[English] 日本語
Yorodumi
- PDB-8tvl: Plasminogen binding group A streptococcus M-like protein from AP5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tvl
TitlePlasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen
ComponentsPlasminogen-binding group A streptococcal M-like protein PAM
KeywordsBLOOD CLOTTING / PAM / human plasminogen / M-protein / Group A streptococcus
Function / homology
Function and homology information


plasminogen activation / extracellular region
Similarity search - Function
Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / : / Streptococcal M proteins D repeats region profile. / : / Streptococcal M proteins C repeat profile. / YSIRK Gram-positive signal peptide
Similarity search - Domain/homology
Plasminogen-binding group A streptococcal M-like protein PAM
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsReadnour, B.M. / Tjia-Fleck, S.K. / Castellino, F.J. / McCann, N.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL013424 United States
CitationJournal: To Be Published
Title: Plasminogen binding group A streptococcus M-like protein from AP53 bound to human plasminogen
Authors: Readnour, B.M. / Tjia-Fleck, S.K. / McCann, N.R. / Ayinuola, Y.A. / Ploplis, V.A. / Castellino, F.J.
History
DepositionAug 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references
Category: database_2 / em_db_reference / pdbx_database_related
Item: _database_2.database_code / _em_db_reference.access_code / _pdbx_database_related.db_id
Revision 2.0Aug 21, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / em_buffer ...atom_site / em_buffer / em_buffer_component / em_software / entity / entity_src_gen / pdbx_contact_author / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_ls_restr / struct_conf / struct_ref / 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 / _em_buffer.details / _em_buffer_component.concentration / _em_buffer_component.concentration_units / _em_buffer_component.name / _em_software.category / _em_software.fitting_id / _em_software.image_processing_id / _em_software.imaging_id / _em_software.name / _em_software.version / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Description: Model orientation/position / Provider: author / Type: Coordinate replacement

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plasminogen-binding group A streptococcal M-like protein PAM


Theoretical massNumber of molelcules
Total (without water)40,6601
Polymers40,6601
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 Plasminogen-binding group A streptococcal M-like protein PAM


Mass: 40659.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: AP53 / Gene: pam, emm / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P49054

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Plasminogen Binding Group A Streptococcus M-Like Protein from AP53 bound to human plasminogen
Type: COMPLEX / Details: PAM was bound to the surface of a lentivirus / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.041 MDa / Experimental value: YES
Source (natural)Organism: Streptococcus pyogenes (bacteria) / Strain: AP53 / Cellular location: Cell surface
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T
Buffer solutionpH: 7.4
Details: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4
Buffer componentConc.: 1 X / Name: PBS / Formula: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Plasminogen binding Group A streptococcus M like protein of AP53 bound to human plasminogen on the surface of a lentivirus
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 109000 X / Nominal defocus max: 34000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4054

-
Processing

EM softwareName: PHENIX / Version: 1.21rc1_5054 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212829 / Num. of class averages: 14 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Phenix map to model / Source name: Other / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 149.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00472720
ELECTRON MICROSCOPYf_angle_d1.0933616
ELECTRON MICROSCOPYf_chiral_restr0.0481389
ELECTRON MICROSCOPYf_plane_restr0.0071489
ELECTRON MICROSCOPYf_dihedral_angle_d11.1548363

+
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