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- PDB-1ilq: CXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8 (MINIMIZED MEAN) -

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Basic information

Entry
Database: PDB / ID: 1ilq
TitleCXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8 (MINIMIZED MEAN)
Components
  • INTERLEUKIN-8 PRECURSOR
  • INTERLEUKIN-8 RECEPTOR A
KeywordsCYTOKINE
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 / interleukin-8 receptor activity / 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 ...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 receptor activity / 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 / neutrophil activation / induction of positive chemotaxis / C-C chemokine receptor activity / C-C chemokine binding / positive regulation of neutrophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / dendritic cell chemotaxis / negative regulation of G protein-coupled receptor signaling pathway / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / cellular response to fibroblast growth factor stimulus / neutrophil chemotaxis / Peptide ligand-binding receptors / response to endoplasmic reticulum stress / secretory granule membrane / calcium-mediated signaling / response to molecule of bacterial origin / G protein-coupled receptor activity / receptor internalization / positive regulation of angiogenesis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to tumor necrosis factor / heparin binding / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / Senescence-Associated Secretory Phenotype (SASP) / angiogenesis / Interleukin-4 and Interleukin-13 signaling / G alpha (i) signalling events / cell surface receptor signaling pathway / intracellular signal transduction / immune response / G protein-coupled receptor signaling pathway / inflammatory response / negative regulation of cell population proliferation / negative regulation of gene expression / external side of plasma membrane / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Interleukin-8 / C-X-C chemokine receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsSkelton, N.J. / Quan, C. / Lowman, H.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Structure of a CXC chemokine-receptor fragment in complex with interleukin-8.
Authors: Skelton, N.J. / Quan, C. / Reilly, D. / Lowman, H.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 1997
Title: Peptide Based Inhibitors of Il-8: Structural Simplification and Improved Potency
Authors: Attwood, M.R. / al., et
#2: Journal: Biochemistry / Year: 1990
Title: Three-Dimensional Structure of Il-8 in Solution
Authors: Clore, G.M. / Appella, E. / Yamada, M. / Gronenborn, A.M.
History
DepositionDec 17, 1998Processing site: BNL
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 25, 2016Group: Source and taxonomy
Revision 1.4Feb 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-8 PRECURSOR
B: INTERLEUKIN-8 PRECURSOR
C: INTERLEUKIN-8 RECEPTOR A


Theoretical massNumber of molelcules
Total (without water)18,8723
Polymers18,8723
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 40LEAST RESTRAINT VIOLATION ENERGY
Representative

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Components

#1: Protein INTERLEUKIN-8 PRECURSOR / IL-8


Mass: 8401.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPS0170 / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASM / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P10145
#2: Protein/peptide INTERLEUKIN-8 RECEPTOR A / IL8-RA


Mass: 2068.220 Da / Num. of mol.: 1 / Fragment: 9-29 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P25024
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111ASSIGNMENT: SEE REFERENCE 1; RESTRAINTS: 3D 15N-EDITED-NOESY HSQC
1213D 13C-FILTERED
13113C-EDITED-NOESY HMQC
1412D 15N-FILTERED NOESY
1512D 13C-FILTERED NOESY (100MS)
16115N-FILTERED NOESY (ALL MIXING TIMES = 100 MS)
NMR detailsText: THE ASSIGNMENTS WERE MADE USING TRIPLE RESONANCE NMR EXPERIMENTS CONDUCTED ON 13C/15N LABELED IL-8 BOUND TO UNLABELED CXCR-1 PEPTIDE (SEE JRNL ENTRY FOR MORE DETAILS) NOE RESTRAINTS WERE ...Text: THE ASSIGNMENTS WERE MADE USING TRIPLE RESONANCE NMR EXPERIMENTS CONDUCTED ON 13C/15N LABELED IL-8 BOUND TO UNLABELED CXCR-1 PEPTIDE (SEE JRNL ENTRY FOR MORE DETAILS) NOE RESTRAINTS WERE OBTAINED FROM 15N EDITED EXPERIMENTS (INTRA IL8), 13C OR 15N FILTERED EXPERIMENTS (INTRA CXCR-1) OR 13C-FILTERED/ EDITED EXPERIMENTS (INTERMOLECULAR RESTRAINTS)

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Sample preparation

Sample conditionsIonic strength: 0.15 M / pH: 5.5 / Pressure: 1 atm / Temperature: 308.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 500 / Manufacturer: Bruker / Model: AMX 500 / Field strength: 500 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionDeveloperClassification
DiscoverBIOSYMrefinement
MSI DISCOVER DISCOVERDISCOVERstructure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: INITIAL COORDINATES FOR IL-8 WERE TAKEN FROM PDB ENTRY 1IL8; A LINEAR CHAIN FOR THE CXCR-1 FRAGMENT WAS BUILT IN INSIGHT (MSI). THE CXCR-1 FRAGMENT WAS POSITIONED RANDOMLY WITH RESPECT TO ...Details: INITIAL COORDINATES FOR IL-8 WERE TAKEN FROM PDB ENTRY 1IL8; A LINEAR CHAIN FOR THE CXCR-1 FRAGMENT WAS BUILT IN INSIGHT (MSI). THE CXCR-1 FRAGMENT WAS POSITIONED RANDOMLY WITH RESPECT TO IL8 - OBTAIN 40 STARTING CONFORMATIONS. THE INITIAL STRUCTURES WERE THEN REFINED USING RMD WITH THE AMBER ALL ATOM FORCE FIELD AS IMPLIMENTED WITHIN DISCOVER. ALL OF IL8 MONOMER B AND PARTS OF IL8 MONOMER A (2-7, 22-38 AND 51-72) WERE KEPT FIXED DURING THE REFINEMENT SINCE CHEMICAL SHIFT CHANGES INDICATED THAT THESE PORTION OF THE MOLECULE WERE NOT PERTURBED BY PEPTIDE BINDING. THIS MODEL IS THE RESULT OF RESTRAINED ENERGY MINIMIZATION OF THE GEOMETRIC MEAN OF 20 STRUCTURES FROM THE ENSEMBLE (ENTRY 1ILP) SEE JRNL ENTRY FOR MORE DETAILS.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION ENERGY
Conformers calculated total number: 40 / Conformers submitted total number: 1

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