[English] 日本語
Yorodumi
- PDB-3fpu: The crystallographic structure of the Complex between Evasin-1 an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fpu
TitleThe crystallographic structure of the Complex between Evasin-1 and CCL3
Components
  • C-C motif chemokine 3
  • Evasin-1
KeywordsIMMUNE SYSTEM / protein:protein complex / chemokine / Glycoprotein / Secreted / Chemotaxis / Cytokine / Inflammatory response
Function / homology
Function and homology information


negative regulation of chemokine activity / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / chemokine binding / positive regulation of natural killer cell chemotaxis / signaling / regulation of behavior / astrocyte cell migration / CCR5 chemokine receptor binding ...negative regulation of chemokine activity / granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / chemokine binding / 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 / lymphocyte chemotaxis / cell activation / T cell chemotaxis / C-C chemokine binding / 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 / positive regulation of calcium ion import / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / macrophage chemotaxis / 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 / response to toxic substance / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of inflammatory response / osteoblast differentiation / calcium ion transport / chemotaxis / positive regulation of tumor necrosis factor production / MAPK cascade / positive regulation of neuron apoptotic process / cell-cell signaling / kinase activity / cellular response to tumor necrosis factor / 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 / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #100 / Evasins Class A / Evasins Class A / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / 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 ...Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #100 / Evasins Class A / Evasins Class A / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / 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) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Evasin-1 / C-C motif chemokine 3
Similarity search - Component
Biological speciesRhipicephalus sanguineus (brown dog tick)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsShaw, J.P. / Dias, J.M.
Citation
Journal: Plos One / Year: 2009
Title: Structural basis of chemokine sequestration by a tick chemokine binding protein: the crystal structure of the complex between Evasin-1 and CCL3
Authors: Dias, J.M. / Losberger, C. / Deruaz, M. / Power, C.A. / Proudfoot, A.E.I. / Shaw, J.P.
#1: Journal: J.Biol.Chem. / Year: 2007
Title: Molecular cloning and characterization of a highly selective chemokine-binding protein from the tick Rhipicephalus sanguineus.
Authors: Frauenschuh, A. / Power, C.A. / Deruaz, M. / Ferreira, B.R. / Silva, J.S. / Teixeira, M.M. / Dias, J.M. / Martin, T. / Wells, T.N.C. / Proudfoot, A.E.I.
#2: Journal: J.Exp.Med. / Year: 2008
Title: Ticks produce highly selective chemokine binding proteins with antiinflammatory activity
Authors: Deruaz, M. / Frauenschuh, A. / Alessandri, A.L. / Dias, J.M. / Coelho, F.M. / Russo, R.C. / Ferreira, B.R. / Graham, G.J. / Shaw, J.P. / Wells, T.N.C. / Teixeira, M.M. / Power, C.A. / Proudfoot, A.E.I.
History
DepositionJan 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Derived calculations
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Evasin-1
B: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3084
Polymers19,1902
Non-polymers1172
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-11 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.384, 104.384, 104.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-101-

NI

21A-102-

NI

31B-71-

HOH

-
Components

#1: Protein Evasin-1


Mass: 11306.446 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus sanguineus (brown dog tick)
Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P0C8E7
#2: Protein C-C motif chemokine 3 / 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: 7883.808 Da / Num. of mol.: 1 / Mutation: A10T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P10147
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 24% (w/v) PEG 3350, 200mM Ammonium sulfate, 100mM HEPES, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.976 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 17, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 19881 / Num. obs: 19881 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 40.4 % / Rsym value: 0.09 / Net I/σ(I): 13.7
Reflection shellResolution: 1.76→1.9 Å / Mean I/σ(I) obs: 7.8 / Rsym value: 0.828 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3fpr

3fpr


Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.868 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28467 1015 5.1 %RANDOM
Rwork0.23133 ---
all0.23398 18797 --
obs0.23398 18797 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.301 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 2 160 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211347
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.941832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48124.20369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4215212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.595159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021063
X-RAY DIFFRACTIONr_nbd_refined0.210.2570
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2906
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.219
X-RAY DIFFRACTIONr_mcbond_it1.3181.5845
X-RAY DIFFRACTIONr_mcangle_it2.27521341
X-RAY DIFFRACTIONr_scbond_it2.9813565
X-RAY DIFFRACTIONr_scangle_it4.294.5491
LS refinement shellResolution: 1.761→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 75 -
Rwork0.265 1371 -
obs--100 %

+
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://pdbjlvh1.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