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- PDB-6xmn: Solution NMR CXCL8-CXCR1 N-domain complex structure -

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Basic information

Entry
Database: PDB / ID: 6xmn
TitleSolution NMR CXCL8-CXCR1 N-domain complex structure
Components
  • C-X-C chemokine receptor type 1
  • Interleukin-8
KeywordsCYTOKINE / Chemokine / CXCL8 / CXCR1 / CXCL8-CXCR1 N-domain complex
Function / homology
Function and homology information


interleukin-8 receptor activity / regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / interleukin-8 binding / : / chemokine receptor activity / negative regulation of cell adhesion molecule production / CXCR chemokine receptor binding / ATF4 activates genes in response to endoplasmic reticulum stress ...interleukin-8 receptor activity / regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / interleukin-8 binding / : / chemokine receptor activity / negative regulation of cell adhesion molecule production / CXCR chemokine receptor binding / ATF4 activates genes in response to endoplasmic reticulum stress / embryonic digestive tract development / C-C chemokine receptor activity / neutrophil activation / C-C chemokine binding / 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 / dendritic cell chemotaxis / negative regulation of G protein-coupled receptor signaling pathway / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / neutrophil chemotaxis / response to endoplasmic reticulum stress / Peptide ligand-binding receptors / secretory granule membrane / G protein-coupled receptor activity / calcium-mediated signaling / response to molecule of bacterial origin / receptor internalization / positive regulation of angiogenesis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to tumor necrosis factor / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / Senescence-Associated Secretory Phenotype (SASP) / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cell surface receptor signaling pathway / intracellular signal transduction / inflammatory response / immune response / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / external side of plasma membrane / negative regulation of gene expression / Neutrophil degranulation / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / plasma membrane
Similarity search - Function
CXC chemokine receptor 1 / CXC chemokine receptor 1/2 / 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 ...CXC chemokine receptor 1 / CXC chemokine receptor 1/2 / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Interleukin-8 / C-X-C chemokine receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSepuru, K.M. / Rajarathnam, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 HL107152 United States
CitationJournal: To Be Published
Title: Solution NMR CXCL8-CXCR1 N-domain complex structure
Authors: Sepuru, K.M. / Rajarathnam, K.
History
DepositionJun 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-8
B: C-X-C chemokine receptor type 1


Theoretical massNumber of molelcules
Total (without water)11,0652
Polymers11,0652
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1940 Å2
ΔGint-3 kcal/mol
Surface area6980 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Interleukin-8 / IL-8 / CXCL8 / C-X-C motif chemokine 8 / Chemokine (C-X-C motif) ligand 8 / Emoctakin / Granulocyte ...IL-8 / CXCL8 / 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 / Fragment: residues 28-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL8, IL8 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P10145
#2: Protein/peptide C-X-C chemokine receptor type 1 / CXCR-1 / CDw128a / High affinity interleukin-8 receptor A / IL-8R A / IL-8 receptor type 1


Mass: 3350.576 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-29
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCR1, CMKAR1, IL8RA / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25024

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D C(CO)NH
161isotropic23D HBHA(CO)NH
171isotropic23D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY
191isotropic23D 1H-13C NOESY
1101isotropic13D 13C-filter NOESY
1112isotropic12D 1H-15N HSQC
1122isotropic12D 1H-13C HSQC
1132isotropic13D CBCA(CO)NH
1142isotropic13D HN(CA)CB
1152isotropic13D C(CO)NH
1162isotropic23D HBHA(CO)NH
1172isotropic23D (H)CCH-TOCSY
1182isotropic13D 1H-15N NOESY
1192isotropic23D 1H-13C NOESY
1202isotropic13D 13C-filter NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.4 mM [U-13C; U-15N] CXCL8, 1.2 mM CXCR1, 50 mM sodium phosphate, 0.01 % sodium azide, 10 % [U-100% 2H] D2O, 90% H2O/10% D2OCXCL8-CXCR1 complex sample Labeled CXCL8 mixed with unlabeled CXCR1 N-domainCXCL8-CXCR1_complex_sample_190% H2O/10% D2O
solution21.2 mM CXCL8, 0.5 mM [U-13C; U-15N] CXCR1, 50 mM sodium phosphate, 0.01 % sodium azide, 10 % [U-100% 2H] D2O, 90% H2O/10% D2OCXCL8-CXCR1 complex sample Labeled CXCR1 N-domain mixed with unlabeled CXCL8CXCL8-CXCR1_complex_sample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMCXCL8[U-13C; U-15N]1
1.2 mMCXCR1natural abundance1
50 mMsodium phosphatenatural abundance1
0.01 %sodium azidenatural abundance1
10 %D2O[U-100% 2H]1
1.2 mMCXCL8natural abundance2
0.5 mMCXCR1[U-13C; U-15N]2
50 mMsodium phosphatenatural abundance2
0.01 %sodium azidenatural abundance2
10 %D2O[U-100% 2H]2
Sample conditionsDetails: CXCL8-CXCR1 complex sample Labeled CXCL8 mixed with unlabeled CXCR1 N-domain
Ionic strength: 50 mM / Label: CXCL8-CXCR1_complex_sample_1 / pH: 6 / Pressure: 1 bar / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III8001TCI cryoprobe
Bruker AVANCE IIIBrukerAVANCE III7502TCI cryoprobe

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgesrefinement
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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