[English] 日本語
Yorodumi
- PDB-1eqt: MET-RANTES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eqt
TitleMET-RANTES
ComponentsT-CELL SPECIFIC RANTES PROTEIN
KeywordsCYTOKINE / CHEMOATTRACTANT / RANTES
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: 1.6 Å
AuthorsHoover, D.M. / Shaw, J. / Gryczynski, Z. / Proudfoot, A.E.I. / Wells, T.
Citation
Journal: PROTEIN PEPT.LETT. / Year: 2000
Title: The Crystal Structure of MET-RANTES: Comparison with Native RANTES and AOP-RANTES
Authors: Hoover, D.M. / Shaw, J. / Gryczynski, Z. / Proudfoot, A.E.I. / Wells, T.
#1: Journal: Chem.Biol. / Year: 1999
Title: Total Chemical Synthesis and High-resolution Crystal Structure of the Potent anti-HIV Protein AOP-RANTES
Authors: Wilken, J. / Hoover, D. / Thompson, D.A. / Barlow, P.N. / McSparron, H. / Picard, L. / Wlodawer, A. / Lubkowski, J. / Kent, S.B.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Extension of Recombinant Human RANTES by the Retention of the Initiating Methionine Produces a Potent Antagonist
Authors: Proudfoot, A.E. / Power, C.A. / Hoogewerf, A.J. / Montjovent, M.O. / Borlat, F. / Offord, R.E. / Wells, T.N.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-CELL SPECIFIC RANTES PROTEIN
B: T-CELL SPECIFIC RANTES PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9604
Polymers15,7682
Non-polymers1922
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.019, 56.809, 93.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is likely a dimer constructed of both chain A and B.

-
Components

#1: Protein T-CELL SPECIFIC RANTES PROTEIN / SMALL INDUCIBLE CYTOKINE A5


Mass: 7884.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINITIATING MET RETAINED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 35000, ammonium sulfate, sodium succinate, MES, sodium acetate, ethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: other / Details: Wilken, J., (1999) Chem.Biol., 6, 43.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMsodium acetate11
215 mg/mlprotein11
30.1 Mammonium sulfate11
4225 mMsodium succinate11
5275 mMMES11
615 %ethanol11
70.1 Mammonium sulfate12
8225 mMsodium succinate12
9275 mMMES12
1015 %ethanol12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 23, 1998 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 44155 / Num. obs: 17136 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 21.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1650 / % possible all: 96
Reflection
*PLUS
Num. measured all: 44155

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RANTES (NMR MODEL 1RTN)

1rtn


Resolution: 1.6→20 Å / Num. parameters: 513 / Num. restraintsaints: 451 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1655 10 %RANDOM
Rwork0.1868 ---
all0.178 17136 --
obs0.178 16548 84.2 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1281
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 10 187 1281
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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