[English] 日本語
Yorodumi
- PDB-9kr6: Cryo-EM structure of MPXV core protease in complex with the subst... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kr6
TitleCryo-EM structure of MPXV core protease in complex with the substrate derivative I-G18
Components
  • Core protease I7
  • Core protein VP8
KeywordsVIRAL PROTEIN / ORTHOPOXVIRUSES / MONKEYPOX / PROTEASE / VIRAL REPLICATION / DRUG DISCOVERY
Function / homology
Function and homology information


cysteine-type peptidase activity / virion component / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis
Similarity search - Function
Poxvirus VP8/L4R, nucleic acid binding / Poxvirus nucleic acid binding protein VP8/L4R / Peptidase C57, Vaccinia virus protein I7 / Vaccinia virus I7 processing peptidase / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Core protein VP8 / MPXVgp068
Similarity search - Component
Biological speciesMonkeypox virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLan, W. / You, T. / Li, D. / Dong, X. / Wang, H. / Xu, J. / Wang, W. / Gao, Y. / Yang, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902063 China
National Natural Science Foundation of China (NSFC)81902063 China
CitationJournal: To Be Published
Title: Cryo-Em Structure Of Mpox Core Protease In Complex With The Substrate Analogue I-G18
Authors: Lan, W. / You, T. / Li, D. / Dong, X. / Wang, H. / Xu, J. / Wang, W. / Gao, Y. / Yang, H.
History
DepositionNov 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Mar 26, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Data processing / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / em_3d_reconstruction / em_admin / em_ctf_correction / em_euler_angle_assignment / em_image_processing / em_image_recording / em_software / em_start_model / entity / entity_poly / entity_poly_seq / pdbx_audit_support / pdbx_contact_author / pdbx_database_related / pdbx_modification_feature / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / refine / struct_conn / struct_ref_seq / struct_ref_seq_dif
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _em_admin.last_update / _entity.formula_weight / _entity.pdbx_mutation / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_main_chain_plane.improper_torsion_angle / _refine.ls_d_res_high / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq.pdbx_auth_seq_align_end
Description: Ligand identity / Provider: author / Type: Coordinate replacement
Revision 2.0Mar 26, 2025Data content type: EM metadata
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Group: Data collection / Data processing ...Data collection / Data processing / Database references / Experimental summary / Other / Structure summary
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Category: em_3d_reconstruction / em_admin ...em_3d_reconstruction / em_admin / em_ctf_correction / em_euler_angle_assignment / em_image_processing / em_image_recording / em_software / em_start_model / entity / entity_poly / pdbx_database_related / struct_ref_seq / struct_ref_seq_dif
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _chem_comp.name / _em_admin.last_update ..._chem_comp.name / _em_admin.last_update / _entity.formula_weight / _entity.pdbx_mutation / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _struct_ref_seq.pdbx_auth_seq_align_end
Revision 2.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Data updated
Revision 2.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Data updated
Revision 2.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Data updated

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Core protease I7
C: Core protein VP8
B: Core protease I7
D: Core protein VP8


Theoretical massNumber of molelcules
Total (without water)100,4314
Polymers100,4314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Core protease I7 / I7L / MPXV-COP-062 / MPXV-SL-062 / MPXV-WRAIR062 / MPXVgp068 / Viral core cysteine proteinase / ...I7L / MPXV-COP-062 / MPXV-SL-062 / MPXV-WRAIR062 / MPXVgp068 / Viral core cysteine proteinase / Virion core cysteine protease


Mass: 49088.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
Gene: I7L, MPXV-CAM1990_02-060, MPXV-COP-062, MPXV-GAB1988_001-061, MPXV-Ikubi-060, MPXV-M2940_FCT-066, MPXV-M2957_Lagos-066, MPXV-M3021_Delta-066, MPXV-M5320_M15_Bayelsa-059, MPXV-Nig_SEV71_2_82- ...Gene: I7L, MPXV-CAM1990_02-060, MPXV-COP-062, MPXV-GAB1988_001-061, MPXV-Ikubi-060, MPXV-M2940_FCT-066, MPXV-M2957_Lagos-066, MPXV-M3021_Delta-066, MPXV-M5320_M15_Bayelsa-059, MPXV-Nig_SEV71_2_82-061, MPXV-PCH-063, MPXV-Singapore-066, MPXV-SL-062, MPXV-UK_P1-066, MPXV-UK_P2-066, MPXV-UK_P3-066, MPXV-UTC-057, MPXV-W_Nigeria-061, MPXV-WRAIR062, MPXV297957_057, MPXV298464_048, MPXV_DRC_Yandongi_069, MPXV_LIB1970_184_073, MPXV_RCG2003_358_073, MPXV_SUD2005_01_069, MPXV_ZAI1979_005_073, MPXVgp068, PDLMKLCO_00071
Production host: Escherichia coli (E. coli)
References: UniProt: Q5IXV7, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein/peptide Core protein VP8


Mass: 1127.243 Da / Num. of mol.: 2 / Mutation: G18(ETA) / Source method: obtained synthetically / Source: (synth.) Monkeypox virus / References: UniProt: M1L511
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: DIMER / Type: COMPLEX / Details: MONKEYPOX I7 IS A DIMER / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Monkeypox virus
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1160GATAN K3 (6k x 4k)
2160GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 760440 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å

+
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