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- PDB-5wdz: Structure of monomeric Interleukin-8 (1-66) -

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Basic information

Entry
Database: PDB / ID: 5wdz
TitleStructure of monomeric Interleukin-8 (1-66)
ComponentsInterleukin-8Interleukin 8
KeywordsCYTOKINE / Interleukin-8 / chemokine-fold
Function / homology
Function and homology information


regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / positive regulation of cellular biosynthetic process / negative regulation of cell adhesion molecule production / negative regulation of G protein-coupled receptor signaling pathway / ATF4 activates genes in response to endoplasmic reticulum stress / CXCR chemokine receptor binding / embryonic digestive tract development / neutrophil activation ...regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / positive regulation of cellular biosynthetic process / negative regulation of cell adhesion molecule production / negative regulation of G protein-coupled receptor signaling pathway / ATF4 activates genes in response to endoplasmic reticulum stress / CXCR chemokine receptor binding / embryonic digestive tract development / neutrophil activation / induction of positive chemotaxis / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / response to endoplasmic reticulum stress / Peptide ligand-binding receptors / neutrophil chemotaxis / calcium-mediated signaling / response to molecule of bacterial origin / receptor internalization / positive regulation of angiogenesis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / cellular response to tumor necrosis factor / G alpha (i) signalling events / Senescence-Associated Secretory Phenotype (SASP) / angiogenesis / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / intracellular signal transduction / inflammatory response / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / signal transduction / extracellular space / extracellular region
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsBerkamp, S. / Opella, S.J. / Marassi, F.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)P41EB002031 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM066978 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118186 United States
Citation
Journal: J. Biomol. NMR / Year: 2017
Title: Structure of monomeric Interleukin-8 and its interactions with the N-terminal Binding Site-I of CXCR1 by solution NMR spectroscopy.
Authors: Berkamp, S. / Park, S.H. / De Angelis, A.A. / Marassi, F.M. / Opella, S.J.
#1: Journal: To Be Published
Title: Interaction of Monomeric Interleukin-8 with CXCR1 Mapped by Proton-detected Fast MAS Solid-state NMR and Intermolecular Paramagnetic Relaxation Enhancement
Authors: Park, S.H. / Berkamp, S. / Radoicic, J. / De Angelis, A.A. / Opella, S.J.
History
DepositionJul 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-8


Theoretical massNumber of molelcules
Total (without water)7,7141
Polymers7,7141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, NMR signal specific for monomeric state of the protein.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5510 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Interleukin-8 / Interleukin 8 / IL-8 / C-X-C motif chemokine 8 / Chemokine (C-X-C motif) ligand 8 / Emoctakin / Granulocyte ...IL-8 / C-X-C motif chemokine 8 / Chemokine (C-X-C motif) ligand 8 / Emoctakin / Granulocyte chemotactic protein 1 / GCP-1 / Monocyte-derived neutrophil chemotactic factor / MDNCF / Monocyte-derived neutrophil-activating peptide / MONAP / Neutrophil-activating protein 1 / NAP-1 / Protein 3-10C / T-cell chemotactic factor


Mass: 7714.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL8, IL8 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10145

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HNCA
121isotropic23D HN(CA)CB
131isotropic23D HNCO
141isotropic13D HCC(CO)NH
151isotropic13D CC(CO)NH
162anisotropic12D IPAP
173isotropic13D NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution120 mM [U-13C; U-15N] IL-8 1-66, 20 mM HEPES, 90% H2O/10% D2Olyophilized protein dissolved in 20mM Hepes, pH 7.313C_15N_IL890% H2O/10% D2O
solution320 mM [U-15N] IL-8 1-66, 20 mM HEPES, 90% H2O/10% D2Olyophilized protein dissolved in 20mM Hepes, pH 7.315N_IL890% H2O/10% D2O
solution220 mM [U-15N] IL-8, 20 mM HEPES, 70 mM sodium chloride, 13.5 mg/L Y21M bacteriophage, 90% H2O/10% D2O15N_IL8 RDC90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMIL-8 1-66[U-13C; U-15N]1
20 mMHEPESnatural abundance1
20 mMIL-8 1-66[U-15N]3
20 mMHEPESnatural abundance3
20 mMIL-8[U-15N]2
20 mMHEPESnatural abundance2
70 mMsodium chloridenatural abundance2
13.5 mg/LY21M bacteriophagenatural abundance2
Sample conditionsIonic strength: 20 mM / Label: 13C_15N_IL8 / pH: 7.3 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian VSVarianVS8002

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
X-PLOR NIH2.41.1Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH2.41.1Schwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 5 / Details: Simulated annealing with EEFx implicit solvation.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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