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- PDB-7saf: Fragment of streptococcal M87 protein fused to GCN4 adaptor -

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Basic information

Entry
Database: PDB / ID: 7saf
TitleFragment of streptococcal M87 protein fused to GCN4 adaptor
ComponentsGeneral control transcription factor GCN4/M protein chimera
KeywordsCELL ADHESION / coiled-coil / virulence factor
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
M protein repeat / M protein repeat / 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
PHOSPHATE ION / General control transcription factor GCN4 / M protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2754
Polymers17,0852
Non-polymers1902
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-47 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.223, 97.223, 40.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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.: 2
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)
Gene: GCN4, AAS101, AAS3, ARG9, YEL009C, emm
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P03069, UniProt: Q6TLP8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.6 M monobasic ammonium phosphate, 0.1 M Tris-HCl, pH 8.0

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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: 2.45→43.48 Å / Num. obs: 7580 / % possible obs: 99.75 % / Redundancy: 12.1 % / Biso Wilson estimate: 55.23 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.3865 / Rpim(I) all: 0.1165 / Rrim(I) all: 0.4042 / Net I/σ(I): 31.4
Reflection shellResolution: 2.45→2.538 Å / Rmerge(I) obs: 4.684 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 738 / CC1/2: 0.556 / CC star: 0.846 / Rpim(I) all: 1.459 / Rrim(I) all: 4.911

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Processing

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

1kql


Resolution: 2.45→43.48 Å / SU ML: 0.3889 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.9661
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2717 383 5.06 %
Rwork0.2574 7180 -
obs0.2581 7563 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.91 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 10 2 1058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721070
X-RAY DIFFRACTIONf_angle_d0.86971447
X-RAY DIFFRACTIONf_chiral_restr0.0391157
X-RAY DIFFRACTIONf_plane_restr0.0043189
X-RAY DIFFRACTIONf_dihedral_angle_d16.1067140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.80.38071200.2922330X-RAY DIFFRACTION99.88
2.8-3.530.31841100.3072376X-RAY DIFFRACTION99.92
3.53-43.480.24541530.23312474X-RAY DIFFRACTION99.55
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)
17.378518368793.79837844163-7.676419771273.13013287091-4.15440111749.49861317043-0.1249938871310.3492001143880.15571361220.246293716072-0.1282676032160.0154623846253-0.0299458545529-0.03662732865820.1671669222380.5167872975850.06517112689540.1823612300790.6350411837270.275582061060.534401919528-35.0808537886-11.8872846029-6.01472093243
26.604369801827.87279489152-8.371038167238.00695267918-6.878960585778.13625352993-0.22432843299-0.342485178318-0.741762926371-0.0641115028177-0.523847236182-0.6839189925510.1677226189580.6753478865620.8428770574930.720357350942-0.01197160637270.1555203926041.042683872970.4334335274510.724405496845-29.3954327967-9.69367445621-4.92870465136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 38 through 99)
2X-RAY DIFFRACTION2(chain 'B' and resid 36 through 105)

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