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- PDB-2g2b: NMR structure of the human allograft inflammatory factor 1 -

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Basic information

Entry
Database: PDB / ID: 2g2b
TitleNMR structure of the human allograft inflammatory factor 1
ComponentsAllograft inflammatory factor 1
KeywordsIMMUNE SYSTEM / AIF-1 / Allograft Inflammatory Factor 1 / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


negative regulation of smooth muscle cell chemotaxis / positive regulation of smooth muscle cell chemotaxis / parallel actin filament bundle assembly / positive regulation of fibroblast growth factor production / actin crosslink formation / ruffle assembly / positive regulation of mononuclear cell migration / positive regulation of chemotaxis / positive regulation of monocyte chemotaxis / phagocytosis, engulfment ...negative regulation of smooth muscle cell chemotaxis / positive regulation of smooth muscle cell chemotaxis / parallel actin filament bundle assembly / positive regulation of fibroblast growth factor production / actin crosslink formation / ruffle assembly / positive regulation of mononuclear cell migration / positive regulation of chemotaxis / positive regulation of monocyte chemotaxis / phagocytosis, engulfment / Rac protein signal transduction / actin filament bundle assembly / glial cell projection / phagocytic cup / positive regulation of T cell migration / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of chemokine production / positive regulation of T cell proliferation / ruffle / actin filament polymerization / actin filament / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / microglial cell activation / cellular response to type II interferon / ruffle membrane / positive regulation of interleukin-6 production / actin filament binding / lamellipodium / cellular response to oxidative stress / regulation of gene expression / positive regulation of cell migration / inflammatory response / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Allograft inflammatory factor 1 / : / Allograft inflammatory factor 1 / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Allograft inflammatory factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics,simulated annealing,distance geometry
AuthorsSong, J. / Tyler, R.C. / Newman, C.L. / Vinarov, D. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: NMR structure of the human allograft inflammatory factor 1
Authors: Song, J. / Tyler, R.C. / Newman, C.L. / Vinarov, D. / Markley, J.L.
History
DepositionFeb 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Allograft inflammatory factor 1


Theoretical massNumber of molelcules
Total (without water)16,9951
Polymers16,9951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Allograft inflammatory factor 1 / AIF-1 / Ionized calcium-binding adapter molecule 1 / G1 protein


Mass: 16994.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: AIF1, G1, IBA1 / Plasmid: pEU-HIS / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P55008

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H,15N-HSQC
1211H,13C-HSQC
131HN(CA)CB
1411H,13C-HSQC
151CBCA(CO)NH
161C(CO)NH
171HCCHTOCSY
181HBACONH
19113C-EDITED 1H,1H-NOESY
110115N-EDITED 1H,1H-NOESY

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Sample preparation

DetailsContents: 10 mM MOPS,100mM NaCl, 5 mM DTT, 0.7 mM 13C,15N-LABELED AIF1_HUMAN
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Varian INOVAVarianINOVA6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionDeveloperClassification
VNMR1.1Varian Inc.collection
XWIN3.5Brukercollection
NMRPipe97.027.12.56Delagio,F. et al.processing
Sparky3.72Goddard TD and Kneller, DG.data analysis
CYANA2.1Guntert, P.structural calculation
Xplor-NIH2.9.3SCHWIETERS, KUSZEWSKI, TJANDRA, CLORErefinement
RefinementMethod: torsion angle dynamics,simulated annealing,distance geometry
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 2152 NOE RESTRAINTS (797 INTRA, 462 SEQUENTIAL, 431 MEDIUM, AND 381 LONG RANGE INTERMOLECULR), 81 HBOND RESTRAINTS, AND 162 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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