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- PDB-3kbx: Human macrophage inflammatory protein-1 alpha L3M_V63M -

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Basic information

Entry
Database: PDB / ID: 3kbx
TitleHuman macrophage inflammatory protein-1 alpha L3M_V63M
ComponentsCCL3
KeywordsCYTOKINE / chemokine / Chemotaxis / Inflammatory response / Secreted
Function / homology
Function and homology information


granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / signaling / astrocyte cell migration / eosinophil degranulation / CCR5 chemokine receptor binding / negative regulation of bone mineralization ...granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / signaling / astrocyte cell migration / eosinophil degranulation / CCR5 chemokine receptor binding / negative regulation of bone mineralization / regulation of sensory perception of pain / CCR chemokine receptor binding / positive regulation of microglial cell activation / lymphocyte chemotaxis / cell activation / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / phospholipase activator activity / macrophage chemotaxis / positive regulation of calcium ion import / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / Interleukin-10 signaling / monocyte chemotaxis / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / cytoskeleton organization / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / calcium-mediated signaling / intracellular calcium ion homeostasis / response to toxic substance / osteoblast differentiation / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of neuron apoptotic process / calcium ion transport / chemotaxis / MAPK cascade / positive regulation of tumor necrosis factor production / cell-cell signaling / cellular response to tumor necrosis factor / kinase activity / 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 / G protein-coupled receptor signaling pathway / 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
ACETATE ION / : / C-C motif chemokine 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.652 Å
AuthorsGuo, Q. / Ren, M. / Tang, W.-J.
CitationJournal: To be Published
Title: Structural basis for the oligomerization of macrophage inflammatory protein-1 alpha
Authors: Guo, Q. / Ren, M. / Tang, W.-J.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCL3
B: CCL3
C: CCL3
D: CCL3
E: CCL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7867
Polymers39,6885
Non-polymers982
Water72140
1
A: CCL3
hetero molecules

A: CCL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0716
Polymers15,8752
Non-polymers1964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area1330 Å2
ΔGint-11 kcal/mol
Surface area8320 Å2
MethodPISA
2
B: CCL3
C: CCL3


Theoretical massNumber of molelcules
Total (without water)15,8752
Polymers15,8752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-10 kcal/mol
Surface area8330 Å2
MethodPISA
3
D: CCL3
E: CCL3


Theoretical massNumber of molelcules
Total (without water)15,8752
Polymers15,8752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-9 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.010, 178.010, 77.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-71-

K

21A-80-

HOH

31B-75-

HOH

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Components

#1: Protein
CCL3 / / Small-inducible cytokine A3 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / Tonsillar ...Small-inducible cytokine A3 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / Tonsillar lymphocyte LD78 alpha protein / G0/G1 switch regulatory protein 19-1 / G0S19-1 protein / SIS-beta / PAT 464.1 / MIP-1-alpha(4-69) / LD78-alpha(4-69)


Mass: 7937.557 Da / Num. of mol.: 5
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) / Strain (production host): BL21(DE3) / References: UniProt: P10147
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 4.45 Å3/Da / Density % sol: 72.39 %

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.652→42.796 Å

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementResolution: 2.652→42.796 Å / SU ML: 0.27 / σ(F): 0.07 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2572 1056 5.1 %
Rwork0.2115 --
obs0.2138 20703 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.678 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 60.276 Å2
Baniso -1Baniso -2Baniso -3
1-2.301 Å2-0 Å2-0 Å2
2--2.301 Å20 Å2
3----4.602 Å2
Refinement stepCycle: LAST / Resolution: 2.652→42.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 5 40 2655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112686
X-RAY DIFFRACTIONf_angle_d1.2153620
X-RAY DIFFRACTIONf_dihedral_angle_d19.506965
X-RAY DIFFRACTIONf_chiral_restr0.089395
X-RAY DIFFRACTIONf_plane_restr0.005470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.652-2.77280.3341230.28372176X-RAY DIFFRACTION88
2.7728-2.9190.33891270.27512321X-RAY DIFFRACTION93
2.919-3.10180.32191270.28022391X-RAY DIFFRACTION96
3.1018-3.34120.32051510.23862425X-RAY DIFFRACTION98
3.3412-3.67730.25191330.20742499X-RAY DIFFRACTION99
3.6773-4.2090.23911340.18252526X-RAY DIFFRACTION100
4.209-5.30130.20641260.16422578X-RAY DIFFRACTION100
5.3013-42.80140.22971350.21892731X-RAY DIFFRACTION100

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