[English] 日本語
Yorodumi
- PDB-1lqs: CRYSTAL STRUCTURE OF HUMAN CYTOMEGALOVIRUS IL-10 BOUND TO SOLUBLE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lqs
TitleCRYSTAL STRUCTURE OF HUMAN CYTOMEGALOVIRUS IL-10 BOUND TO SOLUBLE HUMAN IL-10R1
Components
  • INTERLEUKIN-10 RECEPTOR ALPHA CHAIN
  • INTERLEUKIN-10-LIKE PROTEIN
KeywordsIMMUNE SYSTEM / interleukin 10 / helix bundle / receptor complex / molecular recognition / structure mimic
Function / homology
Function and homology information


symbiont-mediated suppression of host dendritic cell mediated immune response / interleukin-10 binding / interleukin-10 receptor activity / interleukin-10-mediated signaling pathway / intestinal epithelial structure maintenance / ubiquitin-dependent endocytosis / regulation of synapse organization / Interleukin-10 signaling / Nuclear events stimulated by ALK signaling in cancer / negative regulation of autophagy ...symbiont-mediated suppression of host dendritic cell mediated immune response / interleukin-10 binding / interleukin-10 receptor activity / interleukin-10-mediated signaling pathway / intestinal epithelial structure maintenance / ubiquitin-dependent endocytosis / regulation of synapse organization / Interleukin-10 signaling / Nuclear events stimulated by ALK signaling in cancer / negative regulation of autophagy / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / negative regulation of inflammatory response / cytokine-mediated signaling pathway / signaling receptor activity / response to lipopolysaccharide / apical plasma membrane / cilium / symbiont-mediated suppression of host innate immune response / immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / extracellular space / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Interleukin-10; domain 2 / Interleukin-10, domain 2 / Interleukin-10, additional helical / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / : / Tissue factor ...Interleukin-10; domain 2 / Interleukin-10, domain 2 / Interleukin-10, additional helical / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III / Fibronectin type III superfamily / Few Secondary Structures / Irregular / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Viral interleukin-10 homolog / Interleukin-10 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 5
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJones, B.C. / Logsdon, N.J. / Josephson, K. / Cook, J. / Barry, P.A. / Walter, M.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of human cytomegalovirus IL-10 bound to soluble human IL-10R1.
Authors: Jones, B.C. / Logsdon, N.J. / Josephson, K. / Cook, J. / Barry, P.A. / Walter, M.R.
History
DepositionMay 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: INTERLEUKIN-10 RECEPTOR ALPHA CHAIN
S: INTERLEUKIN-10 RECEPTOR ALPHA CHAIN
L: INTERLEUKIN-10-LIKE PROTEIN
M: INTERLEUKIN-10-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7396
Polymers85,2964
Non-polymers4422
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.290, 104.680, 91.890
Angle α, β, γ (deg.)90.00, 106.49, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein INTERLEUKIN-10 RECEPTOR ALPHA CHAIN / IL-10R-A / IL-10R1


Mass: 24506.551 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 22-235 / Mutation: N29Q,N53Q,N89Q,N133Q,N156Q,N168Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pmtv5his / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q13651
#2: Protein INTERLEUKIN-10-LIKE PROTEIN


Mass: 18141.646 Da / Num. of mol.: 2 / Fragment: RESIDUES 20-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 / Genus: Cytomegalovirus / Plasmid: pmtv5his / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P17150
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG-6000, 0.1M MgCl2, 100mM ADA, 0.75% PEG-400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris1droppH8.0
3100 mMADA buffer1reservoirpH6.0
46 %PEG60001reservoir
50.1 M1reservoirMgCl2
60.75 %PEG4001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 30, 2001 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 26564 / Num. obs: 26049 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.195 / % possible all: 0.74
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 26564 / % possible obs: 92.5 % / Redundancy: 2.8 % / Num. measured all: 65855 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 73.7 %

-
Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J7V

1j7v


Resolution: 2.7→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.294 1322 random
Rwork0.244 --
all-26564 -
obs-26049 -
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5623 0 28 48 5699
LS refinement shellResolution: 2.7→2.8 Å
RfactorNum. reflection% reflection
Rfree0.426 101 -
Rwork0.375 --
obs-1908 0.67 %
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 24727 / % reflection Rfree: 5 % / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.35

+
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