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- PDB-1ilp: CXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8 -

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Basic information

Entry
Database: PDB / ID: 1ilp
TitleCXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8
Components
  • C-X-C chemokine receptor type 1
  • Interleukin-8 (precursor)
KeywordsCYTOKINE
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 / positive regulation of cellular biosynthetic process / chemokine receptor activity / 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 ...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 / positive regulation of cellular biosynthetic process / chemokine receptor activity / 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 / C-C chemokine receptor activity / C-C chemokine binding / induction of positive chemotaxis / neutrophil activation / 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 / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / response to endoplasmic reticulum stress / Peptide ligand-binding receptors / neutrophil chemotaxis / 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 / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / Senescence-Associated Secretory Phenotype (SASP) / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cellular response to lipopolysaccharide / 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 / Chemokine interleukin-8-like superfamily ...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 / 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) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 4, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_asym_id ..._atom_site.auth_atom_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_nmr_software.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: C-X-C chemokine receptor type 1


Theoretical massNumber of molelcules
Total (without water)18,8723
Polymers18,8723
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3760 Å2
ΔGint-7 kcal/mol
Surface area10970 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40LEAST RESTRAINT VIOLATION ENERGY
Representative

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Components

#1: Protein Interleukin-8 (precursor) / 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: 8401.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL8, IL8 / 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 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: 2068.220 Da / Num. of mol.: 1 / Fragment: 9-29 / Mutation: L15 - G19 REPLACED BY 5-AMINOVALERIC ACID / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P25024

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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 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

NMR software
NameVersionDeveloperClassification
DiscoverBIOSYMrefinement
MSI 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. SEE JRNL ENTRY FOR MORE DETAILS.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION ENERGY
Conformers calculated total number: 40 / Conformers submitted total number: 20

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