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- PDB-2l7u: Structure of CEL-PEP-RAGE V domain complex -

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Basic information

Entry
Database: PDB / ID: 2l7u
TitleStructure of CEL-PEP-RAGE V domain complex
Components
  • Advanced glycosylation end product-specific receptor
  • Serum albumin peptide
KeywordsALLERGEN / V domain / Cleavage on pair of basic residues / Lipid-binding / Metal-binding / Phosphoprotein / Secreted
Function / homology
Function and homology information


regulation of CD4-positive, alpha-beta T cell activation / advanced glycation end-product receptor activity / negative regulation of blood circulation / regulation of T cell mediated cytotoxicity / positive regulation of endothelin production / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of dendritic cell differentiation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process ...regulation of CD4-positive, alpha-beta T cell activation / advanced glycation end-product receptor activity / negative regulation of blood circulation / regulation of T cell mediated cytotoxicity / positive regulation of endothelin production / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of dendritic cell differentiation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / scavenger receptor activity / induction of positive chemotaxis / cellular response to calcium ion starvation / transcytosis / laminin receptor activity / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / enterobactin binding / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / negative regulation of mitochondrial depolarization / positive regulation of heterotypic cell-cell adhesion / positive regulation of p38MAPK cascade / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / response to amyloid-beta / Advanced glycosylation endproduct receptor signaling / transport across blood-brain barrier / toxic substance binding / positive regulation of chemokine production / cellular response to starvation / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / fatty acid binding / astrocyte activation / microglial cell activation / positive regulation of JNK cascade / regulation of synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / fibrillar center / response to wounding / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / neuron projection development / cellular response to amyloid-beta / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / pyridoxal phosphate binding / signaling receptor activity / cell junction / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / postsynapse / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / learning or memory / cell surface receptor signaling pathway / molecular adaptor activity / inflammatory response / positive regulation of protein phosphorylation / apical plasma membrane / protein-containing complex binding / cell surface / protein-containing complex / DNA binding / extracellular space / extracellular region / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Albumin / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsXue, J. / Rai, V. / Schmidt, A. / Frolov, S. / Reverdatto, S. / Singer, D. / Chabierski, S. / Xie, J. / Burz, D. / Shekhtman, A. / Hoffman, R.
CitationJournal: Structure / Year: 2011
Title: Advanced glycation end product recognition by the receptor for AGEs.
Authors: Xue, J. / Rai, V. / Singer, D. / Chabierski, S. / Xie, J. / Reverdatto, S. / Burz, D.S. / Schmidt, A.M. / Hoffmann, R. / Shekhtman, A.
History
DepositionDec 23, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 2.0May 30, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.label_comp_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_torsion.auth_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 3.0Nov 29, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Advanced glycosylation end product-specific receptor
B: Serum albumin peptide


Theoretical massNumber of molelcules
Total (without water)12,4942
Polymers12,4942
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Advanced glycosylation end product-specific receptor / Receptor for advanced glycosylation end products


Mass: 11571.323 Da / Num. of mol.: 1 / Fragment: Ig-like V-type domain residues 23-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli (E. coli) / References: UniProt: Q15109
#2: Protein/peptide Serum albumin peptide / BSA


Mass: 922.889 Da / Num. of mol.: 1 / Fragment: Sequence database residues 148-154 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P02769

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D HN(CA)CO
11023D 1H-15N NOESY
11123D 1H-13C NOESY
11223D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1 mM [U-100% 13C; U-100% 15N] V domain, 0.3 mM CEL-PEP, 90% H2O/10% D2O90% H2O/10% D2O
20.32 mM [U-100% 13C; U-100% 15N] V domain, 1 mM CEL-PEP, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 mMV domain-1[U-100% 13C; U-100% 15N]1
0.3 mMCEL-PEP-21
0.32 mMV domain-3[U-100% 13C; U-100% 15N]2
1 mMCEL-PEP-42
Sample conditionsIonic strength: 130 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CARABartels et al.chemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1027 / NOE intraresidue total count: 328 / NOE long range total count: 0 / NOE medium range total count: 323 / NOE sequential total count: 375 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 79 / Protein psi angle constraints total count: 71
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.54 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 25 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 4 ° / Maximum upper distance constraint violation: 0.17 Å / Torsion angle constraint violation method: CYANA
NMR ensemble rmsDistance rms dev: 0.015 Å / Distance rms dev error: 0.005 Å

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