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- PDB-4j4l: Modular evolution and design of the protein binding interface -

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Basic information

Entry
Database: PDB / ID: 4j4l
TitleModular evolution and design of the protein binding interface
Components
  • Interleukin-6
  • Internalin B,REPEAT MODULES,Variable lymphocyte receptor B
KeywordsPROTEIN BINDING/CYTOKINE / LRR / IL-6 binding / Interleukin 6 / extracellular matrix / PROTEIN BINDING-CYTOKINE complex
Function / homology
Function and homology information


regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / germinal center B cell differentiation / interleukin-6 receptor complex ...regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / germinal center B cell differentiation / interleukin-6 receptor complex / positive regulation of apoptotic DNA fragmentation / positive regulation of type B pancreatic cell apoptotic process / hepatocyte proliferation / positive regulation of extracellular matrix disassembly / regulation of microglial cell activation / response to peptidoglycan / neutrophil apoptotic process / interleukin-6 receptor binding / positive regulation of B cell activation / positive regulation of receptor signaling pathway via STAT / T-helper 17 cell lineage commitment / inflammatory response to wounding / positive regulation of T-helper 2 cell cytokine production / negative regulation of collagen biosynthetic process / endocrine pancreas development / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / positive regulation of neuroinflammatory response / T follicular helper cell differentiation / negative regulation of chemokine production / positive regulation of leukocyte chemotaxis / neutrophil mediated immunity / positive regulation of platelet aggregation / positive regulation of cytokine production involved in inflammatory response / cell surface receptor signaling pathway via STAT / positive regulation of synapse assembly / cell envelope / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / Interleukin-6 signaling / positive regulation of immunoglobulin production / positive regulation of peptidyl-tyrosine phosphorylation / MAPK3 (ERK1) activation / interleukin-6-mediated signaling pathway / maintenance of blood-brain barrier / negative regulation of fat cell differentiation / MAPK1 (ERK2) activation / Interleukin-10 signaling / positive regulation of interleukin-17 production / monocyte chemotaxis / humoral immune response / positive regulation of interleukin-10 production / Transcriptional Regulation by VENTX / negative regulation of lipid storage / positive regulation of vascular endothelial growth factor production / cell surface receptor signaling pathway via JAK-STAT / regulation of angiogenesis / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / response to glucocorticoid / positive regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of peptidyl-serine phosphorylation / positive regulation of glial cell proliferation / regulation of insulin secretion / axonogenesis / positive regulation of DNA-binding transcription factor activity / liver regeneration / positive regulation of interleukin-1 beta production / positive regulation of translation / cytokine activity / acute-phase response / response to activity / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / growth factor activity / cytokine-mediated signaling pathway / cellular response to virus / positive regulation of miRNA transcription / platelet activation / negative regulation of neurogenesis / positive regulation of interleukin-6 production / cellular response to hydrogen peroxide / neuron cellular homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of tumor necrosis factor production / ADORA2B mediated anti-inflammatory cytokines production / glucose homeostasis / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / defense response to virus / positive regulation of MAPK cascade / defense response to Gram-positive bacterium
Similarity search - Function
Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. ...Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Variable lymphocyte receptor, C-terminal / Internalin, N-terminal / Domain of unknown function (DUF3439) / Bacterial adhesion/invasion protein N terminal / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Growth Hormone; Chain: A; - #10 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Internalin B / Interleukin-6 / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
synthetic construct (others)
Eptatretus burgeri (inshore hagfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCheong, H.K. / Kim, H.J.
CitationJournal: To be Published
Title: Modular evolution and design of the protein binding interface
Authors: Lee, J. / Kim, H.J. / Yang, C. / Choi, J. / Kyeong, H. / Yuk, J. / Park, K. / Kim, Y.J. / Heu, W. / Lee, S. / Kim, D. / Jo, E.K. / Cheong, H.K. / Kim, H.S.
History
DepositionFeb 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references / Source and taxonomy
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Internalin B,REPEAT MODULES,Variable lymphocyte receptor B
B: Internalin B,REPEAT MODULES,Variable lymphocyte receptor B
C: Interleukin-6
D: Interleukin-6


Theoretical massNumber of molelcules
Total (without water)98,5124
Polymers98,5124
Non-polymers00
Water2,846158
1
A: Internalin B,REPEAT MODULES,Variable lymphocyte receptor B
C: Interleukin-6


Theoretical massNumber of molelcules
Total (without water)49,2562
Polymers49,2562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Internalin B,REPEAT MODULES,Variable lymphocyte receptor B
D: Interleukin-6


Theoretical massNumber of molelcules
Total (without water)49,2562
Polymers49,2562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.319, 134.001, 148.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Internalin B,REPEAT MODULES,Variable lymphocyte receptor B


Mass: 30059.117 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 43-100,UNP RESIDUES 141-232
Source method: isolated from a genetically manipulated source
Details: CHIMERA OF RESIDUES 43-100 FROM INTERNALIN B, REPEAT MODULES, RESIDUES 141-232 FROM VARIABLE LYMPHOCYTE RECEPTOR B, AND 8 HIS TAGS
Source: (gene. exp.) Listeria monocytogenes (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: VLRB / Production host: Escherichia coli (E. coli) / References: UniProt: A4L9V2, UniProt: Q4G1L3
#2: Protein Interleukin-6 / IL-6 / B-cell stimulatory factor 2 / BSF-2 / CTL differentiation factor / CDF / Hybridoma growth ...IL-6 / B-cell stimulatory factor 2 / BSF-2 / CTL differentiation factor / CDF / Hybridoma growth factor / Interferon beta-2 / IFN-beta-2


Mass: 19196.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6, IFNB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P05231
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE 101-209 REPRESENTS CONSENSUS DESIGNED REPEAT MODULES. THE SEQUENCES OF REPEAT MODULES ...THE RESIDUE 101-209 REPRESENTS CONSENSUS DESIGNED REPEAT MODULES. THE SEQUENCES OF REPEAT MODULES IS BASED ON VARIABLE LYMPHOCYTE.

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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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 8
Details: 0.1M magnesium formate, 15-18% w/v polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→61.09 Å / Num. all: 40127 / Num. obs: 38083 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.36 Å / % possible all: 78.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ALU

1alu


Resolution: 2.3→61.09 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.885 / SU B: 8.243 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26843 2017 5 %RANDOM
Rwork0.20455 ---
all0.20775 40127 --
obs-38083 95.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→61.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6593 0 0 158 6751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.026706
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9759074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.64725.922309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.692151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9511528
X-RAY DIFFRACTIONr_chiral_restr0.1240.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214934
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 99 -
Rwork0.272 1922 -
obs--69.14 %

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