[English] 日本語
Yorodumi
- PDB-8f5n: Identification of an Immunodominant region on a Group A Streptoco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f5n
TitleIdentification of an Immunodominant region on a Group A Streptococcus T-antigen Reveals Temperature-Dependent Motion in Pili
Components
  • Mouse-Human Fab heavy chain
  • Mouse-Human Fab light chain
  • T18.1 Major pilin backbone protein T-antigen
KeywordsSTRUCTURAL PROTEIN / Streptococcus T-antigen major pilin backbone protein
Function / homology
Function and homology information


Streptococcal pilin isopeptide linker / Spy0128-like isopeptide containing domain / Streptococcal pilin isopeptide linker superfamily / : / Domain of unknown function (DUF7601) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major pilin backbone protein T-antigen
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRaynes, J.M. / Young, P.G. / Moreland, N.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Other government New Zealand
CitationJournal: Virulence / Year: 2023
Title: Identification of an immunodominant region on a group A Streptococcus T-antigen reveals temperature-dependent motion in pili.
Authors: Raynes, J.M. / Young, P.G. / Lorenz, N. / Loh, J.M.S. / McGregor, R. / Baker, E.N. / Proft, T. / Moreland, N.J.
History
DepositionNov 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T18.1 Major pilin backbone protein T-antigen
L: Mouse-Human Fab light chain
H: Mouse-Human Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2294
Polymers78,1893
Non-polymers401
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Co-migration as a complex, immunoprecipitation, ELISA confirms Fab binding to T-antigen
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.362, 41.112, 171.600
Angle α, β, γ (deg.)90.00, 110.42, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein T18.1 Major pilin backbone protein T-antigen


Mass: 31038.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M18 / Gene: tee 18.1 / Plasmid: pProExHta / Production host: Escherichia coli (E. coli) / References: UniProt: A0A096ZH83
#2: Antibody Mouse-Human Fab light chain


Mass: 23560.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pComb3X / Production host: Escherichia coli (E. coli) / Strain (production host): Top10F
#3: Antibody Mouse-Human Fab heavy chain


Mass: 23590.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pComb3X / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.3 Mdiethyleneglycol, 0.3 Mtriethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 Mpentaethyleneglycol and 0.1 M MOPS/HEPES-Na pH 7.5

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.9→41.87 Å / Num. obs: 65913 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.425 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4228 / CC1/2: 0.769 / Rpim(I) all: 0.583 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
XDSVERSION Jun 1, 2017data reduction
Aimless1.17.29data scaling
PHASER2.8.2phasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N0A

6n0a


Resolution: 1.9→41.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.804 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24358 3333 5.1 %RANDOM
Rwork0.20164 ---
obs0.20377 62570 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.565 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20.98 Å2
2--2.66 Å20 Å2
3----1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.9→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 1 302 5586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135403
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174791
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.6467350
X-RAY DIFFRACTIONr_angle_other_deg1.3181.57711162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8215698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33824.425226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99615850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3451512
X-RAY DIFFRACTIONr_chiral_restr0.0720.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021070
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0485.0982807
X-RAY DIFFRACTIONr_mcbond_other4.0475.0972806
X-RAY DIFFRACTIONr_mcangle_it5.3557.6173500
X-RAY DIFFRACTIONr_mcangle_other5.3557.6193501
X-RAY DIFFRACTIONr_scbond_it4.7585.3412596
X-RAY DIFFRACTIONr_scbond_other4.7575.3422597
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8597.893851
X-RAY DIFFRACTIONr_long_range_B_refined8.23557.8455532
X-RAY DIFFRACTIONr_long_range_B_other8.20657.7425489
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 253 -
Rwork0.337 4607 -
obs--99.63 %

+
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