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- PDB-3il8: CRYSTAL STRUCTURE OF INTERLEUKIN 8: SYMBIOSIS OF NMR AND CRYSTALL... -

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Basic information

Entry
Database: PDB / ID: 3il8
TitleCRYSTAL STRUCTURE OF INTERLEUKIN 8: SYMBIOSIS OF NMR AND CRYSTALLOGRAPHY
ComponentsINTERLEUKIN-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 / 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 / positive regulation of neutrophil 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 / 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 / positive regulation of neutrophil chemotaxis / chemokine activity / Chemokine receptors bind chemokines / 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 / 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 / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / angiogenesis / Interleukin-4 and Interleukin-13 signaling / G alpha (i) signalling events / intracellular signal transduction / G protein-coupled receptor signaling pathway / inflammatory response / 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)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBaldwin, E.T. / Weber, I.T. / St Charles, R. / Xuan, J.-C. / Appella, E. / Yamada, M. / Matsushima, K. / Edwards, B.F.P. / Clore, G.M. / Gronenborn, A.M. / Wlodawer, A.
Citation
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Crystallization of Human Interleukin-8. A Protein Chemotactic for Neutrophils and T-Lymphocytes
Authors: Baldwin, E.T. / Franklin, K.A. / Appella, E. / Yamada, M. / Matsushima, K. / Wlodawer, A. / Weber, I.T.
History
DepositionDec 7, 1990Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERLEUKIN-8


Theoretical massNumber of molelcules
Total (without water)8,4021
Polymers8,4021
Non-polymers00
Water2,432135
1
A: INTERLEUKIN-8

A: INTERLEUKIN-8


Theoretical massNumber of molelcules
Total (without water)16,8042
Polymers16,8042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)40.300, 40.300, 90.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein INTERLEUKIN-8


Mass: 8401.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: NEUTROPHILS / References: UniProt: P10145
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.1 MTris-HCl1drop
340 %satammonium sulphate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 5879

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.187 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms558 0 0 135 693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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