[English] 日本語
Yorodumi
- PDB-6bz9: Crystal structure of human caspase-1 in complex with Ac-FLTD-CMK -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bz9
TitleCrystal structure of human caspase-1 in complex with Ac-FLTD-CMK
Components
  • (Caspase-1) x 2
  • Ac-FLTD-CMK
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aldose 1-epimerase activity / galactose catabolic process via UDP-galactose / glucose metabolic process / carbohydrate binding / DNA damage response
Similarity search - Function
Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Caspase-like / Rossmann fold - #1460 / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein YphB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsXiao, T.S. / Yang, J. / Liu, Z. / Wang, C. / Yang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR069908 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanism of gasdermin D recognition by inflammatory caspases and their inhibition by a gasdermin D-derived peptide inhibitor.
Authors: Yang, J. / Liu, Z. / Wang, C. / Yang, R. / Rathkey, J.K. / Pinkard, O.W. / Shi, W. / Chen, Y. / Dubyak, G.R. / Abbott, D.W. / Xiao, T.S.
History
DepositionDec 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 19, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caspase-1
B: Caspase-1
C: Ac-FLTD-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8945
Polymers30,6823
Non-polymers2122
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-36 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.830, 63.830, 160.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / p45


Mass: 19869.838 Da / Num. of mol.: 1 / Fragment: UNP residues 120-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Production host: Escherichia coli (E. coli) / References: UniProt: P29466, EC: 3.4.22.36
#2: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / p45


Mass: 10258.755 Da / Num. of mol.: 1 / Fragment: UNP residues 317-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Production host: Escherichia coli (E. coli) / References: UniProt: P29466, EC: 3.4.22.36
#3: Protein/peptide Ac-FLTD-CMK


Mass: 553.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate, 20% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.796→29.66 Å / Num. obs: 31896 / % possible obs: 99.8 % / Redundancy: 21.8 % / CC1/2: 1 / Rpim(I) all: 0.013 / Net I/σ(I): 31.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 21.5 % / Mean I/σ(I) obs: 2 / CC1/2: 0.877 / Rpim(I) all: 0.375 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QBH

