[English] 日本語
Yorodumi
- PDB-7say: Fragment of streptococcal M87 protein fused to GCN4 adaptor in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7say
TitleFragment of streptococcal M87 protein fused to GCN4 adaptor in complex with human cathelicidin
Components
  • Antibacterial peptide LL-37
  • General control transcription factor GCN4/M protein chimera
KeywordsIMMUNE SYSTEM / complex / virulence factor / antimicrobial peptide
Function / homology
Function and homology information


cytolysis / killing by host of symbiont cells / protein localization to nuclear periphery / FCERI mediated MAPK activation / specific granule / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation ...cytolysis / killing by host of symbiont cells / protein localization to nuclear periphery / FCERI mediated MAPK activation / specific granule / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / cellular response to peptidoglycan / neutrophil activation / Oxidative Stress Induced Senescence / nitrogen catabolite activation of transcription from RNA polymerase II promoter / cellular response to interleukin-6 / Antimicrobial peptides / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / cellular response to interleukin-1 / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / innate immune response in mucosa / cell projection / lipopolysaccharide binding / RNA polymerase II transcription regulator complex / specific granule lumen / positive regulation of angiogenesis / : / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / cellular response to tumor necrosis factor / antibacterial humoral response / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / RNA polymerase II-specific DNA-binding transcription factor binding / defense response to Gram-negative bacterium / transcription regulator complex / sequence-specific DNA binding / amyloid fibril formation / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / chromatin binding / Neutrophil degranulation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus
Similarity search - Function
M protein repeat / M protein repeat / Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cystatin superfamily ...M protein repeat / M protein repeat / Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cystatin superfamily / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
General control transcription factor GCN4 / Cathelicidin antimicrobial peptide / M protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Streptococcus pyogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKolesinski, P. / Ghosh, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Elife / Year: 2022
Title: An M protein coiled coil unfurls and exposes its hydrophobic core to capture LL-37
Authors: Kolesinski, P. / Wang, K.C. / Hirose, Y. / Nizet, V. / Ghosh, P. / Stallings, C.L. / Dotsch, V.
History
DepositionSep 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: General control transcription factor GCN4/M protein chimera
B: General control transcription factor GCN4/M protein chimera
E: Antibacterial peptide LL-37
C: General control transcription factor GCN4/M protein chimera
D: General control transcription factor GCN4/M protein chimera
F: Antibacterial peptide LL-37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,42710
Polymers43,1796
Non-polymers2484
Water1,820101
1
A: General control transcription factor GCN4/M protein chimera
B: General control transcription factor GCN4/M protein chimera
E: Antibacterial peptide LL-37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7766
Polymers21,5893
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: General control transcription factor GCN4/M protein chimera
D: General control transcription factor GCN4/M protein chimera
F: Antibacterial peptide LL-37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6524
Polymers21,5893
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.230, 57.140, 71.490
Angle α, β, γ (deg.)90.000, 102.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
General control transcription factor GCN4/M protein chimera / Amino acid biosynthesis regulatory protein / General control protein GCN4


Mass: 8542.565 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Amino acids 35-38: partial PreScission protease site; amino acids 39-67: GCN4 adaptor - GCN4 from Saccharomyces cerevisiae (amino acids 250-278); amino acids 68-105: M87 protein fragment ...Details: Amino acids 35-38: partial PreScission protease site; amino acids 39-67: GCN4 adaptor - GCN4 from Saccharomyces cerevisiae (amino acids 250-278); amino acids 68-105: M87 protein fragment from Streptococcus pyogenes (amino acids 68-105)
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Streptococcus pyogenes (bacteria)
Strain: ATCC 204508 / S288c / Gene: GCN4, AAS101, AAS3, ARG9, YEL009C, emm
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P03069, UniProt: Q6TLP8
#2: Protein/peptide Antibacterial peptide LL-37


Mass: 4504.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49913
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% (v/v) acetonitrile, 0.1 M MES-NaOH, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→45.02 Å / Num. obs: 22092 / % possible obs: 94.52 % / Redundancy: 6.1 % / Biso Wilson estimate: 26.42 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.05 / Rrim(I) all: 0.128 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1694 / CC1/2: 0.878 / Rpim(I) all: 0.302 / Rrim(I) all: 0.735

