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- PDB-1lk3: ENGINEERED HUMAN INTERLEUKIN-10 MONOMER COMPLEXED TO 9D7 FAB FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1lk3
TitleENGINEERED HUMAN INTERLEUKIN-10 MONOMER COMPLEXED TO 9D7 FAB FRAGMENT
Components
  • 9D7 Heavy Chain
  • 9D7 Light Chain
  • Interleukin-10
KeywordsIMMUNE SYSTEM / ANTIGEN-ANTIBODY COMPLEX
Function / homology
Function and homology information


Classical antibody-mediated complement activation / FCGR activation / Regulation of Complement cascade / interleukin-10 receptor complex / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of interleukin-18 production / Role of phospholipids in phagocytosis / positive regulation of B cell apoptotic process / regulation of B cell activation ...Classical antibody-mediated complement activation / FCGR activation / Regulation of Complement cascade / interleukin-10 receptor complex / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of interleukin-18 production / Role of phospholipids in phagocytosis / positive regulation of B cell apoptotic process / regulation of B cell activation / negative regulation of interferon-alpha production / negative regulation of cytokine activity / negative regulation of chemokine (C-C motif) ligand 5 production / response to inactivity / negative regulation of membrane protein ectodomain proteolysis / endothelial cell apoptotic process / Regulation of actin dynamics for phagocytic cup formation / positive regulation of plasma cell differentiation / regulation of isotype switching / positive regulation of type IIa hypersensitivity / negative regulation of heterotypic cell-cell adhesion / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / negative regulation of cytokine production involved in immune response / negative regulation of MHC class II biosynthetic process / negative regulation of B cell proliferation / negative regulation of interleukin-1 production / interleukin-10-mediated signaling pathway / negative regulation of interleukin-12 production / complement-dependent cytotoxicity / negative regulation of mitotic cell cycle / negative regulation of interleukin-8 production / negative regulation of nitric oxide biosynthetic process / response to carbon monoxide / positive regulation of type I hypersensitivity / positive regulation of macrophage activation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / positive regulation of heterotypic cell-cell adhesion / B cell proliferation / type 2 immune response / alpha-beta T cell receptor complex / negative regulation of cytokine production / leukocyte chemotaxis / immunoglobulin complex, circulating / phagocytosis, engulfment / CD163 mediating an anti-inflammatory response / response to molecule of bacterial origin / immunoglobulin receptor binding / T-helper 1 cell differentiation / immunoglobulin mediated immune response / positive regulation of immunoglobulin production / negative regulation of interleukin-6 production / positive regulation of tyrosine phosphorylation of STAT protein / complement activation, classical pathway / positive regulation of sprouting angiogenesis / hemopoiesis / Interleukin-10 signaling / regulation of synapse organization / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of tumor necrosis factor production / negative regulation of T cell proliferation / liver regeneration / antigen binding / positive regulation of vascular associated smooth muscle cell proliferation / cell surface receptor signaling pathway via JAK-STAT / B cell differentiation / positive regulation of endothelial cell proliferation / positive regulation of cell cycle / positive regulation of phagocytosis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / FCGR3A-mediated IL10 synthesis / response to glucocorticoid / negative regulation of autophagy / cytokine activity / response to activity / positive regulation of receptor signaling pathway via JAK-STAT / response to insulin / growth factor activity / positive regulation of cytokine production / cellular response to estradiol stimulus / negative regulation of inflammatory response / positive regulation of miRNA transcription / positive regulation of immune response / cytokine-mediated signaling pathway / regulation of gene expression / adaptive immune response / Signaling by ALK fusions and activated point mutants / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / antibacterial humoral response / defense response to bacterium / protein dimerization activity / response to xenobiotic stimulus / immune response / negative regulation of cell population proliferation / external side of plasma membrane / positive regulation of cell population proliferation / negative regulation of apoptotic process
Similarity search - Function
Interleukin-10 / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / : ...Interleukin-10 / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ig kappa chain C region, B allele / Ig gamma-1 chain C region / Interleukin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsJosephson, K. / Jones, B.C. / Walter, L.J. / DiGiacomo, R. / Indelicato, S.R. / Walter, M.R.
Citation
Journal: Structure / Year: 2002
Title: Noncompetitive antibody neutralization of IL-10 revealed by protein engineering and x-ray crystallography.
Authors: Josephson, K. / Jones, B.C. / Walter, L.J. / DiGiacomo, R. / Indelicato, S.R. / Walter, M.R.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Design and Analysis of an Engineered Human Interleukin-10 Monomer
Authors: Josephson, K. / DiGiacomo, R. / Indelicato, S.R. / Iyo, A.H. / Nagabhushan, T.L. / Parker, M.H. / Walter, M.R. / Ayo, A.H.
History
DepositionApr 23, 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: Version format compliance
Revision 1.3Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details
Remark 999SEQUENCE USING BLAST NO APPROPRIATE SEQUENCE DATABASE MATCH WAS FOUND FOR 9D7 LIGHT CHAIN, CHAINS ...SEQUENCE USING BLAST NO APPROPRIATE SEQUENCE DATABASE MATCH WAS FOUND FOR 9D7 LIGHT CHAIN, CHAINS L,M AND 9D7 HEAVY CHAIN, CHAINS H,I.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-10
L: 9D7 Light Chain
H: 9D7 Heavy Chain
B: Interleukin-10
M: 9D7 Light Chain
I: 9D7 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)129,6886
Polymers129,6886
Non-polymers00
Water21,6721203
1
A: Interleukin-10
L: 9D7 Light Chain
H: 9D7 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)64,8443
Polymers64,8443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-10
M: 9D7 Light Chain
I: 9D7 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)64,8443
Polymers64,8443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.554, 75.616, 111.975
Angle α, β, γ (deg.)90.00, 96.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interleukin-10 / IL-10M1 (Engineered monomer of human Interleukin-10) / IL-10 / Cytokine synthesis inhibitory factor / CSIF


Mass: 18520.324 Da / Num. of mol.: 2 / Fragment: Residues 26-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL10 / Plasmid: pET32lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22301
#2: Antibody 9D7 Light Chain


Mass: 22794.438 Da / Num. of mol.: 2 / Fragment: Fab fragment, Residues 1-210 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P01835*PLUS
#3: Antibody 9D7 Heavy Chain


Mass: 23529.443 Da / Num. of mol.: 2 / Fragment: Fab fragment, Residues 1-219 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P20759*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1203 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: peg 4000, sodium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)
110 mg/mlprotein1drop
28 %PEG40001drop
30.1 Msodium acetate1droppH4.6
412-14 %PEG40001reservoir
50.1 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1999
RadiationMonochromator: Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 96708 / Num. obs: 96708 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 23.11 Å2 / Rsym value: 0.049 / Net I/σ(I): 10.5
Reflection shellResolution: 1.91→1.95 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.34 / % possible all: 72.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 357669 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 72.6 % / Rmerge(I) obs: 0.34

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2401 1397 RANDOM
Rwork0.1872 --
all0.1872 96708 -
obs0.1872 96708 -
Refinement stepCycle: LAST / Resolution: 1.91→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8770 0 0 1203 9973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.59
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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