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- PDB-7t1e: Structure of monomeric and dimeric human CCL20 -

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Basic information

Entry
Database: PDB / ID: 7t1e
TitleStructure of monomeric and dimeric human CCL20
ComponentsC-C motif chemokine 20
KeywordsIMMUNE SYSTEM / chemokine / CCR6 / Th17 / inflammation / autoimmune / psoriasis / psoriatic arthritis
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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SUCCINIC ACID / C-C motif chemokine 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.459 Å
AuthorsPeterson, F.C. / Riutta, S.J. / Volkman, B.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI050872 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR063091 United States
CitationJournal: J Psoriasis Psoriatic Arthritis / Year: 2023
Title: The Chemokine, CCL20, and Its Receptor, CCR6, in the Pathogenesis and Treatment of Psoriasis and Psoriatic Arthritis
Authors: Shi, Z.R. / Mabuchi, T. / Riutta, S.J. / Wu, X. / Peterson, F.C. / Volkman, B.F. / Hwang, S.T.
History
DepositionDec 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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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
C: C-C motif chemokine 20
D: C-C motif chemokine 20
E: C-C motif chemokine 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,53518
Polymers40,2185
Non-polymers1,31713
Water7,098394
1
A: C-C motif chemokine 20
B: C-C motif chemokine 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7068
Polymers16,0872
Non-polymers6196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-13 kcal/mol
Surface area8450 Å2
MethodPISA
2
C: C-C motif chemokine 20
D: C-C motif chemokine 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3775
Polymers16,0872
Non-polymers2903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-7 kcal/mol
Surface area8460 Å2
MethodPISA
3
E: C-C motif chemokine 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4525
Polymers8,0441
Non-polymers4084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint1 kcal/mol
Surface area4500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.203, 60.203, 231.268
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: 8043.568 Da / Num. of mol.: 5
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 BL21(DE3) (bacteria) / References: UniProt: P78556
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 292.2 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 14% (w/v) PEG 3,350 and 0.5 M succinct acid

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.459→77.09 Å / Num. obs: 84899 / % possible obs: 98.7 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.017 / Rrim(I) all: 0.053 / Net I/σ(I): 23.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.46-1.543.90.35843635112560.880.1990.4132.891.3
4.61-77.099.70.0392934230320.9990.0130.04153.499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.46 Å77.09 Å
Translation6.46 Å77.09 Å

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Processing

Software
NameVersionClassification
XDSBUILT 20180126data reduction
Aimless0.7.2data scaling
PHASER2.8.0phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1m8a

