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- PDB-2n0x: Three dimensional structure of EPI-X4, a human albumin-derived pe... -

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Basic information

Entry
Database: PDB / ID: 2n0x
TitleThree dimensional structure of EPI-X4, a human albumin-derived peptide that regulates innate immunity through the CXCR4/CXCL12 chemotactic axis and antagonizes HIV-1 entry
ComponentsSerum albumin
KeywordsPEPTIDE BINDING PROTEIN / antagonist / inhibitor peptide
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model1
AuthorsPerez-Castells, J. / Canales, A. / Jimenez-Barbero, J. / Gimenez-Gallego, G.
CitationJournal: Cell Rep / Year: 2015
Title: Discovery and characterization of an endogenous CXCR4 antagonist.
Authors: Zirafi, O. / Kim, K.A. / Standker, L. / Mohr, K.B. / Sauter, D. / Heigele, A. / Kluge, S.F. / Wiercinska, E. / Chudziak, D. / Richter, R. / Moepps, B. / Gierschik, P. / Vas, V. / Geiger, H. ...Authors: Zirafi, O. / Kim, K.A. / Standker, L. / Mohr, K.B. / Sauter, D. / Heigele, A. / Kluge, S.F. / Wiercinska, E. / Chudziak, D. / Richter, R. / Moepps, B. / Gierschik, P. / Vas, V. / Geiger, H. / Lamla, M. / Weil, T. / Burster, T. / Zgraja, A. / Daubeuf, F. / Frossard, N. / Hachet-Haas, M. / Heunisch, F. / Reichetzeder, C. / Galzi, J.L. / Perez-Castells, J. / Canales-Mayordomo, A. / Jimenez-Barbero, J. / Gimenez-Gallego, G. / Schneider, M. / Shorter, J. / Telenti, A. / Hocher, B. / Forssmann, W.G. / Bonig, H. / Kirchhoff, F. / Munch, J.
History
DepositionMar 18, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin


Theoretical massNumber of molelcules
Total (without water)1,8331
Polymers1,8331
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)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Serum albumin /


Mass: 1833.198 Da / Num. of mol.: 1 / Fragment: Albumin 3 domain residues 432-447 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 10 mM sodium phosphate, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 10 mM / Component: sodium phosphate-1
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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