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- PDB-5dnf: Crystal structure of CC chemokine 5 (CCL5) oligomer in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5dnf
TitleCrystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin
ComponentsC-C motif chemokine 5Chemokine
KeywordsCYTOKINE / CC chemokine / high oligomer
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of activation of Janus kinase activity / receptor signaling protein tyrosine kinase activator activity / CCR5 chemokine receptor binding / positive regulation of homotypic cell-cell adhesion / negative regulation of G protein-coupled receptor signaling pathway / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / lymphocyte chemotaxis / phosphatidylinositol phospholipase C activity / positive regulation of T cell apoptotic process / negative regulation of T cell apoptotic process / positive regulation of calcium ion transport / neutrophil activation / eosinophil chemotaxis / positive regulation of innate immune response / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / cellular response to fibroblast growth factor stimulus / dendritic cell chemotaxis / regulation of T cell activation / leukocyte cell-cell adhesion / negative regulation of viral genome replication / positive regulation of macrophage chemotaxis / phospholipase activator activity / positive regulation of smooth muscle cell migration / exocytosis / macrophage chemotaxis / chemoattractant activity / Interleukin-10 signaling / monocyte chemotaxis / regulation of insulin secretion / positive regulation of translational initiation / positive regulation of cell adhesion / negative regulation by host of viral transcription / positive regulation of T cell migration / cellular response to interleukin-1 / positive regulation of viral genome replication / positive regulation of T cell proliferation / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / neutrophil chemotaxis / epithelial cell proliferation / positive regulation of epithelial cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / response to virus / response to toxic substance / cellular response to virus / cellular response to type II interferon / intracellular calcium ion homeostasis / calcium ion transport / : / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / 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 / G protein-coupled receptor signaling pathway / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / 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-galactopyranose / C-C motif chemokine 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.549 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
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
DepositionSep 10, 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 / 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 / _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 / chem_comp ...atom_site / 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_struct_special_symmetry / 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_alt_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 / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C motif chemokine 5
B: C-C motif chemokine 5
C: C-C motif chemokine 5
D: C-C motif chemokine 5
E: C-C motif chemokine 5
F: C-C motif chemokine 5
G: C-C motif chemokine 5
H: C-C motif chemokine 5
I: C-C motif chemokine 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,67549
Polymers67,6329
Non-polymers6,04440
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.190, 210.063, 123.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11F-104-

CL

21B-212-

HOH

31H-221-

HOH

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Components

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Protein , 1 types, 9 molecules ABCDEFGHI

#1: Protein
C-C motif chemokine 5 / Chemokine / EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific ...EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific protein P228 / TCP228 / T-cell-specific protein RANTES


Mass: 7514.645 Da / Num. of mol.: 9 / Fragment: UNP residues 27-91 / Mutation: S4TNR
Source method: isolated from a genetically manipulated source
Details: SERINE at the N-terminal has O-linked glycosylation by glucose.
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501

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Sugars , 3 types, 14 molecules

#2: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 916.769 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-GLA / alpha-D-galactopyranose / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 5
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

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Non-polymers , 4 types, 236 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 5.83 Å3/Da / Density % sol: 78.89 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Tris, pH 7.5; 1.8 M (NH4)2SO4 / PH range: 7.2-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.722 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.722 Å / Relative weight: 1
ReflectionResolution: 2.549→39.695 Å / Num. obs: 51550 / % possible obs: 100 % / Observed criterion σ(I): 5.5 / Redundancy: 64.8 % / Rmerge(I) obs: 0.084 / Rsym value: 0.111 / Net I/σ(I): 54
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 52.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.549→39.695 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.37 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2337 1933 3.9 %
Rwork0.1805 --
obs0.1826 51346 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.549→39.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4725 0 341 210 5276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035221
X-RAY DIFFRACTIONf_angle_d1.7357103
X-RAY DIFFRACTIONf_dihedral_angle_d12.8721929
X-RAY DIFFRACTIONf_chiral_restr0.212816
X-RAY DIFFRACTIONf_plane_restr0.004861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5493-2.58160.38231020.28192501X-RAY DIFFRACTION69
2.5816-2.61550.33991210.25362971X-RAY DIFFRACTION86
2.6155-2.65140.28041400.24293182X-RAY DIFFRACTION89
2.6514-2.68920.23381260.22513268X-RAY DIFFRACTION92
2.6892-2.72940.27221410.22683305X-RAY DIFFRACTION94
2.7294-2.7720.32411460.223421X-RAY DIFFRACTION96
2.772-2.81740.24821380.23123476X-RAY DIFFRACTION98
2.8174-2.8660.31691450.26193478X-RAY DIFFRACTION99
2.866-2.91810.24491530.23363536X-RAY DIFFRACTION100
2.9181-2.97420.20891460.2263534X-RAY DIFFRACTION100
2.9742-3.03490.28731430.24033575X-RAY DIFFRACTION100
3.0349-3.10090.33051390.2323573X-RAY DIFFRACTION100
3.1009-3.1730.3081490.25633483X-RAY DIFFRACTION100
3.173-3.25230.36081450.24743540X-RAY DIFFRACTION100
3.2523-3.34020.28521500.22553586X-RAY DIFFRACTION100
3.3402-3.43840.22271470.18823501X-RAY DIFFRACTION100
3.4384-3.54930.22971540.20293536X-RAY DIFFRACTION100
3.5493-3.67610.26521250.17963542X-RAY DIFFRACTION100
3.6761-3.82320.19581380.15793546X-RAY DIFFRACTION100
3.8232-3.9970.25961440.14563541X-RAY DIFFRACTION100
3.997-4.20750.16441440.14753509X-RAY DIFFRACTION99
4.2075-4.47080.18611440.13463521X-RAY DIFFRACTION100
4.4708-4.81540.1681330.12943545X-RAY DIFFRACTION100
4.8154-5.2990.20991280.13143561X-RAY DIFFRACTION100
5.299-6.06350.14741500.14083545X-RAY DIFFRACTION100
6.0635-7.63040.17541390.14433559X-RAY DIFFRACTION100
7.6304-39.69980.19981380.13763515X-RAY DIFFRACTION99

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