[English] 日本語
Yorodumi
- PDB-7h6g: THE 1.21 A CRYSTAL STRUCTURE OF HUMAN CATHEPSIN G IN COMPLEX WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7h6g
TitleTHE 1.21 A CRYSTAL STRUCTURE OF HUMAN CATHEPSIN G IN COMPLEX WITH N-[2-[6-fluoro-2-[(4-hydroxy-5-methyl-2-oxo-5-phenylfuran-3-yl)-phenylmethyl]-1H-indol-3-yl]ethyl]acetamide
ComponentsCathepsin G
KeywordsHYDROLASE / HUMAN CATHEPSIN G / SERINE PROTEINASE / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / caspase binding / negative regulation of T cell activation / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation ...cathepsin G / biofilm matrix disassembly / neutrophil-mediated killing of gram-positive bacterium / purinergic nucleotide receptor signaling pathway / caspase binding / negative regulation of T cell activation / neutrophil activation / Suppression of apoptosis / Interleukin-1 processing / positive regulation of platelet aggregation / Antimicrobial peptides / Activation of Matrix Metalloproteinases / monocyte chemotaxis / extracellular matrix disassembly / defense response to fungus / Metabolism of Angiotensinogen to Angiotensins / Purinergic signaling in leishmaniasis infection / angiotensin maturation / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / protein maturation / protein processing / positive regulation of immune response / platelet activation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytokine-mediated signaling pathway / cytoplasmic stress granule / azurophil granule lumen / antibacterial humoral response / peptidase activity / heparin binding / : / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / lysosome / protein phosphorylation / defense response to Gram-positive bacterium / immune response / receptor ligand activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / membrane / plasma membrane / cytosol
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsBanner, D.W. / Benz, J.M. / Schlatter, D. / Hilpert, H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Not funded Switzerland
CitationJournal: To be published
Title: Crystal structures of human Chymase and Cathepsin G
Authors: Markus, R. / Tosstorff, A.
History
DepositionApr 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cathepsin G
B: Cathepsin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,45613
Polymers53,6042
Non-polymers1,85211
Water7,927440
1
A: Cathepsin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9298
Polymers26,8021
Non-polymers1,1277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5275
Polymers26,8021
Non-polymers7254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.110, 74.450, 60.650
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Cathepsin G / CG


Mass: 26801.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSG / Production host: Escherichia coli (E. coli) / References: UniProt: P08311, cathepsin G

-
Non-polymers , 5 types, 451 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-A1AOS / N-(2-{6-fluoro-2-[(R)-[(5R)-4-hydroxy-5-methyl-2-oxo-5-phenyl-2,5-dihydrofuran-3-yl](phenyl)methyl]-1H-indol-3-yl}ethyl)acetamide


Mass: 498.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H27FN2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 0.2 M LiSO4 (Salt), 25 %w/v PEG3350 (Precipitant), 0.1 M HEPES 7.5 pH (Buffer), Protein was at 17 mg/mL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.21→60.63 Å / Num. obs: 117974 / % possible obs: 88.9 % / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Net I/σ(I): 16.66 / Num. measured all: 749223
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsRrim(I) allNet I/σ(I) obs
1.21-1.28600.37852422123060.4324.15
1.28-1.3791.80.264113335189390.2897.15
1.37-1.4892.70.168114569175010.18310.84
1.48-1.6293.70.1105298160740.10915.99
1.62-1.8194.70.06996745148130.07521.4
1.81-2.0995.60.05685952132800.06125.91
2.09-2.4996.40.05364705101590.05827.93
2.49-397.10.0715381763890.07629.69
3-4.397.60.0714583856740.07824.04
4.3-60.6393.40.0631654228390.07121.84

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→60.63 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.255 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18106 5916 5 %RANDOM
Rwork0.15677 ---
obs0.15797 112057 88.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.404 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.14 Å2
2---0.73 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.21→60.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 112 440 4173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214110
X-RAY DIFFRACTIONr_bond_other_d0.0010.023813
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9745579
X-RAY DIFFRACTIONr_angle_other_deg0.82938760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66820.196204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62415708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8311579
X-RAY DIFFRACTIONr_chiral_restr0.0960.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024687
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02990
X-RAY DIFFRACTIONr_nbd_refined0.1930.2712
X-RAY DIFFRACTIONr_nbd_other0.1920.24073
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21951
X-RAY DIFFRACTIONr_nbtor_other0.0820.22710
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.2118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5971.53168
X-RAY DIFFRACTIONr_mcbond_other0.6271.5985
X-RAY DIFFRACTIONr_mcangle_it1.89423958
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42831919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0714.51621
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.29239628
X-RAY DIFFRACTIONr_sphericity_free6.1833443
X-RAY DIFFRACTIONr_sphericity_bonded3.18137809
LS refinement shellResolution: 1.21→1.241 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 225 -
Rwork0.226 4458 -
obs--47.84 %

+
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://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