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- PDB-4jr2: Human procaspase-7/caspase-7 heterodimer bound to Ac-DEVD-CMK -

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Basic information

Entry
Database: PDB / ID: 4jr2
TitleHuman procaspase-7/caspase-7 heterodimer bound to Ac-DEVD-CMK
Components
  • Ac-DEVD-CMK
  • Procaspase-7
KeywordsAPOPTOSIS / HYDROLASE/HYDROLASE INHIBITOR / protease / proenzyme / protein-peptide complex / irreversible inhibitor / activity based probe / caspase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / striated muscle cell differentiation / cysteine-type peptidase activity / protein maturation / protein catabolic process / protein processing / fibrillar center / positive regulation of neuron apoptotic process / peptidase activity / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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
Ac-Asp-Glu-Val-Asp-CMK / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsThomsen, N.D. / Wells, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural snapshots reveal distinct mechanisms of procaspase-3 and -7 activation.
Authors: Thomsen, N.D. / Koerber, J.T. / Wells, J.A.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Jun 12, 2013Group: Refinement description
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Sep 20, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 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: Procaspase-7
B: Procaspase-7
C: Ac-DEVD-CMK
D: Ac-DEVD-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7716
Polymers57,7004
Non-polymers712
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-36 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.493, 88.663, 88.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Procaspase-7 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3 / Caspase-7


Mass: 28315.168 Da / Num. of mol.: 2 / Fragment: protease domain (UNP residues 57-303) / Mutation: D198A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: Addgene plasmid 29653 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P55210, caspase-7
#2: Protein/peptide Ac-DEVD-CMK


Type: Peptide-like / Class: Inhibitor / Mass: 534.946 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: Ac-Asp-Glu-Val-Asp-CMK
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mM Tris, pH 8.0, 2 mM DTT, 50 mM sodium chloride, 200 mM sodium/potassium phosphate, 100 mM Bis-Tris propane, pH 6.5, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2011
RadiationMonochromator: double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 55958 / Num. obs: 55958 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.052 / Net I/σ(I): 19.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.65-1.713.30.5942.155031.04998.7
1.71-1.783.40.42554801.0998.9
1.78-1.863.40.30755091.08499.3
1.86-1.963.40.20555231.07499.3
1.96-2.083.50.12955911.05699.9
2.08-2.243.50.0955891.00499.8
2.24-2.463.50.06756171.02799.8
2.46-2.823.50.06256131.0499.6
2.82-3.553.40.04456721.02799.1
3.55-503.40.02458611.07798.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å32.87 Å
Translation2.5 Å32.87 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F1J

