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- PDB-7s5a: Crystal structure of human chemokine CCL8 -

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Basic information

Entry
Database: PDB / ID: 7s5a
TitleCrystal structure of human chemokine CCL8
ComponentsC-C motif chemokine 8Chemokine
KeywordsCYTOKINE / CC Chemokine
Function / homology
Function and homology information


negative regulation of leukocyte proliferation / negative regulation by host of viral genome replication / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / chemokine activity / positive regulation of leukocyte migration / phospholipase activator activity / exocytosis ...negative regulation of leukocyte proliferation / negative regulation by host of viral genome replication / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / chemokine activity / positive regulation of leukocyte migration / phospholipase activator activity / exocytosis / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / response to virus / cellular response to type II interferon / intracellular calcium ion homeostasis / calcium ion transport / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / heparin binding / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space
Similarity search - Function
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
C-C motif chemokine 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsBhusal, R.P. / Devkota, S.R. / Aryal, P. / Wilce, M.C.J. / Stone, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structure-guided engineering of tick evasins for targeting chemokines in inflammatory diseases.
Authors: Bhusal, R.P. / Aryal, P. / Devkota, S.R. / Pokhrel, R. / Gunzburg, M.J. / Foster, S.R. / Lim, H.D. / Payne, R.J. / Wilce, M.C.J. / Stone, M.J.
History
DepositionSep 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C motif chemokine 8
B: C-C motif chemokine 8


Theoretical massNumber of molelcules
Total (without water)17,8572
Polymers17,8572
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-10 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.807, 64.718, 81.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 5 or resid 7...
d_2ens_1(chain "B" and (resid 1 through 5 or resid 7...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNVALA1 - 5
d_12ens_1ILEPHEA9 - 15
d_13ens_1VALPROA19 - 25
d_14ens_1GLNTYRA29 - 34
d_15ens_1ILEGLYA39 - 56
d_16ens_1GLUGLUA58 - 65
d_17ens_1TRPASNA67 - 81
d_21ens_1GLNVALB1 - 5
d_22ens_1ILEPHEB7 - 13
d_23ens_1VALPROB15 - 21
d_24ens_1GLNTYRB23 - 28
d_25ens_1ILEGLYB33 - 50
d_26ens_1GLUGLUB54 - 61
d_27ens_1TRPASNB65 - 79

NCS oper: (Code: givenMatrix: (0.127216106139, -0.970881822492, -0.20298903688), (-0.985454739526, -0.146964981691, 0.0853243839854), (-0.112672173515, 0.189181872576, -0.975456406204)Vector: 155. ...NCS oper: (Code: given
Matrix: (0.127216106139, -0.970881822492, -0.20298903688), (-0.985454739526, -0.146964981691, 0.0853243839854), (-0.112672173515, 0.189181872576, -0.975456406204)
Vector: 155.590141993, 170.988515075, 52.5582735254)

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Components

#1: Protein C-C motif chemokine 8 / Chemokine / HC14 / Monocyte chemoattractant protein 2 / Monocyte chemotactic protein 2 / MCP-2 / Small- ...HC14 / Monocyte chemoattractant protein 2 / Monocyte chemotactic protein 2 / MCP-2 / Small-inducible cytokine A8


Mass: 8928.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL8, MCP2, SCYA10, SCYA8 / Production host: Escherichia coli (E. coli) / References: UniProt: P80075
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium phosphate dibasic 20% w/v Polyethylene glycol 3,350 pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→40.56 Å / Num. obs: 34554 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 1 / Net I/σ(I): 20.6
Reflection shellResolution: 1.37→1.39 Å / Num. unique obs: 1631 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ESR

