[English] 日本語
Yorodumi
- PDB-1eku: CRYSTAL STRUCTURE OF A BIOLOGICALLY ACTIVE SINGLE CHAIN MUTANT OF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eku
TitleCRYSTAL STRUCTURE OF A BIOLOGICALLY ACTIVE SINGLE CHAIN MUTANT OF HUMAN IFN-GAMMA
ComponentsInterferon gamma
KeywordsIMMUNE SYSTEM / CYTOKINE / PROTEIN ENGINEERING / INTERFERON
Function / homology
Function and homology information


positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / positive regulation of iron ion import across plasma membrane / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / negative regulation of tau-protein kinase activity / positive regulation of NMDA glutamate receptor activity / : / positive regulation of vitamin D biosynthetic process ...positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / positive regulation of iron ion import across plasma membrane / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / negative regulation of tau-protein kinase activity / positive regulation of NMDA glutamate receptor activity / : / positive regulation of vitamin D biosynthetic process / positive regulation of cellular respiration / positive regulation of peptidyl-serine phosphorylation of STAT protein / positive regulation of interleukin-23 production / negative regulation of amyloid-beta clearance / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of protein deacetylation / type III interferon-mediated signaling pathway / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of smooth muscle cell apoptotic process / positive regulation of core promoter binding / neuroinflammatory response / positive regulation of exosomal secretion / positive regulation of killing of cells of another organism / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / positive regulation of MHC class II biosynthetic process / negative regulation of interleukin-17 production / positive regulation of signaling receptor activity / positive regulation of membrane protein ectodomain proteolysis / positive regulation of neurogenesis / negative regulation of epithelial cell differentiation / positive regulation of amyloid-beta formation / IFNG signaling activates MAPKs / positive regulation of epithelial cell migration / positive regulation of nitric-oxide synthase biosynthetic process / cell surface receptor signaling pathway via JAK-STAT / regulation of insulin secretion / humoral immune response / macrophage differentiation / positive regulation of autophagy / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / positive regulation of phagocytosis / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-12 production / positive regulation of glycolytic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / cytokine activity / astrocyte activation / positive regulation of protein localization to plasma membrane / negative regulation of smooth muscle cell proliferation / microglial cell activation / positive regulation of protein-containing complex assembly / response to virus / positive regulation of protein serine/threonine kinase activity / cellular response to virus / positive regulation of protein import into nucleus / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Interferon gamma signaling / positive regulation of nitric oxide biosynthetic process / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interferon gamma / Interferon gamma / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsLandar, A. / Curry, B. / Parker, M.H. / DiGiacomo, R. / Indelicato, S.R. / Walter, M.R.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Design, characterization, and structure of a biologically active single-chain mutant of human IFN-gamma.
Authors: Landar, A. / Curry, B. / Parker, M.H. / DiGiacomo, R. / Indelicato, S.R. / Nagabhushan, T.L. / Rizzi, G. / Walter, M.R.
History
DepositionMar 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity_name_com.name / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq_dif.details
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Interferon gamma
B: Interferon gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0199
Polymers62,3472
Non-polymers6727
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-74 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.380, 111.380, 311.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-502-

SO4

21B-501-

SO4

-
Components

#1: Protein Interferon gamma / IFN-gamma / Immune interferon


Mass: 31173.404 Da / Num. of mol.: 2 / Mutation: H111D, L121F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: T-CELLS, NK CELLS / Gene: IFNG / Production host: Escherichia coli (E. coli) / References: UniProt: P01579
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M NaCitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 63 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMHEPES1drop
35 mMbenzamidine1drop
41.4 Msodium citrate1reservoir
5100 mMHEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 16757 / Num. obs: 16757 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 85 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 10 % / Rmerge(I) obs: 0.6 / Num. unique all: 1659 / % possible all: 100
Reflection
*PLUS
Num. measured all: 182491

-
Processing

Software
NameVersionClassification
CNS0.4refinement
SCALEPACKdata scaling
RefinementResolution: 2.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 808 -RANDOM
Rwork0.246 ---
all0.251 16757 --
obs0.251 16183 95.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.44 Å2-12.381 Å20 Å2
2---1.44 Å20 Å2
3---2.881 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 35 2 4232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008008
X-RAY DIFFRACTIONc_angle_deg1.2289
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.749
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2PARAM.WAT
X-RAY DIFFRACTION3PARAM.SO4
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.749

+
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