFRACTION2chain 'A' and (resseq 60:80)A60 - 80
3X-RAY DIFFRACTION3chain 'A' and (resseq 81:121)A81 - 121
4X-RAY DIFFRACTION4chain 'A' and (resseq 122:155)A122 - 155
5X-RAY DIFFRACTION5chain 'A' and (resseq 156:205)A156 - 205
6X-RAY DIFFRACTION6chain 'A' and (resseq 206:257)A206 - 257
7X-RAY DIFFRACTION7chain 'A' and (resseq 258:280)A258 - 280
8X-RAY DIFFRACTION8chain 'A' and (resseq 281:292)A281 - 292
9X-RAY DIFFRACTION9chain 'B' and (resseq 30:44)B30 - 44
10X-RAY DIFFRACTION10chain 'B' and (resseq 45:59)B45 - 59
11X-RAY DIFFRACTION11chain 'B' and (resseq 60:80)B60 - 80
12X-RAY DIFFRACTION12chain 'B' and (resseq 81:132)B81 - 132
13X-RAY DIFFRACTION13chain 'B' and (resseq 133:151)B133 - 151
14X-RAY DIFFRACTION14chain 'B' and (resseq 152:205)B152 - 205
15X-RAY DIFFRACTION15chain 'B' and (resseq 206:258)B206 - 258
16X-RAY DIFFRACTION16chain 'B' and (resseq 259:291)B259 - 291
17X-RAY DIFFRACTION17chain 'C' and (resseq 30:44)C30 - 44
18X-RAY DIFFRACTION18chain 'C' and (resseq 45:59)C45 - 59
19X-RAY DIFFRACTION19chain 'C' and (resseq 60:80)C60 - 80
20X-RAY DIFFRACTION20chain 'C' and (resseq 81:132)C81 - 132
21X-RAY DIFFRACTION21chain 'C' and (resseq 133:151)C133 - 151
22X-RAY DIFFRACTION22chain 'C' and (resseq 152:205)C152 - 205
23X-RAY DIFFRACTION23chain 'C' and (resseq 206:257)C206 - 257
24X-RAY DIFFRACTION24chain 'C' and (resseq 258:280)C258 - 280
25X-RAY DIFFRACTION25chain 'C' and (resseq 281:292)C281 - 292
26X-RAY DIFFRACTION26chain 'D' and (resseq 30:44)D30 - 44
27X-RAY DIFFRACTION27chain 'D' and (resseq 45:80)D45 - 80
28X-RAY DIFFRACTION28chain 'D' and (resseq 81:132)D81 - 132
29X-RAY DIFFRACTION29chain 'D' and (resseq 133:151)D133 - 151
30X-RAY DIFFRACTION30chain 'D' and (resseq 152:205)D152 - 205
31X-RAY DIFFRACTION31chain 'D' and (resseq 206:258)D206 - 258
32X-RAY DIFFRACTION32chain 'D' and (resseq 259:291)D259 - 291
33X-RAY DIFFRACTION33chain 'E'E39 - 50
34X-RAY DIFFRACTION34chain 'F'F39 - 49
35X-RAY DIFFRACTION35chain 'G'G39 - 50
36X-RAY DIFFRACTION36chain 'H'H39 - 50

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