1esr


Resolution: 1.37→40.56 Å / SU ML: 0.1165 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.1387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1893 1691 4.89 %
Rwork0.1694 32861 -
obs0.1704 34552 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.9 Å2
Refinement stepCycle: LAST / Resolution: 1.37→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 0 215 1390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01531237
X-RAY DIFFRACTIONf_angle_d1.39131690
X-RAY DIFFRACTIONf_chiral_restr0.1117197
X-RAY DIFFRACTIONf_plane_restr0.0098220
X-RAY DIFFRACTIONf_dihedral_angle_d5.1061174
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.11757308122 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.410.29611110.23052695X-RAY DIFFRACTION98.32
1.41-1.450.20161410.20712702X-RAY DIFFRACTION99.93
1.45-1.510.21651380.19682720X-RAY DIFFRACTION100
1.51-1.570.2391170.18952733X-RAY DIFFRACTION100
1.57-1.640.22181460.17732713X-RAY DIFFRACTION100
1.64-1.720.19581230.16442771X-RAY DIFFRACTION100
1.72-1.830.16481620.16722682X-RAY DIFFRACTION100
1.83-1.970.19241560.16622727X-RAY DIFFRACTION99.97
1.97-2.170.17151370.15452748X-RAY DIFFRACTION100
2.17-2.490.2111490.17012771X-RAY DIFFRACTION99.86
2.49-3.130.19641510.17992750X-RAY DIFFRACTION99.69
3.13-40.560.17031600.15762849X-RAY DIFFRACTION98.49
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)
14.84654633047-1.407777025543.239949870122.04188006496-0.4599247572912.328215267570.09532970381390.5425430704420.691169928417-0.986832053117-0.570839554508-0.1217289932740.02854167844810.2575751098950.4633548969870.437667570928-0.003541269082540.03728318634320.2457521417190.00315378244860.35976002985875.32490.43415.393
24.084777033532.18392157074-2.342456692792.38422912648-0.9697885911142.731964071930.092589406379-0.273362512406-0.212137348880.0909040482573-0.147017659496-0.119583033370.0005898612070260.01504057994590.06165782916260.113855464273-0.0133379254723-0.01314163568820.1229907903430.007640788451070.12823557255569.8281.92938.112
35.335053321360.562514884452-5.227985749953.9030081233-1.970176988327.207396389810.225808286653-0.1670606641660.2876634665380.140195872850.1292256196830.137924840521-0.05503701074410.217864791968-0.3360918211190.0932981479212-0.0240504941711-0.03013582720350.148469553805-0.01141642308680.14500660078658.37482.19138.015
44.80861708408-1.19378253291-6.391050084080.4437574222181.811153406818.35443846776-0.1126521756430.303166969821-0.259428027991-0.0872878535255-0.1391108980320.08186998308090.165864392302-0.2980796531120.2275466381750.13051636844-0.02221170951970.003011864803530.153033753773-0.0319810889020.16906631872468.38880.75831.615
58.920398750380.685034514733-1.232954780956.256274539112.828555393566.535648702810.247162460821-0.009439318797590.1672873097380.119000454753-0.21879615986-0.209341010766-0.03045311373-0.0854488574875-0.1067027249130.103885928803-0.02792094225450.00176252193350.127042170265-0.0005591417952260.076342087558863.98181.86939.85
65.6170152769-3.881350358083.275554647453.25961091596-1.827304780165.340099443590.1693174587670.197277507757-0.7161631615270.00715641311062-0.04039380185850.3315462454210.315803341410.0160339534987-0.09903688679430.132397886812-0.0515996276775-0.009171932021550.150616291358-0.003496843757620.19642790037255.43575.1637.794
75.34012226304-4.490691718872.025945718124.997057888880.07704639327883.37832609806-0.3277582635860.03787614700630.7940923778290.308317769948-0.289190896157-0.580807707264-1.41704708465-0.6202059490430.4057895404830.4267966651430.113933011319-0.07007538109970.335919059759-0.04966118288640.3808261464749.14989.20533.952
86.893058828450.9010557262-2.445600505552.500316475741.672524375412.620175281290.2860775298290.4582948397960.928080466172-0.584639326052-0.1135454507210.0576831023051-1.56941869592-0.141779589709-0.133216644410.374470108775-0.02875424046640.01377155076170.263325331044-0.007789775040520.26857149144875.29289.40943.331
90.7911270185890.95901857551-0.5113513934284.18715223598-2.968567328311.85048353458-0.05656906468840.070304548209-0.00548483419178-0.32828272221-0.0513419575292-0.1346612248380.04758270708960.04123973770120.1295951566760.153950448085-0.002049333495150.001313248420750.144776900152-0.0008564910046640.13300093561976.69493.20123.905
104.44202798523-1.87519927060.1176714698546.3111483532-5.600867895547.709692107960.04061283422570.0503377920344-0.13236984603-0.06407516880250.2422651127010.3299678275290.0562167061005-0.401590170987-0.257107201030.107741690089-0.0199965125845-0.01972634356130.13176356057-0.00990951584310.13188924600674.199103.71225.556
111.93545664844-2.609136949573.226844999297.00010530049-6.970295769477.69072627006-0.131063360982-0.08335170634390.000218839674030.128026141823-0.046381741776-0.237877031874-0.08443709580660.006674111375340.1668377844720.109347659203-0.00763139007973-0.00977429192980.122650929319-0.006377659309620.13759831350879.3193.90729.41
127.57134181702-1.640134539652.840997996726.66086282118-0.8805530378315.48052751408-0.1065091962090.4381188585360.0426204661515-0.2024657376490.1818667126180.376289425784-0.0235404453349-0.30846101209-0.08276411870110.1257284140270.01677472833930.006749886949420.1390975446990.05093822413940.093587491003875.04599.26221.658
134.00038301886-2.46232383851-3.406219282035.684764382772.321324737127.165228352550.1597191806840.1629148813230.106947685574-0.090204890419-0.159595740985-0.00818541513122-0.278585478631-0.253763118666-0.07025913371810.0832170053249-0.00144365047697-0.02617332791330.09316334814580.01078951320020.095794525939877.462109.19126.66
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:6 )A1 - 6
2X-RAY DIFFRACTION2( CHAIN A AND RESID 7:21 )A7 - 21
3X-RAY DIFFRACTION3( CHAIN A AND RESID 22:31 )A22 - 31
4X-RAY DIFFRACTION4( CHAIN A AND RESID 32:45 )A32 - 45
5X-RAY DIFFRACTION5( CHAIN A AND RESID 46:57 )A46 - 57
6X-RAY DIFFRACTION6( CHAIN A AND RESID 58:69 )A58 - 69
7X-RAY DIFFRACTION7( CHAIN A AND RESID 70:73 )A70 - 73
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1:5 )B1 - 5
9X-RAY DIFFRACTION9( CHAIN B AND RESID 6:21 )B6 - 21
10X-RAY DIFFRACTION10( CHAIN B AND RESID 22:31 )B22 - 31
11X-RAY DIFFRACTION11( CHAIN B AND RESID 32:45 )B32 - 45
12X-RAY DIFFRACTION12( CHAIN B AND RESID 46:57 )B46 - 57
13X-RAY DIFFRACTION13( CHAIN B AND RESID 58:76 )B58 - 76

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