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- PDB-1lqs: CRYSTAL STRUCTURE OF HUMAN CYTOMEGALOVIRUS IL-10 BOUND TO SOLUBLE... -

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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 / ubiquitin-dependent endocytosis / intestinal epithelial structure maintenance / interleukin-10-mediated signaling pathway / 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 / ubiquitin-dependent endocytosis / intestinal epithelial structure maintenance / interleukin-10-mediated signaling pathway / 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 / cytokine-mediated signaling pathway / negative regulation of inflammatory response / signaling receptor activity / response to lipopolysaccharide / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / immune response / apical plasma membrane / extracellular space / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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 %

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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

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