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- PDB-5d65: X-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3)... -

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Basic information

Entry
Database: PDB / ID: 5d65
TitleX-RAY STRUCTURE OF MACROPHAGE INFLAMMATORY PROTEIN-1 ALPHA (CCL3) WITH HEPARIN COMPLEX
ComponentsC-C motif chemokine 3
KeywordsCYTOKINE / CC chemokine / CCL3 / OLIGOMER / SIGNALING PROTEIN / HEPARIN / GAG / COMPLEX
Function / homology
Function and homology information


granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation ...granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain / negative regulation of bone mineralization / CCR chemokine receptor binding / positive regulation of microglial cell activation / 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 / chemoattractant activity / exocytosis / negative regulation of osteoclast differentiation / monocyte chemotaxis / Interleukin-10 signaling / cellular response to interleukin-1 / negative regulation by host of viral transcription / cytoskeleton organization / positive regulation of calcium-mediated signaling / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / calcium-mediated signaling / response to toxic substance / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of inflammatory response / osteoblast differentiation / chemotaxis / calcium ion transport / positive regulation of neuron apoptotic process / MAPK cascade / positive regulation of tumor necrosis factor production / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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
beta-D-glucopyranose / alpha-D-glucopyranose / C-C motif chemokine 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsLiang, W.G. / Hwang, D.Y. / Zulueta, M.M. / Hung, S.C. / Tang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: 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.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jan 15, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,03219
Polymers38,9685
Non-polymers3,06314
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12970 Å2
ΔGint-35 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.061, 181.061, 77.378
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 / 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.: 5 / Fragment: UNP residues 23-92
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: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid


Type: oligosaccharide / Mass: 595.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 4.7 Å3/Da / Density % sol: 73.82 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Tris, pH 7.0; 1.8M (NH4)2SO4; / PH range: 7.0-7.8

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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: 3.095→34.22 Å / Num. obs: 14085 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 12.9 % / Rmerge(I) obs: 0.053 / Rsym value: 0.039 / Net I/σ(I): 48.9
Reflection shellResolution: 3.1→3.13 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: 2X69

2x69


Resolution: 3.1→34.22 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.18 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.243 694 4.99 %
Rwork0.214 --
obs0.215 13915 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→34.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 193 0 2855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032926
X-RAY DIFFRACTIONf_angle_d1.543985
X-RAY DIFFRACTIONf_dihedral_angle_d16.3761100
X-RAY DIFFRACTIONf_chiral_restr0.185489
X-RAY DIFFRACTIONf_plane_restr0.003486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.095-3.33340.30211310.25622473X-RAY DIFFRACTION95
3.3334-3.66850.21111360.21022601X-RAY DIFFRACTION99
3.6685-4.19850.25461390.19352635X-RAY DIFFRACTION100
4.1985-5.28650.20931400.18952683X-RAY DIFFRACTION100
5.2865-34.21940.26391480.23972829X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.7769 Å / Origin y: 73.9483 Å / Origin z: 46.6755 Å
111213212223313233
T0.3452 Å20.2503 Å20.055 Å2-0.8892 Å2-0.0413 Å2--0.4138 Å2
L1.7507 °20.2187 °20.0913 °2-0.5842 °20.0429 °2--1.07 °2
S-0.1617 Å °0.1898 Å °-0.0653 Å °0.1089 Å °0.0414 Å °0.0239 Å °0.1407 Å °-0.5034 Å °0.066 Å °
Refinement TLS groupSelection details: ALL

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