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- PDB-5ur7: Crystal structure of engineered CCL20 disulfide locked dimer -

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Basic information

Entry
Database: PDB / ID: 5ur7
TitleCrystal structure of engineered CCL20 disulfide locked dimer
ComponentsC-C motif chemokine 20
KeywordsIMMUNE SYSTEM / CCL20 / chemokine / Macrophage Inflammatory Protein-3 alpha / MIP3-alpha / chemotaxis / psoriasis / locked dimer / cytokine
Function / homology
Function and homology information


thymocyte migration / CCR6 chemokine receptor binding / T cell migration / CCR chemokine receptor binding / lymphocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / monocyte chemotaxis ...thymocyte migration / CCR6 chemokine receptor binding / T cell migration / CCR chemokine receptor binding / lymphocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / monocyte chemotaxis / : / positive regulation of T cell migration / cellular response to interleukin-1 / neutrophil chemotaxis / cell chemotaxis / cellular response to type II interferon / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / defense response to bacterium / inflammatory response / immune response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region
Similarity search - Function
Chemokine CC, DCCL motif-cointaining domain / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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) ...Chemokine CC, DCCL motif-cointaining domain / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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
ACETATE ION / ISOPROPYL ALCOHOL / C-C motif chemokine 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.0004 Å
AuthorsGetschman, A.E. / Peterson, F.C. / Volkman, B.F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1 AI058072 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM097381 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)RO1 AR063091 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Protein engineering of the chemokine CCL20 prevents psoriasiform dermatitis in an IL-23-dependent murine model.
Authors: Getschman, A.E. / Imai, Y. / Larsen, O. / Peterson, F.C. / Wu, X. / Rosenkilde, M.M. / Hwang, S.T. / Volkman, B.F.
History
DepositionFeb 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C motif chemokine 20
B: C-C motif chemokine 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4758
Polymers16,1192
Non-polymers3556
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-17 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.679, 71.679, 71.561
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsDimer confirmed by non-reducing SDS-PAGE analysis, mass spectrometry

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Components

#1: Protein C-C motif chemokine 20 / Beta-chemokine exodus-1 / CC chemokine LARC / Liver and activation-regulated chemokine / Macrophage ...Beta-chemokine exodus-1 / CC chemokine LARC / Liver and activation-regulated chemokine / Macrophage inflammatory protein 3 alpha / MIP-3-alpha / Small-inducible cytokine A20


Mass: 8059.634 Da / Num. of mol.: 2 / Mutation: S64C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL20, LARC, MIP3A, SCYA20 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P78556
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 302 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M ammonium acetate, 0.1 M sodium HEPES, 25% v/v 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14186 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 22.08 Å2 / Rmerge(I) obs: 0.042 / Χ2: 1.169 / Net I/σ(I): 20.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID% possible all
2-2.039.50.20813601.031100
2.03-2.0710.20.191.051199.4
2.07-2.1110.20.1781.132199.7
2.11-2.1510.20.1561.1111100
2.15-2.210.20.1251.194199.9
2.2-2.2510.20.1191.219199.9
2.25-2.3110.30.1121.217199.9
2.31-2.3710.40.1011.2271100
2.37-2.4410.30.0931.2191100
2.44-2.5210.40.0851.21100
2.52-2.6110.40.0751.221100
2.61-2.7110.40.061.121100
2.71-2.8410.50.0541.1341100
2.84-2.9910.50.0491.2221100
2.99-3.1710.50.0381.1541100
3.17-3.4210.50.0311.1251100
3.42-3.7610.60.0281.1961100
3.76-4.3110.60.0231.0851100
4.31-5.4310.60.0211.0381100
5.43-5010.20.0251.461199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å46.89 Å
Translation2 Å46.89 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
HKL-2000708cdata collection
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
HKL-2000708cdata reduction
HKL-2000708cdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CCL20 (PDB ID 1M8A)

1m8a


Resolution: 2.0004→46.892 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.44
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1398 9.95 %Random selection
Rwork0.1598 ---
obs0.1634 14051 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.65 Å2 / Biso mean: 26.3401 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: final / Resolution: 2.0004→46.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 24 104 1194
Biso mean--48.52 32.9 -
Num. residues----132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071126
X-RAY DIFFRACTIONf_angle_d0.8661516
X-RAY DIFFRACTIONf_chiral_restr0.055171
X-RAY DIFFRACTIONf_plane_restr0.004188
X-RAY DIFFRACTIONf_dihedral_angle_d12.677690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0004-2.07190.24891340.17841226136098
2.0719-2.15490.21441430.16741273141698
2.1549-2.2530.19221430.14761244138799
2.253-2.37170.20751410.1561241138299
2.3717-2.52030.21681360.15941266140299
2.5203-2.71490.21981450.16551263140899
2.7149-2.98810.21731380.180812761414100
2.9881-3.42030.19551390.158812661405100
3.4203-4.30880.19551400.144112981438100
4.3088-46.90460.15791390.16213001439100

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