[English] 日本語
Yorodumi
- PDB-2ila: STRUCTURE OF INTERLEUKIN 1ALPHA AT 2.7-ANGSTROMS RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ila
TitleSTRUCTURE OF INTERLEUKIN 1ALPHA AT 2.7-ANGSTROMS RESOLUTION
ComponentsINTERLEUKIN-1 ALPHA
KeywordsCYTOKINE
Function / homology
Function and homology information


negative regulation of establishment of Sertoli cell barrier / positive regulation of neutrophil migration / positive regulation of steroid biosynthetic process / connective tissue replacement involved in inflammatory response wound healing / response to L-ascorbic acid / response to ozone / positive regulation of stress-activated MAPK cascade / positive regulation of immature T cell proliferation in thymus / positive regulation of prostaglandin secretion / fever generation ...negative regulation of establishment of Sertoli cell barrier / positive regulation of neutrophil migration / positive regulation of steroid biosynthetic process / connective tissue replacement involved in inflammatory response wound healing / response to L-ascorbic acid / response to ozone / positive regulation of stress-activated MAPK cascade / positive regulation of immature T cell proliferation in thymus / positive regulation of prostaglandin secretion / fever generation / intracellular sodium ion homeostasis / Interleukin-1 processing / response to copper ion / interleukin-1 receptor binding / keratinization / Interleukin-10 signaling / positive regulation of cell division / positive regulation of vascular endothelial growth factor production / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Pyroptosis / ectopic germ cell programmed cell death / Purinergic signaling in leishmaniasis infection / regulation of ERK1 and ERK2 cascade / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / positive regulation of cytokine production / cytokine activity / response to gamma radiation / positive regulation of protein secretion / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / Interleukin-1 signaling / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / cellular response to heat / heart development / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / positive regulation of canonical NF-kappaB signal transduction / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / immune response / inflammatory response / copper ion binding / negative regulation of cell population proliferation / apoptotic process / positive regulation of gene expression / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleus / cytosol
Similarity search - Function
Interleukin-1 alpha / Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsGraves, B.J. / Hatada, M.H.
CitationJournal: Biochemistry / Year: 1990
Title: Structure of interleukin 1 alpha at 2.7-A resolution.
Authors: Graves, B.J. / Hatada, M.H. / Hendrickson, W.A. / Miller, J.K. / Madison, V.S. / Satow, Y.
History
DepositionMay 1, 1991Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INTERLEUKIN-1 ALPHA


Theoretical massNumber of molelcules
Total (without water)17,6181
Polymers17,6181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.970, 54.520, 45.630
Angle α, β, γ (deg.)90.00, 108.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein INTERLEUKIN-1 ALPHA / Coordinate model: Cα atoms only


Mass: 17618.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01583

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 mg/mlprotein1drop
20.1 Mcitrate1reservior
30.2 Mammonium sulphate1reservoir
430 %(w/v)PEG4001reservoir

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.19 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms145 0 0 0 145
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

+
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