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- PDB-2zks: Structural insights into the proteolytic machinery of apoptosis-i... -

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Basic information

Entry
Database: PDB / ID: 2zks
TitleStructural insights into the proteolytic machinery of apoptosis-inducing Granzyme M
Components
  • Granzyme M
  • hGzmM inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Serine protease / granzyme / Cytolysis / Glycoprotein / Hydrolase / Secreted / Zymogen / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Alternative complement activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / protein maturation / T cell mediated cytotoxicity / killing of cells of another organism / innate immune response / serine-type endopeptidase activity / apoptotic process / proteolysis ...Alternative complement activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / protein maturation / T cell mediated cytotoxicity / killing of cells of another organism / innate immune response / serine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / membrane
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWu, L.F. / Wang, L. / Hua, G.Q. / Liu, K. / Yang, X. / Zhai, Y.J. / Sun, F. / Fan, Z.S.
CitationJournal: J.Immunol. / Year: 2009
Title: Structural basis for proteolytic specificity of the human apoptosis-inducing granzyme M
Authors: Wu, L. / Wang, L. / Hua, G. / Liu, K. / Yang, X. / Zhai, Y. / Bartlam, M. / Sun, F. / Fan, Z.
History
DepositionMar 28, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2024Group: 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.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_comp_id / _struct_conn.ptnr2_auth_seq_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 1.4Nov 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: Granzyme M
C: hGzmM inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0326
Polymers26,6482
Non-polymers3844
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-51 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.671, 74.671, 113.557
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Granzyme M / Met-ase / Natural killer cell granular protease / HU-Met-1 / Met-1 serine protease


Mass: 26132.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Refolding from E. coli inclusion bodies / Source: (gene. exp.) Homo sapiens (human) / Strain: CTLs, NK cells / Gene: GZMM, MET1 / Plasmid: pET26b-GzmM / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P51124, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide hGzmM inhibitor


Mass: 515.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.2M Li2SO4, 0.1M Bicine, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9789 Å
DetectorType: MARRESEARCH Flat Panel / Detector: FLAT PANEL / Date: Mar 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→64.68 Å / Num. all: 10499 / Num. obs: 9978 / % possible obs: 95.04 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GZC

2gzc


Resolution: 2.7→56.19 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.843 / SU B: 24.538 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.539 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29308 501 4.8 %RANDOM
Rwork0.22279 ---
obs0.22609 9978 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.7→56.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 20 83 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221842
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9912498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3775232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36521.09464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65615309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0181519
X-RAY DIFFRACTIONr_chiral_restr0.1080.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021339
X-RAY DIFFRACTIONr_nbd_refined0.2360.2922
X-RAY DIFFRACTIONr_nbtor_refined0.320.21222
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3280.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.25
X-RAY DIFFRACTIONr_mcbond_it0.7751.51199
X-RAY DIFFRACTIONr_mcangle_it1.34821884
X-RAY DIFFRACTIONr_scbond_it2.0183717
X-RAY DIFFRACTIONr_scangle_it3.2194.5614
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 38 -
Rwork0.326 723 -
obs--99.74 %
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)
11.7491-1.5221-0.8994.38482.22553.66890.0336-0.07040.080.09230.1245-0.0619-0.05850.3025-0.1581-0.12950.02420.01-0.09670.0093-0.087-21.2686-13.291317.8701
247.1949-7.631942.87546.6992-7.572439.0259-0.0020.4777-1.453-0.17370.37750.3739-0.1001-0.8215-0.3755-0.01060.07360.05070.1805-0.00950.2545-28.3112-23.841714.2796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 231
2X-RAY DIFFRACTION2C2 - 5

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