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- PDB-1iau: HUMAN GRANZYME B IN COMPLEX WITH AC-IEPD-CHO -

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Basic information

Entry
Database: PDB / ID: 1iau
TitleHUMAN GRANZYME B IN COMPLEX WITH AC-IEPD-CHO
Components
  • GRANZYME B
  • acetyl-isoleucyl-glutamyl-prolyl-aspartyl-aldehyde peptide INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


granzyme B / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / 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 ...granzyme B / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / 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 / serine-type peptidase activity / proteolysis involved in protein catabolic process / killing of cells of another organism / negative regulation of translation / serine-type endopeptidase activity / intracellular membrane-bounded organelle / 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 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
N-acetyl-L-isoleucyl-L-alpha-glutamyl-N-[(1S)-2-carboxy-1-formylethyl]-L-prolinamide / Granzyme B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRotonda, J. / Garcia-Calvo, M. / Bull, H.G. / Geissler, W.M. / McKeever, B.M. / Willoughby, C.A. / Thornberry, N.A. / Becker, J.W.
CitationJournal: Chem.Biol. / Year: 2001
Title: The three-dimensional structure of human granzyme B compared to caspase-3, key mediators of cell death with cleavage specificity for aspartic acid in P1.
Authors: Rotonda, J. / Garcia-Calvo, M. / Bull, H.G. / Geissler, W.M. / McKeever, B.M. / Willoughby, C.A. / Thornberry, N.A. / Becker, J.W.
History
DepositionMar 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.3Apr 4, 2012Group: Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRANZYME B
B: acetyl-isoleucyl-glutamyl-prolyl-aspartyl-aldehyde peptide INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7139
Polymers26,0672
Non-polymers1,6467
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-106 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.873, 75.081, 80.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein GRANZYME B /


Mass: 25582.607 Da / Num. of mol.: 1
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: Protein/peptide acetyl-isoleucyl-glutamyl-prolyl-aspartyl-aldehyde peptide INHIBITOR / ACE-ILE-GLU-PRO-ASP-CHO


Type: Peptide-like / Class: Inhibitor / Mass: 484.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
References: N-acetyl-L-isoleucyl-L-alpha-glutamyl-N-[(1S)-2-carboxy-1-formylethyl]-L-prolinamide

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1098.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[DManpb1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-1-3-4/a4-b1_a6-f1_b4-c1_c4-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 63 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHERE IS A COVALENT BOND BETWEEN ATOM OG OF SER195A AND ATOM C OF ASJ405B, FORMING A HEMIACETAL
Sequence detailsTHE RESIDUE NUMBERS FOR CHAIN A ARE NOT SEQUENTIAL. THE NUMBERING SCHEME IS BASED ON THE FAMILY OF ...THE RESIDUE NUMBERS FOR CHAIN A ARE NOT SEQUENTIAL. THE NUMBERING SCHEME IS BASED ON THE FAMILY OF SERINE PROTEASES AND IS BASED ON THE ZYMOGEN CHYMOTRYPSINOGEN

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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: 2.71 Å3/Da / Density % sol: 54.32 %
Crystal growpH: 6.5
Details: 0.5 UL DROPS OF PROTEIN-INHIBITOR SOLUTION (12.2 MG/ML IN 20 MM TRIS-HCL PH 8.0, 200 MM NACL) WERE MIXED WITH AN EQUAL VOLUME OF PRECIPITANT SOLUTION (25% PEG MONOMETHYLETHER-550 (V/V), 0.10 ...Details: 0.5 UL DROPS OF PROTEIN-INHIBITOR SOLUTION (12.2 MG/ML IN 20 MM TRIS-HCL PH 8.0, 200 MM NACL) WERE MIXED WITH AN EQUAL VOLUME OF PRECIPITANT SOLUTION (25% PEG MONOMETHYLETHER-550 (V/V), 0.10 M MES PH 6.5, 10 MM ZNSO(4), 12 MM ZNCL(2)) AND INCUBATED AT ROOM TEMPERATURE OVER A RESERVOIR OF 24% W/V PEG-3350, 12.8% V/V PEG MME-550, 50 MM MES PH 6.5, 5 MM ZNSO(4), AND 6 MM ZNCL(2).
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal amounts of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112.2 mg/mlprotein1drop
220 mmTris-HCl1drop
3200 mM1dropNaCl
425 %(v/v)mPEG5501dropprecipitant
50.1 MMES1dropprecipitant
610 mM1dropZnSO4precipitant
712 mM1dropZnCl2precipitant
824 %(w/v)PEG33501reservoir
912.8 %(v/v)mPEG5501reservoir
1050 mMMES1reservoir
115 mM1reservoirZnSO4
126 mM1reservoirZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2000 / Details: NON-FOCUSING
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.9 Å / Num. obs: 19956 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.32 / % possible all: 88.8
Reflection
*PLUS
Num. measured all: 163991
Reflection shell
*PLUS
% possible obs: 88.8 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNXrefinement
HKL-2000data reduction
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CATHEPSIN G (PDB ENTRY 1CGH)

1cgh


Resolution: 2→19.9 Å / Cross valid method: FREE-R
Details: RESIDUE 245 IS MISSING IN THE ELECTRON DENSITY. SHELX WAS ALSO USED FOR THE FINAL REFINEMENT TO MODEL DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2027 10.2 %RANDOM
Rwork0.2391 ---
obs-19942 96.6 %-
Displacement parametersBiso mean: 42.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.2793 Å
Refinement stepCycle: LAST / Resolution: 2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 93 58 1966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg0.025
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 1.998→2.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.33 2340 -
obs--89.8 %
Software
*PLUS
Name: CNX / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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