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- PDB-8gdh: Solution structure of the Neutrophil Serine Protease Inhibitor, EapH1 -

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Basic information

Entry
Database: PDB / ID: 8gdh
TitleSolution structure of the Neutrophil Serine Protease Inhibitor, EapH1
ComponentsCell surface protein map-w
KeywordsIMMUNE SYSTEM/INHIBITOR / protease / protease inhibitor / enzyme kinetics / innate immunity / immune evasion / IMMUNE SYSTEM / IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


extracellular region
Similarity search - Function
MAP domain / MAP domain / MAP repeat profile. / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
MAP domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMishra, N.B. / Geisbrecht, B.V. / Prakash, O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1S10OD026726 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Simultaneous inhibition of two neutrophil serine proteases by the S. aureus innate immune evasion protein EapH2.
Authors: Mishra, N. / Herdendorf, T.J. / Prakash, O. / Geisbrecht, B.V.
History
DepositionMar 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 19, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell surface protein map-w


Theoretical massNumber of molelcules
Total (without water)12,7221
Polymers12,7221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Cell surface protein map-w / MAP domain-containing protein / Outer membrane protein


Mass: 12722.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: map, G6Y24_08670, GZ128_06505, GZ156_01355, SA0759_01852, SA950122_01799, SAJPND4_02182
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2W3EU09

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D HNCA
131isotropic23D HNCO
141isotropic23D HN(CA)CB
151isotropic13D 1H-15N NOESY
161isotropic12D 1H-15N HSQC
171isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] EapH1, 95% H2O/5% D2O
Details: 15N_13C_EapH1 was dissolved in 95% H2O/5% D2O / Label: 15N_13C_EapH1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: EapH1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 mM / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Agilent DD2AgilentDD27002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.9.1Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1Keller and Wuthrichpeak picking
TopSpin4.1Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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