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- PDB-2il8: THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN 8 IN SOLUTION -

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Basic information

Entry
Database: PDB / ID: 2il8
TitleTHREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN 8 IN SOLUTION
ComponentsINTERLEUKIN-8Interleukin 8
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 / 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 / induction of positive chemotaxis ...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 / 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 / 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 / cellular response to tumor necrosis factor / heparin binding / 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
AuthorsClore, G.M.
Citation
Journal: Biochemistry / Year: 1990
Title: Three-dimensional structure of interleukin 8 in solution.
Authors: Clore, G.M. / Appella, E. / Yamada, M. / Matsushima, K. / Gronenborn, A.M.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Determination of the Secondary Structure of Interleukin-8 by Nuclear Magnetic Resonance Spectroscopy
Authors: Clore, G.M. / Appella, E. / Yamada, M. / Matsushima, K. / Gronenborn, A.M.
History
DepositionMar 8, 1990Processing site: BNL
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERLEUKIN-8
B: INTERLEUKIN-8


Theoretical massNumber of molelcules
Total (without water)16,8042
Polymers16,8042
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / -
Representative

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Components

#1: Protein INTERLEUKIN-8 / Interleukin 8


Mass: 8401.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POTENTIAL / References: UniProt: P10145

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR software
NameDeveloperClassification
DISGEOHAVEL,WUTHRICHrefinement
X-PLORBRUNGERrefinement
RefinementSoftware ordinal: 1
Details: STRUCTURE DETERMINATION. THE METHOD USED TO DETERMINE AND REFINE THE STRUCTURE IS THE HYBRID DISTANCE GEOMETRY-SIMULATED ANNEALING METHOD (M.NILGES, G.M.CLORE, A.M. GRONENBORN, FEBS LETT. ...Details: STRUCTURE DETERMINATION. THE METHOD USED TO DETERMINE AND REFINE THE STRUCTURE IS THE HYBRID DISTANCE GEOMETRY-SIMULATED ANNEALING METHOD (M.NILGES, G.M.CLORE, A.M. GRONENBORN, FEBS LETT. 229, 317 (1988)) USING THE PROGRAMS *DISGEO* (T.F. HAVEL, QCPE NO. 507, INDIANA UNIVERSITY) AND *XPLOR* (A.T. BRUNGER, YALE UNIVERSITY, NEW HAVEN, CT 06511). STRUCTURAL STATISTICS - THESE ARE CALCULATED FROM ALL THE 30 MODELS GIVEN IN THIS ENTRY. NUMBERS ENCLOSED IN PARENTHESIS REPRESENT THE MINIMIZED MEAN STRUCTURE OBTAINED BY RESTRAINED MINIMIZATION OF THE AVERAGE RMS. RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)* RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS) ALL 1880 0.031(0.029) INTRASUBUNIT SHORT RANGE 784 0.019(0.020) INTERRESIDUE LONG RANGE 370 0.027(0.026) INTRARESIDUE 540 0.044(0.042) HBOND *(2)* 104 0.031(0.028) INTERSUBUNIT INTERPROTON 70 0.022(0.014) HBOND 12 0.004(0.000) TORSION ANGLES (DEGREES) 362 0.203 (0.211) POTENTIAL ENERGY TERMS TYPE ENERGY (KCAL/MOL) F(NOE) *(3)* 53(48) F(TOR) *(4)* 0.94(0.98) F(REPEL) *(5)* 38(37) F(SYM) *(6)* 0.15(424) LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS -542(-474) KCAL/MOL. DEVIATIONS FROM IDEALIZED GEOMETRY *(6)* TYPE TOTAL NUMBER RMS DEVIATION BONDS 2392 0.006(0.011) (ANGSTROMS) ANGLES 4362 2.016(2.458) (DEGREES) IMPROPERS 882 0.504(0.485) (DEGREES) NOTES. *(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL RESTRAINTS IS CALCULATED WITH RESPECT TO THE UPPER AND LOWER LIMITS OF THE DISTANCE RESTRAINTS. NONE OF THE STRUCTURES EXHIBITED VIOLATIONS GREATER THAN 0.3 ANGSTROMS. *(2)* FOR EACH BACKBONE HYDROGEN BOND THERE ARE TWO RESTRAINTS - R(NH-O) 1.7 TO 2.3 ANGSTROMS AND R(N-O) 2.4 TO 3.3 ANGSTROMS. *(3)* THE VALUES OF THE SQUARE-WELL NOE POTENTIAL 50 KCAL/MOL/ANGSTROM**2. *(4)* THE VALUES OF F(PHI) ARE CALCULATED WITH A FORCE CONSTANT OF 200 KCAL/MOL/RAD**2. F(PHI) IS A SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO RESTRICT THE RANGES OF TORSION ANGLES. *(5)* THE VALUE OF THE VAN DER WAALS REPULSION TERM F(REPEL) IS CALCULATED WITH A FORCE CONSTANT OF 4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE VAN DER WAALS RADII SET TO 0.8 TIMES THE STANDARD VALUES USED IN THE *CHARMM* EMPIRICAL ENERGY FUNCTION. *(6)* F(SYM) IS AN EFFECTIVE HARMONIC POTENTIAL USED TO MAINTAIN SYMMETRY BETWEEN THE TWO SUBUNITS WITH A FORCE CONSTANT SET TO 300.0 KCAL/MOL/ANGSTROMS**2 *(7)* THE IMPROPER TERMS SERVE TO MAINTAIN PLANARITY AND APPROPRIATE CHIRALITY. THEY ALSO MAINTAIN THE PEPTIDE BONDS OF ALL RESIDUES (WITH THE EXCEPTION OF PROLINES) IN THE TRANS CONFORMATION. IN THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS. THE 3D STRUCTURE OF THE INTERLEUKIN-8 DIMER IN SOLUTION DERIVED FROM NMR EXPERIMENTS IS BASED ON 1880 EXPERIMENTAL DISTANCE RESTRAINTS (OF WHICH 82 ARE INTERSUBUNIT) AND 362 TORSION ANGLE RESTRAINTS DERIVED FROM NOE AND COUPLING CONSTANT MEASUREMENTS. A COMPLETE LIST OF EXPERIMENTAL RESTRAINTS HAS BEEN DEPOSITED WITH THE BROOKHAVEN PROTEIN DATA BANK AND IS LOCATED IN ENTRY R1IL8MR. A TOTAL OF 30 STRUCTURES CONSISTENT WITH THE NMR DATA WERE CALCULATED AND ARE GIVEN IN THIS ENTRY. THE PROTEIN DATA BANK ENTRY *1IL8* CONTAIN THE COORDINATES OBTAINED BY AVERAGING THE COORDINATES OF THESE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO FURTHER RESTRAINED MINIMIZATION. THE FIVE N-TERMINAL RESIDUES ARE ILL-DEFINED. THE CYS 9 - CYS 50 DISULFIDE BRIDGE IS LEFT-HANDED.
NMR ensembleConformers submitted total number: 30

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