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- PDB-1orf: The Oligomeric Structure of Human Granzyme A Reveals the Molecula... -

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Basic information

Entry
Database: PDB / ID: 1orf
TitleThe Oligomeric Structure of Human Granzyme A Reveals the Molecular Determinants of Substrate Specificity
ComponentsGranzyme A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


granzyme A / negative regulation of endodeoxyribonuclease activity / cytotoxic T cell pyroptotic cell death / granzyme-mediated programmed cell death signaling pathway / negative regulation of oxidoreductase activity / pyroptotic inflammatory response / negative regulation of DNA binding / protein maturation / immunological synapse / proteolysis involved in protein catabolic process ...granzyme A / negative regulation of endodeoxyribonuclease activity / cytotoxic T cell pyroptotic cell death / granzyme-mediated programmed cell death signaling pathway / negative regulation of oxidoreductase activity / pyroptotic inflammatory response / negative regulation of DNA binding / protein maturation / immunological synapse / proteolysis involved in protein catabolic process / response to bacterium / killing of cells of another organism / immune response / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / protein homodimerization activity / extracellular space / nucleus / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Granzyme A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBell, J.K. / Goetz, D.H. / Mahrus, S. / Harris, J.L. / Fletterick, R.J. / Craik, C.S.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: The oligomeric structure of human granzyme A is a determinant of its extended substrate specificity.
Authors: Bell, J.K. / Goetz, D.H. / Mahrus, S. / Harris, J.L. / Fletterick, R.J. / Craik, C.S.
History
DepositionMar 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: 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 1.3Feb 27, 2013Group: Other
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_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_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 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Granzyme A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4203
Polymers25,8701
Non-polymers5502
Water2,306128
1
A: Granzyme A
hetero molecules

A: Granzyme A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8406
Polymers51,7402
Non-polymers1,1004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1600 Å2
ΔGint-40 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.034, 145.022, 39.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer generated by the two fold axis: -x, y, 1/2-z

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Components

#1: Protein Granzyme A / / Cytotoxic T-lymphocyte proteinase 1 / Hanukkah factor / H factor / HF / Granzyme 1 / CTL tryptase / ...Cytotoxic T-lymphocyte proteinase 1 / Hanukkah factor / H factor / HF / Granzyme 1 / CTL tryptase / Fragmentin 1


Mass: 25870.066 Da / Num. of mol.: 1 / Mutation: N170E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GZMA / Plasmid: pPicZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P12544, granzyme A
#2: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / Details: solid phase peptide synthesis / References: D-Phe-Pro-Arg-CH2Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER A ...THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER A 195, 2) VIA A METHYLENE GROUP TO NE2 HIS A 57.

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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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris pH 8.5, PEG 4000, lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMMES1droppH6.0
250 mM1dropNaCl
310 mg/mlprotein1drop
42.9 mMD-Phe-Pro-Arg-CMK1drop
50.1 MTris1reservoirpH8.5
60.2 mM1reservoirLi2SO4
713-18 %(v/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 13319 / Num. obs: 12664 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 94.3
Reflection
*PLUS
Num. obs: 13373 / % possible obs: 99 % / Num. measured all: 175040 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DST

1dst


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.903 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23245 660 5 %RANDOM
Rwork0.19137 ---
all0.19339 13319 --
obs0.19137 12664 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.985 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2--2.91 Å20 Å2
3----0.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.223 Å0.295 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 35 128 1937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211856
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9712514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455234
X-RAY DIFFRACTIONr_chiral_restr0.1050.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021372
X-RAY DIFFRACTIONr_nbd_refined0.2070.2832
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.40.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.27
X-RAY DIFFRACTIONr_mcbond_it0.7131.51164
X-RAY DIFFRACTIONr_mcangle_it1.3921882
X-RAY DIFFRACTIONr_scbond_it2.0393691
X-RAY DIFFRACTIONr_scangle_it3.4334.5629
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 46
Rwork0.242 873
Refinement
*PLUS
Highest resolution: 2.4 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.544

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