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- PDB-2q8t: Crystal Structure of the CC chemokine CCL14 -

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Basic information

Entry
Database: PDB / ID: 2q8t
TitleCrystal Structure of the CC chemokine CCL14
ComponentsCCL14
KeywordsCYTOKINE / common CC chemokine fold
Function / homology
Function and homology information


CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / intracellular calcium ion homeostasis / cellular response to type II interferon ...CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / chemokine activity / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / intracellular calcium ion homeostasis / cellular response to type II interferon / cellular response to tumor necrosis factor / positive regulation of ERK1 and ERK2 cascade / inflammatory response / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsBlain, K.Y.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and Functional Characterization of CC Chemokine CCL14
Authors: Blain, K.Y. / Kwiatkowski, W. / Zhao, Q. / La Fleur, D. / Naik, C. / Chun, T.-W. / Tsareva, T. / Kanakaraj, P. / Laird, M.W. / Shah, R. / George, L. / Sanyal, I. / Moore, P.A. / Demeler, B. / Choe, S.
History
DepositionJun 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE AUTHORS STATE THAT THE MONOMER AND THE DIMER SEEM TO BE BIOLOGICALLY RELEVANT, AND THE CONVERSION BETWEEN THE TWO APPEARS TO BE IMPORTANT. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCL14
B: CCL14
C: CCL14
D: CCL14


Theoretical massNumber of molelcules
Total (without water)34,7634
Polymers34,7634
Non-polymers00
Water3,315184
1
A: CCL14
B: CCL14


Theoretical massNumber of molelcules
Total (without water)17,3822
Polymers17,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
MethodPISA
2
C: CCL14
D: CCL14


Theoretical massNumber of molelcules
Total (without water)17,3822
Polymers17,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.345, 78.073, 59.639
Angle α, β, γ (deg.)90.000, 121.650, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer. There are four monomers presented monomers A, B, C, and D.

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Components

#1: Protein
CCL14 / Small inducible cytokine A14 / Chemokine CC-1/CC-3 / HCC-1/HCC-3 / HCC-1(1-74) / NCC-2


Mass: 8690.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16627
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2 M sodium formate, 20% w/v PEG 3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2004
Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 17814 / % possible obs: 98.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.039 / Χ2: 0.996 / Net I/σ(I): 30.98
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 14.3 / Num. unique all: 1764 / Χ2: 0.93 / % possible all: 99.2

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å30.95 Å
Translation2.5 Å30.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1B3A

1b3a


Resolution: 2.23→30.95 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.599 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 910 5.1 %RANDOM
Rwork0.187 ---
obs0.19 17814 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.739 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å2-1.08 Å2
2--0.3 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.23→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 0 184 2314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222202
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9342983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56223.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89215380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0791512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021664
X-RAY DIFFRACTIONr_nbd_refined0.2240.2909
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21476
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2166
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.213
X-RAY DIFFRACTIONr_mcbond_it1.2371.51318
X-RAY DIFFRACTIONr_mcangle_it1.99422124
X-RAY DIFFRACTIONr_scbond_it3.24531033
X-RAY DIFFRACTIONr_scangle_it4.7194.5859
LS refinement shellResolution: 2.23→2.289 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 71 -
Rwork0.181 1250 -
obs-1321 98.8 %
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)
11.7356-0.49990.98411.4123-1.56422.847-0.0313-0.2952-0.10450.01220.08780.0365-0.0949-0.1043-0.0565-0.12380.02160.0256-0.03950.0255-0.0946-6.848866.926318.0724
21.65830.0135-0.50650.84710.12683.35450.05560.0655-0.098-0.06990.2223-0.01420.0513-0.0829-0.278-0.0864-0.0355-0.0194-0.119-0.0087-0.063-15.999868.6708-5.6783
31.33070.16031.09421.7295-0.84953.7407-0.056-0.19980.10820.15290.26530.0307-0.2822-0.1851-0.2093-0.0490.08630.0092-0.1012-0.0297-0.0886-15.046787.92857.9298
41.252-0.6349-0.28861.0886-1.0163.41180.08040.16930.1035-0.0341-0.0755-0.056-0.0496-0.0623-0.0049-0.09250.0018-0.0293-0.08490.0279-0.0877-9.604689.1859-17.2286
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA10 - 7110 - 71
22BB10 - 7410 - 74
33CC10 - 7410 - 74
44DD10 - 7310 - 73

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