[English] 日本語
Yorodumi
- PDB-6aez: Crystal structure of human CCL5 trimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aez
TitleCrystal structure of human CCL5 trimer
Components(C-C motif chemokine 5Chemokine) x 2
KeywordsCYTOKINE / CCL5 / RANTES / Chemokine / Oligomer / dimer / CC-type
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 / positive regulation of homotypic cell-cell adhesion / CCR5 chemokine receptor binding / positive regulation of T cell chemotaxis / negative regulation of G protein-coupled receptor signaling pathway / CCR chemokine receptor binding / lymphocyte chemotaxis / neutrophil activation / phosphatidylinositol phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / positive regulation of calcium ion transport / eosinophil chemotaxis / positive regulation of innate immune response / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / regulation of T cell activation / leukocyte cell-cell adhesion / positive regulation of macrophage chemotaxis / negative regulation of viral genome replication / phospholipase activator activity / macrophage chemotaxis / positive regulation of smooth muscle cell migration / exocytosis / chemoattractant activity / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of translational initiation / regulation of insulin secretion / positive regulation of cell adhesion / negative regulation by host of viral transcription / positive regulation of T cell migration / positive regulation of viral genome replication / cellular response to interleukin-1 / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / 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 / intracellular calcium ion homeostasis / response to toxic substance / cellular response to virus / cellular response to type II interferon / : / calcium ion transport / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / 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 / 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
C-C motif chemokine 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsChen, Y.C. / Li, K.M. / Chen, P.J. / Zarivach, R. / Sun, Y.J. / Sue, S.C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)106-2113-M-007 -020 - Taiwan
Ministry of Science and Technology (Taiwan)107-2113-M-007 -011 - Taiwan
Citation
Journal: J.Mol.Biol. / Year: 2020
Title: Integrative Model to Coordinate the Oligomerization and Aggregation Mechanisms of CCL5.
Authors: Chen, Y.C. / Chen, S.P. / Li, J.Y. / Chen, P.C. / Lee, Y.Z. / Li, K.M. / Zarivach, R. / Sun, Y.J. / Sue, S.C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2018
Title: Human CCL5 trimer: expression, purification and initial crystallographic studies.
Authors: Chen, Y.C. / Li, K.M. / Zarivach, R. / Sun, Y.J. / Sue, S.C.
History
DepositionAug 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-C motif chemokine 5
B: C-C motif chemokine 5
C: C-C motif chemokine 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4729
Polymers23,8963
Non-polymers5766
Water3,495194
1
B: C-C motif chemokine 5
C: C-C motif chemokine 5
hetero molecules

B: C-C motif chemokine 5
C: C-C motif chemokine 5
hetero molecules

A: C-C motif chemokine 5
hetero molecules

A: C-C motif chemokine 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,94418
Polymers47,7916
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
crystal symmetry operation3_555-y+1/2,x+1/2,z+1/41
crystal symmetry operation5_445-x-1/2,y-1/2,-z+1/41
Buried area6510 Å2
ΔGint-134 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.556, 56.556, 154.103
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

21C-249-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSERAA6 - 656 - 65
21SERSERSERSERBB6 - 656 - 65
12SERSERMETMETAA6 - 686 - 68
22SERSERMETMETCC6 - 686 - 68
13PROPROSERSERBB3 - 653 - 65
23PROPROSERSERCC3 - 653 - 65

NCS ensembles :
ID
1
2
3
DetailsAUTHOR DETERMINED BIOLOGICAL ASSEMBLY: UNKNOWN.

-
Components

#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: 7951.170 Da / Num. of mol.: 2 / Mutation: E67S
Source method: isolated from a genetically manipulated source
Details: The CCL5 trimer was prepared by mixing native protein (E67) and mutant (S67) with molar ratio of 1:2.
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501
#2: 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: 7993.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M ammonium sulfate, 0.1M BIS-TRIS pH 5, 16% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→53.09 Å / Num. obs: 30546 / % possible obs: 94.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 48.73
Reflection shellResolution: 1.63→1.66 Å / Rmerge(I) obs: 0.889

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EQT monomer
Resolution: 1.63→53.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.531 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22844 1504 4.9 %RANDOM
Rwork0.20127 ---
obs0.2026 28967 94.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.535 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å20 Å2
2---1.54 Å2-0 Å2
3---3.08 Å2
Refinement stepCycle: 1 / Resolution: 1.63→53.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 30 194 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.021664
X-RAY DIFFRACTIONr_bond_other_d0.0060.021488
X-RAY DIFFRACTIONr_angle_refined_deg2.481.9642268
X-RAY DIFFRACTIONr_angle_other_deg1.3833460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4865196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25621.6971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82915268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3491515
X-RAY DIFFRACTIONr_chiral_restr0.1590.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211787
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02364
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_it2.3242.143780
X-RAY DIFFRACTIONr_mcbond_other2.3242.145779
X-RAY DIFFRACTIONr_mcangle_it3.3283.198971
X-RAY DIFFRACTIONr_mcangle_other3.3273.196972
X-RAY DIFFRACTIONr_scbond_it3.5882.777882
X-RAY DIFFRACTIONr_scbond_other3.0972.655857
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6783.7771258
X-RAY DIFFRACTIONr_long_range_B_refined8.38128.011889
X-RAY DIFFRACTIONr_long_range_B_other8.1626.8661842
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A34680.11
12B34680.11
21A35980.15
22C35980.15
31B35420.14
32C35420.14
LS refinement shellResolution: 1.631→1.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 72 -
Rwork0.356 1483 -
obs--66.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.81750.0381.55370.6917-0.10333.16790.0576-0.0350.0802-0.0177-0.0714-0.0909-0.1407-0.00950.01390.11460.0214-0.00310.10580.00790.0218-15.862632.366211.6922
23.35450.3288-0.98450.9651-0.23891.1056-0.05340.1306-0.3826-0.0516-0.0663-0.11420.0985-0.12960.11970.08080.0199-0.01120.0803-0.02130.0687-16.001811.22314.1798
31.4010.7150.61350.50550.01651.56030.05710.0509-0.269-0.06430.0422-0.0448-0.02020.105-0.09930.20550.0337-0.02080.12190.02230.33585.62217.5042-8.3545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 69
2X-RAY DIFFRACTION2B3 - 66
3X-RAY DIFFRACTION3C3 - 69

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more