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- PDB-5uc6: Structural insights into IL-1 alpha recognition by a naphthyl-mod... -

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Basic information

Entry
Database: PDB / ID: 5uc6
TitleStructural insights into IL-1 alpha recognition by a naphthyl-modified aptamer that mimics IL-1RI Domain III
Components
  • DNA (5'-D(*CP*G)-R(P*(85Y))-D(P*GP*AP*G)-R(P*(85Y)P*(85Y))-D(P*A)-R(P*(85Y))-D(P*GP*GP*G)-R(P*(85Y)P*(85Y))-D(P*AP*GP*AP*G)-R(P*(85Y))-D(P*CP*GP*(ATD))-3')
  • Interleukin-1 alpha
KeywordsIMMUNE SYSTEM/DNA / SOMAmer / IMMUNE SYSTEM-DNA complex
Function / homology
Function and homology information


negative regulation of establishment of Sertoli cell barrier / positive regulation of neutrophil migration / positive regulation of steroid biosynthetic process / connective tissue replacement involved in inflammatory response wound healing / response to L-ascorbic acid / response to ozone / positive regulation of stress-activated MAPK cascade / positive regulation of immature T cell proliferation in thymus / positive regulation of prostaglandin secretion / fever generation ...negative regulation of establishment of Sertoli cell barrier / positive regulation of neutrophil migration / positive regulation of steroid biosynthetic process / connective tissue replacement involved in inflammatory response wound healing / response to L-ascorbic acid / response to ozone / positive regulation of stress-activated MAPK cascade / positive regulation of immature T cell proliferation in thymus / positive regulation of prostaglandin secretion / fever generation / intracellular sodium ion homeostasis / Interleukin-1 processing / interleukin-1 receptor binding / response to copper ion / : / keratinization / Interleukin-10 signaling / positive regulation of cell division / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular endothelial growth factor production / ectopic germ cell programmed cell death / Pyroptosis / Purinergic signaling in leishmaniasis infection / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / positive regulation of cytokine production / cytokine activity / positive regulation of protein secretion / response to gamma radiation / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / Interleukin-1 signaling / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / heart development / cellular response to heat / Senescence-Associated Secretory Phenotype (SASP) / cellular response to lipopolysaccharide / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / inflammatory response / immune response / copper ion binding / negative regulation of cell population proliferation / positive regulation of gene expression / apoptotic process / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleus / cytosol
Similarity search - Function
Interleukin-1 alpha / Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 ...Interleukin-1 alpha / Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Interleukin-1 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRen, X. / Pyle, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for IL-1 alpha recognition by a modified DNA aptamer that specifically inhibits IL-1 alpha signaling.
Authors: Ren, X. / Gelinas, A.D. / von Carlowitz, I. / Janjic, N. / Pyle, A.M.
History
DepositionDec 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2017Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.0Aug 22, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 alpha
B: DNA (5'-D(*CP*G)-R(P*(85Y))-D(P*GP*AP*G)-R(P*(85Y)P*(85Y))-D(P*A)-R(P*(85Y))-D(P*GP*GP*G)-R(P*(85Y)P*(85Y))-D(P*AP*GP*AP*G)-R(P*(85Y))-D(P*CP*GP*(ATD))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6478
Polymers26,4312
Non-polymers2156
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-31 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.790, 74.790, 86.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-375-

HOH

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein Interleukin-1 alpha / IL-1 alpha / Hematopoietin-1


Mass: 18064.486 Da / Num. of mol.: 1 / Fragment: residues 113-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1A, IL1F1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01583
#2: DNA chain DNA (5'-D(*CP*G)-R(P*(85Y))-D(P*GP*AP*G)-R(P*(85Y)P*(85Y))-D(P*A)-R(P*(85Y))-D(P*GP*GP*G)-R(P*(85Y)P*(85Y))-D(P*AP*GP*AP*G)-R(P*(85Y))-D(P*CP*GP*(ATD))-3')


Mass: 8366.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 151 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.2 M NaCl, 0.1 M Na acetate, and 22% polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.1→64.77 Å / Num. obs: 16642 / % possible obs: 99.5 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ILA

2ila


Resolution: 2.1→64.77 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 787 4.73 %RANDOM
Rwork0.1776 ---
obs0.1794 16627 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→64.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 548 9 145 1916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071863
X-RAY DIFFRACTIONf_angle_d1.3442581
X-RAY DIFFRACTIONf_dihedral_angle_d20.686966
X-RAY DIFFRACTIONf_chiral_restr0.097279
X-RAY DIFFRACTIONf_plane_restr0.006244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.23160.26481300.21442626X-RAY DIFFRACTION100
2.2316-2.40390.27621200.22782625X-RAY DIFFRACTION100
2.4039-2.64580.27071320.2172598X-RAY DIFFRACTION100
2.6458-3.02870.23141640.21062601X-RAY DIFFRACTION99
3.0287-3.81580.18531230.16482658X-RAY DIFFRACTION99
3.8158-64.80060.20091180.14972732X-RAY DIFFRACTION97

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