[English] 日本語
Yorodumi
- PDB-9sm8: Zuzalysin zymogen pentamer E439A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9sm8
TitleZuzalysin zymogen pentamer E439A
ComponentsZinc-dependent metalloprotease
KeywordsHYDROLASE / metallopeptidase / pentamer / zymogen / prophyromonas gingivalis
Function / homology
Function and homology information


metallopeptidase activity
Similarity search - Function
EcxA, zinc-binding / Domain of unknown function DUF5117 / Domain of unknown function DUF5118 / Bacterial MMP-like domain / Domain of unknown function (DUF5117) / Domain of unknown function (DUF5118) / Met-zincin / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
Zinc-dependent metalloprotease
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsRodriguez-Banqueri, A. / Madej, M. / Eckhard, U. / Potempa, J. / Gomis Ruth, F.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Zuzalysin zymogen pentamer E439A at 3.59 Angstroms resolution
Authors: Rodriguez-Banqueri, A. / Madej, M. / Eckhard, U. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionSep 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc-dependent metalloprotease
B: Zinc-dependent metalloprotease
C: Zinc-dependent metalloprotease
D: Zinc-dependent metalloprotease
E: Zinc-dependent metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)486,04415
Polymers485,5175
Non-polymers52710
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNHISHISAA43 - 90130 - 847
d_12CACACACAAF1001
d_21GLNGLNHISHISBB43 - 90130 - 847
d_22CACACACABH1001
d_31GLNGLNHISHISCC43 - 90130 - 847
d_32CACACACACJ1001
d_41GLNGLNHISHISDD43 - 90130 - 847
d_42CACACACADL1001
d_51GLNGLNHISHISEE43 - 90130 - 847
d_52CACACACAEN1001

NCS oper:
IDCodeMatrixVector
1given(0.308869418577, 0.95109980508, -0.00297372555933), (-0.951104452435, 0.308868083152, -0.000909817888489), (5.31612969278E-5, 0.00310933854202, 0.999995164582)-23.8094331656, 152.799788121, -0.317527471203
2given(-0.811421395768, 0.584461276857, -0.000578225814832), (-0.584461046326, -0.811418966177, 0.00213228894696), (0.000777056927682, 0.00206813533827, 0.999997559496)114.303305789, 222.593290507, -0.301252388636
3given(-0.806893818147, -0.590693694004, 0.0018237598136), (0.590696411063, -0.806891619609, 0.0019142000441), (0.00034087061466, 0.00262184455882, 0.999996504863)222.874763152, 112.86182575, -0.309849875778
4given(0.308792080809, -0.95112516544, 0.00289318117704), (0.951128716629, 0.308794441108, 0.00039691986739), (-0.00127091873913, 0.00262922198813, 0.99999573597)152.448452185, -24.1003588861, -0.169078950424

-
Components

#1: Protein
Zinc-dependent metalloprotease


Mass: 97103.305 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: NY149_10785 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAF0BD41
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Zuzalysin zymogen E439A / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: OTHER / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2700 nm / Nominal defocus min: 1700 nm
Image recordingElectron dose: 38.58 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0rc1_5617model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212348 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 200.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007833585
ELECTRON MICROSCOPYf_angle_d1.707845470
ELECTRON MICROSCOPYf_chiral_restr0.0884920
ELECTRON MICROSCOPYf_plane_restr0.010310025
ELECTRON MICROSCOPYf_dihedral_angle_d3.59224515
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints2.93953588753E-13
ens_1d_3AAELECTRON MICROSCOPYNCS constraints3.85159991285E-13
ens_1d_4AAELECTRON MICROSCOPYNCS constraints5.31009667405E-13
ens_1d_5AAELECTRON MICROSCOPYNCS constraints6.29663650414E-13

+
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