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- PDB-7say: Fragment of streptococcal M87 protein fused to GCN4 adaptor in co... -

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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 / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / specific granule / mediator complex binding ...cytolysis / killing by host of symbiont cells / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / specific granule / mediator complex binding / cellular response to peptidoglycan / neutrophil activation / Oxidative Stress Induced Senescence / cellular response to interleukin-6 / Antimicrobial peptides / TFIID-class transcription factor complex binding / amino acid biosynthetic process / cellular response to interleukin-1 / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / 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 / cellular response to tumor necrosis factor / antibacterial humoral response / tertiary granule lumen / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to Gram-negative bacterium / transcription regulator complex / sequence-specific DNA binding / amyloid fibril formation / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to Gram-positive bacterium / intracellular signal transduction / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / chromatin binding / 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) / : / Streptococcal M proteins C repeat profile. / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like ...M protein repeat / M protein repeat / Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / : / Streptococcal M proteins C repeat profile. / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / : / Basic region leucine zipper / Cystatin superfamily / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


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

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Experimental details

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Experiment

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

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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

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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

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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)

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