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- PDB-1fq3: CRYSTAL STRUCTURE OF HUMAN GRANZYME B -

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Basic information

Entry
Database: PDB / ID: 1fq3
TitleCRYSTAL STRUCTURE OF HUMAN GRANZYME B
ComponentsGRANZYME B
KeywordsHYDROLASE / chymotrypsin-like serine proteinase
Function / homology
Function and homology information


cytolytic granule lumen / granzyme B / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / positive regulation of establishment of protein localization to mitochondrion / Activation, myristolyation of BID and translocation to mitochondria / NOTCH2 intracellular domain regulates transcription / natural killer cell mediated cytotoxicity / pyroptotic inflammatory response / protein maturation ...cytolytic granule lumen / granzyme B / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / positive regulation of establishment of protein localization to mitochondrion / Activation, myristolyation of BID and translocation to mitochondria / NOTCH2 intracellular domain regulates transcription / natural killer cell mediated cytotoxicity / pyroptotic inflammatory response / protein maturation / immunological synapse / Pyroptosis / Nuclear events stimulated by ALK signaling in cancer / serine-type peptidase activity / proteolysis involved in protein catabolic process / killing of cells of another organism / negative regulation of translation / intracellular membrane-bounded organelle / serine-type endopeptidase activity / apoptotic process / extracellular region / membrane / nucleus / cytosol / 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 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsEstebanez-Perpina, E. / Fuentes-Prior, P. / Belorgey, D. / Rubin, H. / Bode, W.
CitationJournal: Biol.Chem. / Year: 2000
Title: Crystal structure of the caspase activator human granzyme B, a proteinase highly specific for an Asp-P1 residue.
Authors: Estebanez-Perpina, E. / Fuentes-Prior, P. / Belorgey, D. / Braun, M. / Kiefersauer, R. / Maskos, K. / Huber, R. / Rubin, H. / Bode, W.
History
DepositionSep 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRANZYME B
B: GRANZYME B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4726
Polymers51,1072
Non-polymers1,3654
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.74, 114.31, 135.52
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Detailsdimer constructed from chain A and chain B not related by a two-fold symmetry

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Components

#1: Protein GRANZYME B


Mass: 25553.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10144, granzyme B
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: PEG-8000, ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 31, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→15 Å / Num. all: 40709 / Num. obs: 11275 / Rmerge(I) obs: 0.199
Reflection shellResolution: 3.1→15 Å / Rmerge(I) obs: 0.199 / Num. unique all: 9106

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cathepsin G

Resolution: 3.1→15 Å / Stereochemistry target values: Engh & Huber /
Rfactor% reflection
all0.227 -
Rfree-32.5 %
Refinement stepCycle: LAST / Resolution: 3.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 88 0 3670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.511

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