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- PDB-2x69: X-ray Structure of Macrophage Inflammatory Protein-1 alpha polymer -

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Basic information

Entry
Database: PDB / ID: 2x69
TitleX-ray Structure of Macrophage Inflammatory Protein-1 alpha polymer
ComponentsC-C MOTIF CHEMOKINE 3
KeywordsIMMUNE SYSTEM / INFLAMMATORY RESPONSE / CYTOKINE / CHEMOTAXIS
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 / positive regulation of calcium ion transport / response to cholesterol / chemokine activity / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / phospholipase activator activity / Interleukin-10 signaling / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / exocytosis / negative regulation of osteoclast differentiation / monocyte chemotaxis / cellular response to interleukin-1 / negative regulation by host of viral transcription / cytoskeleton organization / neutrophil chemotaxis / 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 / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / calcium ion transport / positive regulation of tumor necrosis factor production / osteoblast differentiation / kinase activity / positive regulation of neuron apoptotic process / MAPK cascade / cellular response to tumor necrosis factor / cell-cell signaling / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / 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 / cytosol / cytoplasm
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 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGuo, Q. / Ren, M. / Tang, W.
CitationJournal: Embo J. / Year: 2010
Title: Polymerization of Mip-1 Chemokine (Ccl3 and Ccl4) and Clearance of Mip-1 by Insulin-Degrading Enzyme.
Authors: Ren, M. / Guo, Q. / Guo, L. / Lenz, M. / Qian, F. / Koenen, R.R. / Xu, H. / Schilling, A.B. / Weber, C. / Ye, R.D. / Dinner, A.R. / Tang, W.
History
DepositionFeb 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)38,9685
Polymers38,9685
Non-polymers00
Water23413
1
B: C-C MOTIF CHEMOKINE 3
C: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,5872
Polymers15,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-11.7 kcal/mol
Surface area8310 Å2
MethodPISA
2
A: C-C MOTIF CHEMOKINE 3

A: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,5872
Polymers15,5872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area1330 Å2
ΔGint-9.9 kcal/mol
Surface area8300 Å2
MethodPISA
3
D: C-C MOTIF CHEMOKINE 3
E: C-C MOTIF CHEMOKINE 3


Theoretical massNumber of molelcules
Total (without water)15,5872
Polymers15,5872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-9.5 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.541, 181.541, 76.845
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein
C-C MOTIF CHEMOKINE 3 / SMALL-INDUCIBLE CYTOKINE A3 / MACROPHAGE INFLAMMATORY PROTEIN 1-ALPHA / TONSILLAR LYMPHOCYTE LD78 ...SMALL-INDUCIBLE CYTOKINE A3 / MACROPHAGE INFLAMMATORY PROTEIN 1-ALPHA / TONSILLAR LYMPHOCYTE LD78 ALPHA PROTEIN / G0/G1 SWITCH REGULATORY PROTEIN 19-1 / SIS- BETA / PAT 464.1 / MIP-1-ALPHA(4-69) / LD78-ALPHA(4-69) / MIP- 1-ALPHA


Mass: 7793.664 Da / Num. of mol.: 5 / Fragment: RESIDUES 23-92 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P10147
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.69 Å3/Da / Density % sol: 73.78 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 22235 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 40.7
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 11 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→157.22 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.787 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26461 1133 5.1 %RANDOM
Rwork0.2227 ---
obs0.23483 21083 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.689 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.65→157.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 0 13 2618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222675
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0991.9463640
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5365325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53324.4125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.74315430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.211515
X-RAY DIFFRACTIONr_chiral_restr0.1590.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212045
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0441.51660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04522705
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.99631015
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1374.5935
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.647→2.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 95 -
Rwork0.314 1504 -
obs--99.94 %

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