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- PDB-5cor: X-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3)... -

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Basic information

Entry
Database: PDB / ID: 5cor
TitleX-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3) N-TERMINAL-SWITCH POLYMER
ComponentsC-C motif chemokine 3
KeywordsCYTOKINE / CC chemokine / CCL3 / OLIGOMER / SIGNALING PROTEIN
Function / homology
Function and homology information


lymphocyte chemotaxis / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / CCR chemokine receptor binding ...lymphocyte chemotaxis / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / CCR chemokine receptor binding / regulation of sensory perception of pain / signaling / negative regulation of bone mineralization / positive regulation of microglial cell activation / cell activation / T cell chemotaxis / chemokine-mediated signaling pathway / eosinophil chemotaxis / response to cholesterol / positive regulation of calcium ion transport / chemokine activity / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / phospholipase activator activity / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / negative regulation of osteoclast differentiation / Interleukin-10 signaling / monocyte chemotaxis / exocytosis / cellular response to interleukin-1 / host-mediated suppression of viral transcription / neutrophil chemotaxis / cytoskeleton organization / positive regulation of calcium-mediated signaling / positive regulation of interleukin-1 beta production / cell chemotaxis / calcium-mediated signaling / cellular response to type II interferon / response to toxic substance / intracellular calcium ion homeostasis / chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / antimicrobial humoral immune response mediated by antimicrobial peptide / osteoblast differentiation / cellular response to tumor necrosis factor / calcium ion transport / kinase activity / cell-cell signaling / positive regulation of neuron apoptotic process / MAPK cascade / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / inflammatory response / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytoplasm / cytosol
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
ACETATE ION / HEXANE-1,6-DIOL / C-C motif chemokine 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.548 Å
AuthorsLiang, W.G. / Tang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3.
Authors: Liang, W.G. / Triandafillou, C.G. / Huang, T.Y. / Zulueta, M.M. / Banerjee, S. / Dinner, A.R. / Hung, S.C. / Tang, W.J.
#1: Journal: To Be Published
Title: X-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3) N-TERMINAL-SWITCH POLYMER
Authors: Liang, W.G. / Tang, W.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 4, 2016Group: Database references
Revision 1.3May 18, 2016Group: Database references
Revision 1.4Jan 15, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C motif chemokine 3
B: C-C motif chemokine 3
C: C-C motif chemokine 3
D: C-C motif chemokine 3
E: C-C motif chemokine 3
F: C-C motif chemokine 3
G: C-C motif chemokine 3
H: C-C motif chemokine 3
I: C-C motif chemokine 3
J: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,29623
Polymers77,93710
Non-polymers1,35913
Water2,504139
1
A: C-C motif chemokine 3
C: C-C motif chemokine 3
E: C-C motif chemokine 3
G: C-C motif chemokine 3
I: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,79513
Polymers38,9685
Non-polymers8278
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-C motif chemokine 3
D: C-C motif chemokine 3
F: C-C motif chemokine 3
H: C-C motif chemokine 3
J: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,50010
Polymers38,9685
Non-polymers5325
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.073, 112.592, 179.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
C-C motif chemokine 3 / G0/G1 switch regulatory protein 19-1 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / PAT ...G0/G1 switch regulatory protein 19-1 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / PAT 464.1 / SIS-beta / Small-inducible cytokine A3 / Tonsillar lymphocyte LD78 alpha protein


Mass: 7793.664 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL3, G0S19-1, MIP1A, SCYA3 / Production host: Escherichia coli (E. coli) / References: UniProt: P10147
#2: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.69 Å3/Da / Density % sol: 66.68 %
Crystal growTemperature: 291.16 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Cobalt (II) chloride hexahydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 1.0 M 1,6-Hexanediol
PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.746 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 11, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.746 Å / Relative weight: 1
ReflectionResolution: 2.548→50 Å / Num. obs: 38583 / % possible obs: 100 % / Observed criterion σ(I): 1.9 / Redundancy: 9.1 % / Rmerge(I) obs: 0.078 / Rsym value: 0.058 / Net I/σ(I): 26.4
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 0.868 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X69

2x69


Resolution: 2.548→48.966 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.72 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2204 1891 5.29 %
Rwork0.1802 --
obs0.1823 37824 85.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.548→48.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 92 139 5613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025601
X-RAY DIFFRACTIONf_angle_d0.5627546
X-RAY DIFFRACTIONf_dihedral_angle_d12.2342041
X-RAY DIFFRACTIONf_chiral_restr0.022837
X-RAY DIFFRACTIONf_plane_restr0.002971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5484-2.58480.4232630.29631162X-RAY DIFFRACTION40
2.5848-2.62340.2801760.29361351X-RAY DIFFRACTION47
2.6234-2.66440.3057890.27291545X-RAY DIFFRACTION54
2.6644-2.70810.3221940.26041666X-RAY DIFFRACTION58
2.7081-2.75480.27381010.2421826X-RAY DIFFRACTION64
2.7548-2.80490.33311120.21971982X-RAY DIFFRACTION69
2.8049-2.85880.27041230.22782111X-RAY DIFFRACTION73
2.8588-2.91710.33441240.2272210X-RAY DIFFRACTION79
2.9171-2.98060.27171500.22382506X-RAY DIFFRACTION86
2.9806-3.04990.30481470.21962628X-RAY DIFFRACTION92
3.0499-3.12620.25871590.20522855X-RAY DIFFRACTION99
3.1262-3.21070.3151630.22352859X-RAY DIFFRACTION100
3.2107-3.30510.25821590.22112892X-RAY DIFFRACTION100
3.3051-3.41180.25521590.18072892X-RAY DIFFRACTION100
3.4118-3.53370.22941600.17442876X-RAY DIFFRACTION100
3.5337-3.67510.19061580.16622817X-RAY DIFFRACTION100
3.6751-3.84230.15241640.15582892X-RAY DIFFRACTION100
3.8423-4.04480.20581570.16442879X-RAY DIFFRACTION100
4.0448-4.29810.19691610.14662854X-RAY DIFFRACTION100
4.2981-4.62970.17221550.13782882X-RAY DIFFRACTION100
4.6297-5.09520.16191630.14222881X-RAY DIFFRACTION100
5.0952-5.83140.18861540.15492865X-RAY DIFFRACTION100
5.8314-7.3430.20461580.18722891X-RAY DIFFRACTION100
7.343-48.97530.1881580.1682858X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 37.7045 Å / Origin y: 64.6923 Å / Origin z: 76.2111 Å
111213212223313233
T0.1894 Å20.0037 Å20.0466 Å2-0.2266 Å20.0088 Å2--0.2344 Å2
L0.1469 °2-0.0555 °20.0928 °2-0.3608 °20.0751 °2--0.3033 °2
S-0.075 Å °-0.0407 Å °-0.0324 Å °-0.0454 Å °-0.0437 Å °0.059 Å °0.1051 Å °0.0357 Å °0.12 Å °
Refinement TLS groupSelection details: all

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