2qbh
PDB Unreleased entry


Resolution: 1.796→29.657 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 1998 6.29 %
Rwork0.178 --
obs0.18 31762 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.796→29.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 14 125 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062166
X-RAY DIFFRACTIONf_angle_d0.7412910
X-RAY DIFFRACTIONf_dihedral_angle_d5.0791834
X-RAY DIFFRACTIONf_chiral_restr0.054320
X-RAY DIFFRACTIONf_plane_restr0.005375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7964-1.84130.34051380.28582046X-RAY DIFFRACTION97
1.8413-1.89110.24131380.23492058X-RAY DIFFRACTION99
1.8911-1.94680.20121410.212077X-RAY DIFFRACTION99
1.9468-2.00960.21511400.18632101X-RAY DIFFRACTION100
2.0096-2.08140.2381400.19492084X-RAY DIFFRACTION100
2.0814-2.16470.25981400.192084X-RAY DIFFRACTION100
2.1647-2.26320.24121420.19082119X-RAY DIFFRACTION100
2.2632-2.38250.26031410.19382099X-RAY DIFFRACTION100
2.3825-2.53160.19521420.19542126X-RAY DIFFRACTION100
2.5316-2.7270.21681430.19752127X-RAY DIFFRACTION100
2.727-3.00120.23571430.20022133X-RAY DIFFRACTION100
3.0012-3.43490.23951450.19362163X-RAY DIFFRACTION100
3.4349-4.32550.17351490.14762209X-RAY DIFFRACTION100
4.3255-29.66120.18741560.15792338X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.01741.13413.47257.057-3.07093.5575-0.51121.0723-1.33160.51540.00630.18831.1160.00580.43620.7739-0.1260.15430.4023-0.16890.4922-21.3746-49.61-9.1762
22.95222.00311.84852.5987-0.40823.78860.1632-0.8037-1.3349-0.23970.16472.51810.7457-2.1422-0.20750.6504-0.3235-0.00821.018-0.09451.1427-37.1961-40.6052-9.9491
35.1462-4.9646-4.9126.97172.0847.55360.05660.9369-0.4422-0.2142-0.44970.50430.9426-0.56530.45760.3895-0.0954-0.00140.5835-0.12670.3409-25.4498-37.729-19.7432
42.61562.87260.45235.0922.00633.17220.03030.3079-0.44960.28540.3622-1.1870.14841.4996-0.31580.29150.0401-0.03510.7338-0.1010.49510.9974-31.4017-4.8669
52.69111.4611.07014.68961.54914.4794-0.0950.0868-0.18680.1960.1831-0.36420.50980.61-0.09110.31490.05690.03420.3758-0.06810.2711-7.7057-38.073-10.6386
67.14371.96241.76731.72151.14297.9014-0.0450.61530.1387-0.18330.0837-0.0968-0.20980.4689-0.0450.26740.00890.04450.3145-0.02920.3027-11.2127-28.0866-17.3107
72.6808-2.4376-3.37566.77683.39934.20410.2416-0.27220.66210.26210.3785-0.1162-0.681.0291-0.60640.4149-0.124-0.00810.5938-0.09250.4996-3.7865-21.6478-0.2315
84.53610.5488-0.14852.0733-0.07082.94470.11130.06060.5235-0.0215-0.004-0.2748-0.42460.5221-0.03350.2806-0.06780.05980.3347-0.03050.3227-10.5987-21.5938-10.3459
97.2652-1.9915-5.48472.10872.57349.1849-0.1618-0.6844-0.28690.3252-0.1951-0.03490.34531.0170.32420.3588-0.0589-0.06730.3872-0.04070.3181-10.906-25.35217.1023
105.4266-3.34563.37357.8386-5.96164.59240.09660.2595-0.038-0.33150.12260.13690.3152-0.1665-0.23930.2776-0.04420.04620.33350.00510.2491-26.0794-18.1357-16.8407
117.0445-5.12620.87887.1455-0.24252.87380.1223-0.2827-0.15930.29780.0763-0.35950.52860.6897-0.22480.36630.0363-0.04130.39950.00260.3081-7.9592-31.46325.6252
123.3574-0.3486-0.28481.73331.52746.6863-0.26710.0632-0.36360.49490.05660.25190.8107-0.10710.18760.4487-0.0330.090.220.00660.2617-21.147-37.68681.5977
137.2691.1447-1.88666.28055.01376.87260.156-0.43-0.64950.79640.1754-0.18161.15650.5763-0.22390.44590.0183-0.03440.2726-0.0120.304-15.0106-31.096110.4918
143.7348-2.5812-0.85982.83762.88814.6373-0.18820.3547-0.2463-0.0231-0.09830.76830.4913-0.51940.24360.2613-0.09980.04460.3459-0.02120.2123-27.2305-32.9106-9.7443
156.42824.8431-1.93614.10780.41748.3476-0.0086-0.49420.18030.89180.2392-1.40610.05241.1193-0.21960.54440.1922-0.1010.6794-0.14240.5227-1.5865-33.13368.1168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 151 )
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 163 )
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 207 )
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 235 )
7X-RAY DIFFRACTION7chain 'A' and (resid 236 through 245 )
8X-RAY DIFFRACTION8chain 'A' and (resid 246 through 283 )
9X-RAY DIFFRACTION9chain 'A' and (resid 284 through 297 )
10X-RAY DIFFRACTION10chain 'B' and (resid 317 through 328 )
11X-RAY DIFFRACTION11chain 'B' and (resid 329 through 347 )
12X-RAY DIFFRACTION12chain 'B' and (resid 348 through 377 )
13X-RAY DIFFRACTION13chain 'B' and (resid 378 through 390 )
14X-RAY DIFFRACTION14chain 'B' and (resid 391 through 404 )
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 5 )

+
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