[English] 日本語
Yorodumi
- PDB-1ilp: CXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8 -

+
Open data


ID or keywords:

Loading...

-
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


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 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
Revision 3.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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
Has protein modificationY

-
Experimental details

-
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)

-
Sample preparation

Sample conditionsIonic strength: 0.15 M / pH: 5.5 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more