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQL

1kql


Resolution: 2.1→45.02 Å / SU ML: 0.2193 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.5329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.271 1131 5.15 %
Rwork0.2257 20827 -
obs0.2281 21958 94.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 4 101 2653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00142604
X-RAY DIFFRACTIONf_angle_d0.31963482
X-RAY DIFFRACTIONf_chiral_restr0.0276379
X-RAY DIFFRACTIONf_plane_restr0.0014450
X-RAY DIFFRACTIONf_dihedral_angle_d10.3856338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.34581450.27452426X-RAY DIFFRACTION89.58
2.2-2.310.32071640.2582564X-RAY DIFFRACTION94.95
2.31-2.460.27111400.23422634X-RAY DIFFRACTION95.69
2.46-2.650.29431360.22372672X-RAY DIFFRACTION97.36
2.65-2.910.24521270.22522520X-RAY DIFFRACTION91.66
2.91-3.330.27581350.23112699X-RAY DIFFRACTION97.29
3.33-4.20.24831530.20652585X-RAY DIFFRACTION93.48
4.2-45.020.26061310.222727X-RAY DIFFRACTION96.03
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)
10.651577435927-0.477289797091-1.134214632721.566957533271.466320120547.59951421007-0.0293837995621-0.0370749941501-0.003937130578820.04169679250880.259810388053-0.0221032084524-0.1256494168950.802121300659-0.1013354963420.347795209861-0.0538736693250.02949606383290.1134421782210.00223770084360.1955339396281.92993979816-0.75091396738910.0383467993
20.207514353453-0.060052097241-0.01909869554281.437775421322.835007411977.088735474260.03296526981570.0302106943562-0.00846372084616-0.286193879058-0.0870101139443-0.0120907558984-0.594376523945-0.171336695635-0.01191050291880.408075965392-0.06396447040050.03728895181280.1216145627570.007466097720410.171499471973-3.332766359642.8562103895515.7342734592
31.533048622950.3266234930660.1750607705065.134896683434.534674024716.11124678765-0.1249373134140.0451191994909-0.1522077989340.253125177883-0.2554751940370.3036594864570.680076834817-1.206813169170.3295522342010.441302769112-0.1151469477790.09487895700910.162766222215-0.0134653901420.283971643879-7.03776703693.1263745438247.697839173
41.56627203860.3353399509782.0856541330.1571387036030.1668736798313.96411674550.366006978325-0.354812875185-0.186794932218-0.342654980752-0.1836860637910.3097288451951.63652146178-0.690768814374-0.06052974142240.8425655048670.0575981031732-0.1330099411140.4853893959130.05434396389930.33598528109516.42442834496.0022776138314.4023338909
51.29934688856-0.2493806017710.2731693457340.683439224828-1.221758551832.07511231287-0.134168800316-0.7736743245220.05975068509570.304666152834-0.0182875960355-0.086014190535-1.28967487272-0.657265411666-0.03036445654080.388603427374-0.0493836912283-0.01234211559080.459863706855-0.005090139021510.20708591073114.085912888715.27736314946.31789446436
62.062422811430.2065972318531.999163344992.672847263210.9383551630156.61534194076-0.0277761774319-0.2710853483760.1175360412350.2184753584150.237134702763-0.1006852370680.06440838037132.096882464340.02252867858930.1896260066120.0525413176453-0.0133080269370.589981050199-0.06420752120730.24888777566522.790306087310.7554722011-11.006032582
71.737665246540.1116110138170.5264079739963.794375096440.2817167558742.72446079670.188778153364-0.7020533681370.2255233431391.055944663850.209930555379-0.158704802107-0.3767436379490.4075396226920.3911793467310.6354157177190.075383171449-0.07992489933031.577733684130.04392907379310.22429175561417.190560949811.989697636153.9502692515
86.19532990257-0.2753672091111.054756601337.06411319774-1.509174087442.146954269360.0816648161549-0.200401730252-0.7733421895850.8548904805850.607489123633-0.4065741445830.06238519711741.6678847118-0.6996305399930.7515902162470.123136400539-0.09123892434171.00499652132-0.003457006642560.51782018565726.76554707218.9307372675655.7219457565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 38 through 93)
2X-RAY DIFFRACTION2(chain 'B' and resid 35 through 301)
3X-RAY DIFFRACTION3(chain 'E' and resid 2 through 101)
4X-RAY DIFFRACTION4(chain 'C' and resid 56 through 93)
5X-RAY DIFFRACTION5(chain 'D' and resid 56 through 104)
6X-RAY DIFFRACTION6(chain 'F' and resid 3 through 36)
7X-RAY DIFFRACTION7(chain 'C' and resid 41 through 55)
8X-RAY DIFFRACTION8(chain 'D' and resid 38 through 55)

+
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