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- PDB-1s4v: The 2.0 A crystal structure of the KDEL-tailed cysteine endopepti... -

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Basic information

Entry
Database: PDB / ID: 1s4v
TitleThe 2.0 A crystal structure of the KDEL-tailed cysteine endopeptidase functioning in programmed cell death of Ricinus communis endosperm
Components
  • DVA-LEU-LYS-0QE peptide
  • cysteine endopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / KDEL ER RETENTION SIGNAL / ENDOSPERM / RICINOSOMES / SEED GERMINATION / SENESCENCE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cysteine-type peptidase activity / cytoplasmic vesicle / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis
Similarity search - Function
Endoplasmic reticulum targeting sequence. / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : ...Endoplasmic reticulum targeting sequence. / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
D-valyl-N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-L-leucinamide / : / Vignain
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThan, M.E. / Helm, M. / Simpson, D.J. / Lottspeich, F. / Huber, R. / Gietl, C.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The 2.0 A crystal structure and substrate specificity of the KDEL-tailed cysteine endopeptidase functioning in programmed cell death of Ricinus communis endosperm.
Authors: Than, M.E. / Helm, M. / Simpson, D.J. / Lottspeich, F. / Huber, R. / Gietl, C.
History
DepositionJan 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 23, 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_sheet / 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.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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cysteine endopeptidase
B: cysteine endopeptidase
C: DVA-LEU-LYS-0QE peptide
D: DVA-LEU-LYS-0QE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0785
Polymers49,9824
Non-polymers961
Water6,161342
1
A: cysteine endopeptidase
C: DVA-LEU-LYS-0QE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0873
Polymers24,9912
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-17 kcal/mol
Surface area9860 Å2
MethodPISA
2
B: cysteine endopeptidase
D: DVA-LEU-LYS-0QE peptide


Theoretical massNumber of molelcules
Total (without water)24,9912
Polymers24,9912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-6 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.448, 68.162, 163.780
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 cysteine endopeptidase


Mass: 24599.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ricinus communis (castor bean) / Tissue: endosperm / References: GenBank: 2944446, UniProt: O65039*PLUS
#2: Protein/peptide DVA-LEU-LYS-0QE peptide


Type: Peptide-like / Class: Inhibitor / Mass: 391.956 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ricinus communis (castor bean) / Tissue: endosperm
References: D-valyl-N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-L-leucinamide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE REACTION BETWEEN THE THIOL GROUP OF ACTIVE SITE CYS 26 (CHAINS A AND B) AND DVA-LEU-LYS- ...THE REACTION BETWEEN THE THIOL GROUP OF ACTIVE SITE CYS 26 (CHAINS A AND B) AND DVA-LEU-LYS-CHLOROMETHYL KETONE (CHAINS C AND D) RESULTS IN THE FORMATION OF THE COVALENT BOND BETWEEN THE INHIBITOR AND THE PROTEIN IN WHICH CHLORINE OF CHLOROMETHYLKETONE MOIETY 0QE IS LEAVING.
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: 2.07 Å3/Da / Density % sol: 41 %
Description: THE DIFFRACTION LIMIT OF THE CRYSTAL WAS BEYOND 1.7 A USING ROTATING ANODE X-RAY RADIATION. THE RESOLUTION WAS CUT AT 2.0 A DURING DATA COLLECTION IN ORDER TO PREVENT POTENTIAL SPOT ...Description: THE DIFFRACTION LIMIT OF THE CRYSTAL WAS BEYOND 1.7 A USING ROTATING ANODE X-RAY RADIATION. THE RESOLUTION WAS CUT AT 2.0 A DURING DATA COLLECTION IN ORDER TO PREVENT POTENTIAL SPOT OVERLAP DUE TO HIGH MOSAIC SPREAD AND RELATIVELY LARGE CELL CONSTANTS.
Crystal growTemperature: 291 K / pH: 5.04
Details: PEG 4000, Li2SO4, pH 5.04, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlprotein1drop
23 mMMES/NaOH1droppH5.5
31 mMbeta-mercaptoethanol1drop
431 %(w/v)PEG40001reservoir
50.1 Msodium citrate1reservoirpH5.04
60.2 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→24.2 Å / Num. obs: 28159 / % possible obs: 98.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.066
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.137 / % possible all: 89.3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 24.4 Å / Num. measured all: 179209 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 89.3 % / Rmerge(I) obs: 0.137

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CQD

1cqd


Resolution: 2→24.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2615176.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1508 5.4 %SHELLS
Rwork0.181 ---
obs0.181 28102 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.16 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.23 Å20 Å20 Å2
2--0.19 Å20 Å2
3---4.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 2→24.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 5 342 3790
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.532.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.212 160 3.7 %
Rwork0.176 4181 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MY_PROTEIN_REP3.PARAMMY_PROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5MY_CMK.PARAMMY_CMK.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 24.3 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.469
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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