[English] 日本語
Yorodumi
- PDB-1fi8: RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD] -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fi8
TitleRAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD]
Components
  • (ECOTIN) x 2
  • NATURAL KILLER CELL PROTEASE 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / complex (serine protease-inhibitor) / protease substrate interactions / beta strand structure / chymotrypsin fold / granzyme B / ecotin / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Activation, myristolyation of BID and translocation to mitochondria / granzyme B / granzyme-mediated apoptotic signaling pathway / : / cytolytic granule / cytolysis / positive regulation of necroptotic process / natural killer cell mediated cytotoxicity / serine-type peptidase activity / serine-type endopeptidase inhibitor activity ...Activation, myristolyation of BID and translocation to mitochondria / granzyme B / granzyme-mediated apoptotic signaling pathway / : / cytolytic granule / cytolysis / positive regulation of necroptotic process / natural killer cell mediated cytotoxicity / serine-type peptidase activity / serine-type endopeptidase inhibitor activity / T cell mediated cytotoxicity / defense response / outer membrane-bounded periplasmic space / early endosome / negative regulation of translation / serine-type endopeptidase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Ecotin, trypsin inhibitor / Ecotin, trypsin inhibitor / Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / Few Secondary Structures / Irregular ...Ecotin, trypsin inhibitor / Ecotin, trypsin inhibitor / Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / Few Secondary Structures / Irregular / 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 / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWaugh, S.M. / Harris, J.L. / Fletterick, R.J. / Craik, C.S.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The structure of the pro-apoptotic protease granzyme B reveals the molecular determinants of its specificity
Authors: Waugh, S.M. / Harris, J.L. / Fletterick, R. / Craik, C.S.
History
DepositionAug 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NATURAL KILLER CELL PROTEASE 1
C: ECOTIN
D: ECOTIN
B: NATURAL KILLER CELL PROTEASE 1
E: ECOTIN
F: ECOTIN


Theoretical massNumber of molelcules
Total (without water)82,8006
Polymers82,8006
Non-polymers00
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17410 Å2
ΔGint-90 kcal/mol
Surface area29350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.64, 154.6, 57.24
Angle α, β, γ (deg.)90, 119.76, 90
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is the tetramer in the asymmetric unit.

-
Components

#1: Protein NATURAL KILLER CELL PROTEASE 1 / GRANZYME B


Mass: 25225.396 Da / Num. of mol.: 2 / Mutation: N66Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: CYTOTOXIC LYMPHOCYTE GRANULES / Plasmid: PPICZAA / Production host: Pichia pastoris (fungus)
References: UniProt: P18291, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein ECOTIN


Mass: 9528.733 Da / Num. of mol.: 2 / Fragment: RESIDUES 28 - 111 / Mutation: V81I, S82E, T83P, M84D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTACTAC / Production host: Escherichia coli (E. coli) / References: UniProt: P23827
#3: Protein ECOTIN


Mass: 6645.746 Da / Num. of mol.: 2 / Fragment: RESIDUES 112 - 169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTACTAC / Production host: Escherichia coli (E. coli) / References: UniProt: P23827
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: sodium acetate, PEGmme 2000, ammonium acetate,, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150-1500 mM1dropNaCl
25 mg/mlprotein1drop
3100 mMsodium acetate1reservoirpH5.8
4100 mMammonium sulfate1reservoir
525 %(w/v)PEG2000MME1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1851
2851
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-111.08
SYNCHROTRONSSRL BL7-121.08
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEAug 3, 1999
MARRESEARCH2IMAGE PLATENov 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→35.8 Å / Num. all: 98218 / Num. obs: 98218 / % possible obs: 90.3 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.8
Reflection shellResolution: 2.21→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.58 / Num. unique all: 48837 / % possible all: 90.7
Reflection
*PLUS
Num. obs: 48837 / Num. measured all: 121975
Reflection shell
*PLUS
% possible obs: 90 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.2→35.7 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
Details: Crystal 1 data was used for initial molecular replacement and refinement. Crystal 2 data was given the same Rfree set and used for final refinement. Molecular replacement used 1AZZ and 1AUG.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1305 0.05 %5% of observed reflections
Rwork0.218 ---
obs0.222 25137 90.2 %-
all-27853 --
Displacement parametersBiso mean: 43.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.42 Å
Luzzati sigma a0.5 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.2→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 0 370 5638
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 35.7 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more