1f1j


Resolution: 1.65→32.867 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 18.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 2819 5.04 %RANDOM
Rwork0.1611 ---
obs0.1629 55899 99.27 %-
all-55901 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78 Å2 / Biso mean: 22.0648 Å2 / Biso min: 7.03 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 2 382 4104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074027
X-RAY DIFFRACTIONf_angle_d1.1045467
X-RAY DIFFRACTIONf_chiral_restr0.082595
X-RAY DIFFRACTIONf_plane_restr0.005712
X-RAY DIFFRACTIONf_dihedral_angle_d13.3451562
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 (%)
1.65-1.67850.29941280.23812580270898
1.6785-1.7090.2531560.22452611276799
1.709-1.74190.27991200.20972619273999
1.7419-1.77750.23581190.20292633275299
1.7775-1.81610.2471320.19232617274999
1.8161-1.85830.20651240.18512632275699
1.8583-1.90480.19371440.17872625276999
1.9048-1.95630.24581230.17492627275099
1.9563-2.01390.19221600.165226512811100
2.0139-2.07890.23861410.157926362777100
2.0789-2.15310.20381440.154326512795100
2.1531-2.23930.20321450.150826482793100
2.2393-2.34120.191610.154926562817100
2.3412-2.46460.19151380.15226602798100
2.4646-2.6190.20961530.158126592812100
2.619-2.82110.18131440.17192652279699
2.8211-3.10480.18281620.16732650281299
3.1048-3.55360.18621290.14842724285399
3.5536-4.47540.16321400.13072721286199
4.4754-32.87370.19261560.16542828298499
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)
11.55290.95680.40230.68640.15310.23260.1680.6854-0.3481-0.769-0.2194-0.50580.85910.8335-0.15270.37410.15590.03080.31770.00190.192622.9903-8.3419-34.3665
21.0837-1.0296-0.80822.68541.15022.01130.12870.2071-0.1213-0.3188-0.31740.4845-0.0907-0.3048-0.09840.11620.02420.00280.1550.00090.10797.2357.1033-27.4639
30.11710.02340.0520.02480.01570.02370.2688-0.17860.19680.4807-0.07450.375-0.6905-0.37760.00470.41140.03080.1810.366-0.0440.3267-0.932217.9256-8.1363
41.4381-0.3462-0.32851.8115-0.33211.43680.08090.01010.0357-0.0232-0.03470.2321-0.0161-0.1304-0.01020.075-0.00120.0020.11640.02390.10237.52797.8403-24.3378
51.1325-0.23010.02420.7773-0.04490.58680.0105-0.1074-0.2630.0709-0.03140.44170.2439-0.25170.01770.1607-0.02740.0210.140.03650.17218.2983-2.7559-20.2486
61.5539-0.3708-0.29670.9424-0.29241.38120.0175-0.19380.15060.3116-0.0175-0.061-0.05850.0003-0.0010.1176-0.02320.00880.14610.01560.080417.28157.4723-15.9955
72.6086-0.42610.05271.0808-1.01881.11380.1242-0.18340.5082-0.1129-0.1547-0.3054-0.26550.11750.21170.1485-0.01090.0480.12160.08810.216225.738613.4594-22.5954
81.62770.46610.23461.7869-0.37721.21840.079-0.22380.34930.214-0.261-0.0115-0.04060.0077-0.17780.11430.00390.0090.12160.00880.161223.13746.5503-18.1911
90.68840.1048-0.87240.1691-0.1241.11210.0990.53610.9176-0.3223-0.0155-0.4495-0.38390.5240.9628-0.1441-0.31670.17170.44740.43080.424941.63056.0116-21.3089
100.9698-0.08980.13561.43990.21631.0143-0.01210.0322-0.03170.1223-0.1988-0.4566-0.04120.41050.12210.06290.0258-0.01560.15470.06270.139539.8679-9.1863-3.6608
111.0904-0.45940.87251.5945-0.02771.41370.04090.03390.08340.069-0.0314-0.10570.1720.28660.0030.09710.04570.00960.10280.00590.10535.8051-14.8699-1.0635
121.1992-0.2029-0.16941.4042-0.39972.16360.0045-0.08340.35330.1653-0.053-0.0147-0.19590.1886-0.03090.09690.00180.00260.10050.00960.131132.1783-2.6718-2.2165
130.6435-0.40320.04340.4571-0.36570.4582-0.31060.18340.0722-0.82120.2127-0.1852-0.1165-0.076-0.01420.4371-0.12940.06250.38280.09650.358720.1252-5.2542-15.7859
140.79520.42350.22240.6499-0.46961.35680.02860.01810.0778-0.0018-0.0160.10180.14780.0127-00.09640.01360.01890.08450.00980.087425.839-13.2172-10.1181
151.1814-0.44410.33721.1789-0.20510.8894-0.08810.2275-0.0688-0.4058-0.0815-0.21020.26130.0775-0.03590.14130.0650.07670.12420.02210.05629.2506-15.8816-19.2895
160.6918-0.46190.45621.02340.49661.0710.11810.04240.12970.0416-0.2249-0.03450.0550.1042-0.01740.06930.01060.02410.10940.04060.074425.9271-8.8224-15.8289
170.6620.04060.25040.1671-0.06990.14010.26970.08640.4597-0.0567-0.0767-0.0244-0.31790.1066-0.02340.2576-0.04770.08130.1813-0.03610.21114.583521.5676-11.6728
180.27360.26080.36260.24660.34340.4750.1873-0.0951-0.22030.06920.0964-0.0660.47930.01160.04440.16150.0175-0.01320.0623-0.00390.116422.5004-23.1989-5.2262
190.536-0.35350.38360.9886-0.48421.01440.00150.02970.0614-0.0691-0.0206-0.03110.0380.0605-0.00130.1533-0.00470.04980.19670.01080.178223.2351-3.3877-14.5473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 56:63A56 - 63
2X-RAY DIFFRACTION2chain A and resseq 64:78A64 - 78
3X-RAY DIFFRACTION3chain A and resseq 79:84A79 - 84
4X-RAY DIFFRACTION4chain A and resseq 85:152A85 - 152
5X-RAY DIFFRACTION5chain A and resseq 153:184A153 - 184
6X-RAY DIFFRACTION6chain A and resseq 185:243A185 - 243
7X-RAY DIFFRACTION7chain A and resseq 244:280A244 - 280
8X-RAY DIFFRACTION8chain A and resseq 281:302A281 - 302
9X-RAY DIFFRACTION9chain B and resseq 56:63B56 - 63
10X-RAY DIFFRACTION10chain B and resseq 64:78B64 - 78
11X-RAY DIFFRACTION11chain B and resseq 79:121B79 - 121
12X-RAY DIFFRACTION12chain B and resseq 122:191B122 - 191
13X-RAY DIFFRACTION13chain B and resseq 192:215B192 - 215
14X-RAY DIFFRACTION14chain B and resseq 216:243B216 - 243
15X-RAY DIFFRACTION15chain B and resseq 244:280B244 - 280
16X-RAY DIFFRACTION16chain B and resseq 281:302B281 - 302
17X-RAY DIFFRACTION17chain C and resseq 1:6C1 - 6
18X-RAY DIFFRACTION18chain D and resseq 1:6D1 - 6
19X-RAY DIFFRACTION19( chain A and resseq 501:665 ) or ( chain B and resseq 501:704 ) or ( chain C and resseq 201:205 ) or ( chain D and resseq 201:208 )A501 - 665
20X-RAY DIFFRACTION19( chain A and resseq 501:665 ) or ( chain B and resseq 501:704 ) or ( chain C and resseq 201:205 ) or ( chain D and resseq 201:208 )B501 - 704
21X-RAY DIFFRACTION19( chain A and resseq 501:665 ) or ( chain B and resseq 501:704 ) or ( chain C and resseq 201:205 ) or ( chain D and resseq 201:208 )C201 - 205
22X-RAY DIFFRACTION19( chain A and resseq 501:665 ) or ( chain B and resseq 501:704 ) or ( chain C and resseq 201:205 ) or ( chain D and resseq 201:208 )D201 - 208

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