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- PDB-1gqf: Crystal structure of human procaspase-7 -

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Basic information

Entry
Database: PDB / ID: 1gqf
TitleCrystal structure of human procaspase-7
ComponentsCaspase-7
KeywordsHYDROLASE / CASPASE-7 / APOPTOSIS / ZYMOGEN
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 / peptidase activity / positive regulation of neuron apoptotic process / 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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRiedl, S. / Bode, W. / Fuentes-Prior, P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2001
Title: Structural basis for the activation of human procaspase-7.
Authors: Riedl, S.J. / Fuentes-Prior, P. / Renatus, M. / Kairies, N. / Krapp, S. / Huber, R. / Salvesen, G.S. / Bode, W.
History
DepositionNov 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Nov 7, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.3Dec 13, 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_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Caspase-7
B: Caspase-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0477
Polymers60,5672
Non-polymers4805
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-85.9 kcal/mol
Surface area29490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.210, 90.210, 183.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 30283.334 Da / Num. of mol.: 2 / Mutation: C187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.55 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 50 MM MES, PH 5.6, 10 MM MAGNESIUM CHLORIDE, 100 MM AMMONIUM SULFATE, 20% (W/V) PEG 8000
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprocaspase-7 solution1drop
2100 mMammonium sulfate solution1drop
350 mMMES1reservoirpH5.6
4100 mMammonium sulfate1reservoir
510 mM1reservoirMgCl2
620 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.9→59.76 Å / Num. obs: 19487 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 74.2 Å2 / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.386 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 180534
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F1J

1f1j


Resolution: 2.9→21.73 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1166291.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: COMPETITION FOR THE LIMITED INTERMONOMER SPACE (THE "CENTRAL CAVITY") BY THE TWO INTERDOMAIN LINKERS MANIFESTS ITSELF IN POOR OR AMBIGOUS ELECTRON DENSITY FOR RESIDUES N-TERMINAL OF ILE321. ...Details: COMPETITION FOR THE LIMITED INTERMONOMER SPACE (THE "CENTRAL CAVITY") BY THE TWO INTERDOMAIN LINKERS MANIFESTS ITSELF IN POOR OR AMBIGOUS ELECTRON DENSITY FOR RESIDUES N-TERMINAL OF ILE321. ALTERNATE CONFORMATIONS, HOWEVER, ARE NOT SEPARABLE AT THE CURRENT RESOLUTION. ELECTRON DENSITY IS ALSO POOR OR MISSING FOR RESIDUES THR288 - LYS320 (THE INTERDOMAIN LINKER), GLY336 - GLY346 (THE SUBSTRATE BINDING LOOP), AS WELL AS FOR THE INSERTION LOOP GLU381-GLU382. RESIDUES N-TERMINAL OF PRO149 AND THE C-TERMINAL HISTIDINE TAG ARE FLEXIBLY DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 947 4.9 %RANDOM
Rwork0.268 ---
obs0.268 19487 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 210.532 Å2 / ksol: 0.237854 e/Å3
Displacement parametersBiso mean: 80.7 Å2
Baniso -1Baniso -2Baniso -3
1-11.14 Å27.01 Å20 Å2
2--11.14 Å20 Å2
3----22.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.9→21.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4242 0 25 20 4287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 141 4.4 %
Rwork0.313 3075 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 59.76 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor obs: 0.313

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