1m8a


Resolution: 1.459→34.6 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1731 1991 2.35 %
Rwork0.1626 82789 -
obs0.1629 84780 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.67 Å2 / Biso mean: 25.4961 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 1.459→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 100 400 3185
Biso mean--37.36 35.41 -
Num. residues----333
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4593-1.49580.23731170.2214510786
1.4958-1.53630.20611390.1953560995
1.5363-1.58150.17851480.17395920100
1.5815-1.63250.16291420.16375883100
1.6325-1.69080.18621420.16785902100
1.6908-1.75850.17491430.16285926100
1.7585-1.83860.19131440.15915952100
1.8386-1.93550.15731420.15835965100
1.9355-2.05680.17871410.15795938100
2.0568-2.21550.15961440.15516007100
2.2155-2.43840.17931460.15976010100
2.4384-2.79120.21191490.17336047100
2.7912-3.5160.16761420.1666140100
3.516-34.60.15131520.1536383100
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)
11.8384-0.99310.1570.6105-0.17770.59110.04110.00270.0526-0.0429-0.0165-0.04280.01090.0071-0.02860.14510.00350.0020.0936-0.010.140271.979666.193234.2418
29.8244-2.8677-2.18417.6411-0.44623.7094-0.39060.0003-0.1475-0.1966-0.0309-0.54050.40210.66190.33040.23030.0010.06250.25310.05590.26283.776366.580529.4245
31.59911.53370.60694.6451-1.45852.51720.0330.17030.00870.12590.08730.191-0.1436-0.2588-0.05620.13720.02110.00770.0920.0010.180668.567560.770235.9404
41.58250.76351.74891.2240.94032.20890.1289-0.1648-0.0230.0931-0.0406-0.0339-0.0398-0.0661-0.08040.1836-0.01820.00230.1026-0.00170.171779.023859.816846.4078
54.2945-1.0017-1.3592.77380.68991.53820.11810.452-0.084-0.218-0.19680.0534-0.0117-0.30470.13130.1478-0.0154-0.00990.1387-0.01440.138288.411578.83144.295
63.26440.85230.35771.8356-0.01592.4411-0.0040.2346-0.1347-0.1491-0.0690.0564-0.06720.0070.08890.1555-0.0045-0.00910.0886-0.03150.166185.078773.281142.7301
72.73611.28552.1272.01691.60493.97770.192-0.3425-0.15820.122-0.29060.32520.2931-0.71040.06230.1817-0.0570.00990.2276-0.02780.25475.07769.186750.3952
84.0812-1.6858-0.19053.57330.41012.940.22220.13920.4126-0.20770.0521-0.1954-0.04250.0994-0.25370.16750.0209-0.00540.17310.03260.1576104.050470.251680.0382
92.6095-0.08150.33343.5058-0.82062.96760.0580.1279-0.1009-0.53330.0529-0.14780.44230.2752-0.03720.26830.0562-0.00690.2010.01730.1108103.203271.481870.4803
101.5917-0.656-0.39932.5528-0.7381.60190.0977-0.05590.0382-0.0262-0.0928-0.22650.08770.0677-0.01830.18420.0051-0.02640.18680.01520.1361101.917574.654776.6386
110.8328-2.02552.04164.4223-4.48474.80160.1228-0.2721-0.24810.16910.38080.7959-0.1955-0.2887-0.42810.183-0.0203-0.01970.24010.07680.258389.698675.696371.6562
120.6776-0.1457-0.22221.43561.55661.7412-0.0775-0.07710.01610.1770.1393-0.01960.31330.27-0.0990.22880.0097-0.01860.1643-0.00670.1361101.269289.361462.2951
130.68090.28610.40632.21550.30451.22650.00050.01230.00620.10010.0211-0.00550.15970.1820.00210.18090.009500.15010.00280.117598.339885.416165.7803
143.5421-0.72540.86273.03060.11062.3148-0.1227-0.00860.03460.00530.1731-0.3336-0.0230.5051-0.03670.1688-0.01230.00180.2098-0.03210.1331101.180184.64360.2605
153.1878-0.20010.7171.4568-0.50943.02880.1618-0.3061-0.40790.3125-0.07730.0160.70710.0627-0.10080.3419-0.0298-0.03080.15660.02630.164894.064173.157761.8694
161.51860.8466-1.3511.6186-1.7093.7323-0.0021-0.1597-0.09980.0358-0.0816-0.12970.11910.14770.03940.1938-0.0073-0.01410.1604-0.0120.1408110.440795.740360.4985
171.6336-0.39340.15280.948-0.70334.50390.0586-0.244-0.00630.06560.0245-0.01560.08760.2518-0.09290.1687-0.0123-0.01460.17380.00120.1629117.2564102.288759.369
184.20420.157-0.2092.32060.46733.37950.1425-0.1645-0.36190.0282-0.1323-0.11340.29450.2963-0.0330.19040.0115-0.00520.16680.00770.1584115.158596.494862.7744
193.06040.6731.4752.11360.48631.5258-0.1791-0.37940.39410.26050.2159-0.1456-0.190.3444-0.00820.2049-0.0297-0.00090.2714-0.08430.1581112.8345103.696670.2991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 41 )A1 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 46 )A42 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 53 )A47 - 53
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 70 )A54 - 70
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 16 )B4 - 16
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 53 )B17 - 53
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 70 )B54 - 70
8X-RAY DIFFRACTION8chain 'C' and (resid 5 through 16 )C5 - 16
9X-RAY DIFFRACTION9chain 'C' and (resid 17 through 35 )C17 - 35
10X-RAY DIFFRACTION10chain 'C' and (resid 36 through 53 )C36 - 53
11X-RAY DIFFRACTION11chain 'C' and (resid 54 through 70 )C54 - 70
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 16 )D1 - 16
13X-RAY DIFFRACTION13chain 'D' and (resid 17 through 41 )D17 - 41
14X-RAY DIFFRACTION14chain 'D' and (resid 42 through 53 )D42 - 53
15X-RAY DIFFRACTION15chain 'D' and (resid 54 through 70 )D54 - 70
16X-RAY DIFFRACTION16chain 'E' and (resid 5 through 16 )E5 - 16
17X-RAY DIFFRACTION17chain 'E' and (resid 17 through 35 )E17 - 35
18X-RAY DIFFRACTION18chain 'E' and (resid 36 through 53 )E36 - 53
19X-RAY DIFFRACTION19chain 'E' and (resid 54 through 64 )E54 - 64

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