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- PDB-4jr1: Human procaspase-7 bound to Ac-DEVD-CMK -

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Basic information

Entry
Database: PDB / ID: 4jr1
TitleHuman procaspase-7 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 / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / 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 / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / cysteine-type peptidase activity / striated muscle cell differentiation / protein catabolic process / protein processing / 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 / RNA binding / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol
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
Ac-Asp-Glu-Val-Akz-CMK / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.149 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 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Sep 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

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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)57,7756
Polymers57,7044
Non-polymers712
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-37 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.284, 100.016, 161.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-527-

HOH

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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: 536.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: Ac-Asp-Glu-Val-Akz-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.: 203 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM Tris, pH 8.0, 2 mM DTT, 50 mM sodium chloride, 200 mM ammonium formate, 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: 2.149→50 Å / Num. all: 25681 / Num. obs: 25681 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.092 / Χ2: 1.05 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.149-2.233.80.7761.724971.00598.3
2.23-2.324.80.61725331.04599.9
2.32-2.426.80.51425191.056100
2.42-2.5570.38525381.076100
2.55-2.7170.28525581.093100
2.71-2.9270.18725641.07100
2.92-3.2170.1125631.049100
3.21-3.6870.06225621.013100
3.68-4.636.90.05526170.989100
4.63-506.60.04727301.07599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.24 Å49.71 Å
Translation7.24 Å49.71 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F1J

1f1j


Resolution: 2.149→49.708 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.27 / σ(F): 0 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1303 5.08 %RANDOM
Rwork0.1969 ---
all0.1984 25646 --
obs0.1984 25641 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.56 Å2 / Biso mean: 32.7264 Å2 / Biso min: 0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.149→49.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 2 203 3878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023757
X-RAY DIFFRACTIONf_angle_d0.5545060
X-RAY DIFFRACTIONf_chiral_restr0.042547
X-RAY DIFFRACTIONf_plane_restr0.002649
X-RAY DIFFRACTIONf_dihedral_angle_d10.3441391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.149-2.23460.35211410.28872576271796
2.2346-2.33630.28341270.255126812808100
2.3363-2.45950.28931370.239226812818100
2.4595-2.61360.28051440.222527132857100
2.6136-2.81540.25141660.214526502816100
2.8154-3.09860.27231520.20727042856100
3.0986-3.54690.20351400.186427252865100
3.5469-4.46830.18661430.162227582901100
4.4683-49.72140.19261530.183328503003100
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)
11.28530.16330.13391.9950.53293.2428-0.00250.00840.0229-0.16030.064-0.0836-0.32980.24290.04660.1172-0.06580.0350.1674-0.00380.17261.4006-11.543419.649
21.19360.24070.25342.49120.27052.3319-0.0153-0.0316-0.0343-0.0638-0.0067-0.47590.03680.40670.0410.1276-0.03560.02040.2121-0.02460.22214.1312-23.449215.1625
32.45440.3513-0.32432.9645-0.24112.1816-0.20060.0682-0.16790.15530.1545-0.19320.7129-0.1444-0.07040.4267-0.07640.02690.1258-0.05880.1614-9.352-43.915620.4957
42.66980.4872-0.21893.41590.01812.9078-0.25850.28290.1325-0.3140.28590.29190.3535-0.38690.02220.2266-0.12880.02340.18820.03190.1654-12.1242-31.764812.1357
50.0418-0.0198-0.00480.0139-0.0018-0.001-0.0449-0.2028-0.231-0.1746-0.4017-0.3966-0.04451.0682-0.0090.2863-0.0168-0.0810.60670.07090.824615.0625-21.584732.7925
60.3822-0.61120.14570.9974-0.03781.6514-0.13130.1341-0.1379-0.0874-0.02350.60710.1729-0.2978-0.9692-0.1207-0.4671-0.10840.39820.28830.6039-26.2904-32.151618.1096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 56:203A56 - 203
2X-RAY DIFFRACTION2chain A and resseq 204:302A204 - 302
3X-RAY DIFFRACTION3chain B and resseq 56:192B56 - 192
4X-RAY DIFFRACTION4chain B and resseq 212:302B212 - 302
5X-RAY DIFFRACTION5chain CC - A1 - 401
6X-RAY DIFFRACTION6chain DD - B1 - 401

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