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- PDB-6n2u: IL-8 Structure from Bacterial Expression Source -

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Basic information

Entry
Database: PDB / ID: 6n2u
TitleIL-8 Structure from Bacterial Expression Source
ComponentsInterleukin-8Interleukin 8
KeywordsIMMUNE SYSTEM / IL-8
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.254 Å
AuthorsPark, H. / Jung, J.H. / Luo, J.L.
CitationJournal: To Be Published
Title: IL-8 Structure from Bacterial Expression Source
Authors: Park, H. / Jung, J.H. / Luo, J.L.
History
DepositionNov 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-8


Theoretical massNumber of molelcules
Total (without water)11,1161
Polymers11,1161
Non-polymers00
Water1,62190
1
A: Interleukin-8

A: Interleukin-8


Theoretical massNumber of molelcules
Total (without water)22,2322
Polymers22,2322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)39.701, 39.701, 89.971
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 / Interleukin 8 / 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: 11116.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL8, IL8 / Production host: Escherichia coli (E. coli) / References: UniProt: P10145
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.4 M Ammonium Phosphate dibasic, 0.1 M Tris HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.254→32.12 Å / Num. obs: 13693 / % possible obs: 58.82 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02608 / Rpim(I) all: 0.02608 / Rrim(I) all: 0.03688 / Net I/σ(I): 15.99
Reflection shellResolution: 1.254→1.299 Å / Rmerge(I) obs: 0.3216 / Num. unique obs: 122 / CC1/2: 0.752 / Rpim(I) all: 0.752 / Rrim(I) all: 0.3216 / % possible all: 5.34

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D14

5d14


Resolution: 1.254→32.12 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.99
RfactorNum. reflection% reflection
Rfree0.2233 1205 8.8 %
Rwork0.1874 --
obs0.1905 13688 58.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.254→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 0 90 657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01578
X-RAY DIFFRACTIONf_angle_d0.99775
X-RAY DIFFRACTIONf_dihedral_angle_d12.141230
X-RAY DIFFRACTIONf_chiral_restr0.08585
X-RAY DIFFRACTIONf_plane_restr0.00698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2541-1.30440.3327130.2993130X-RAY DIFFRACTION6
1.3044-1.36370.2841230.2788239X-RAY DIFFRACTION10
1.3637-1.43560.2851390.2515413X-RAY DIFFRACTION18
1.4356-1.52560.2557680.2602723X-RAY DIFFRACTION31
1.5256-1.64340.24171340.23981417X-RAY DIFFRACTION60
1.6434-1.80870.25842210.22152305X-RAY DIFFRACTION99
1.8087-2.07040.20622280.18772350X-RAY DIFFRACTION100
2.0704-2.60840.22752330.17872387X-RAY DIFFRACTION100
2.6084-32.120.21622460.17582519X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.267-0.5632-1.94085.5702-1.11173.36230.30450.01730.22460.163-0.54880.3765-0.5581-0.47430.36630.2033-0.02730.01240.3936-0.03470.2269-22.001816.882918.2521
23.35961.0602-0.17682.0333-0.54746.6597-0.02850.252-0.1166-0.17670.0340.10820.32190.24350.00970.09270.0083-0.0280.1316-0.00670.0908-12.60729.87086.3003
31.76570.1090.0521.44070.96384.6258-0.06640.0223-0.0057-0.0454-0.01380.1090.1874-0.22840.05120.1273-0.05320.00190.1363-0.00770.1212-16.857311.526814.1607
44.17481.39470.72442.65630.63463.15110.1816-0.0183-0.5457-0.09950.0376-0.65420.51520.35770.03030.15380.0357-0.02040.0967-0.03080.2011-5.32165.59589.0164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 26 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 69 )

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