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- PDB-1mpv: Structure of bhpBR3, the BAFF-binding loop of BR3 embedded in a b... -

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Basic information

Entry
Database: PDB / ID: 1mpv
TitleStructure of bhpBR3, the BAFF-binding loop of BR3 embedded in a beta-hairpin peptide
ComponentsBLyS Receptor 3
KeywordsPROTEIN BINDING / beta-hairpin
Function / homology
Function and homology information


B cell costimulation / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of B cell proliferation / positive regulation of T cell proliferation / tumor necrosis factor-mediated signaling pathway / T cell costimulation / TNFR2 non-canonical NF-kB pathway / signaling receptor activity / adaptive immune response / external side of plasma membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / Tumor necrosis factor receptor 13C/17
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 13C
Similarity search - Component
MethodSOLUTION NMR / hybrid distance geometry, simulated annealing, restrained molecular dynamics.
AuthorsKayagaki, N. / Yan, M. / Seshasayee, D. / Wang, H. / Lee, W. / French, D.M. / Grewal, I.S. / Cochran, A.G. / Gordon, N.C. / Yin, J. ...Kayagaki, N. / Yan, M. / Seshasayee, D. / Wang, H. / Lee, W. / French, D.M. / Grewal, I.S. / Cochran, A.G. / Gordon, N.C. / Yin, J. / Starovasnik, M.A. / Dixit, V.M.
CitationJournal: Immunity / Year: 2002
Title: BAFF/BLyS receptor 3 binds the B cell survival factor BAFF ligand through a discrete surface loop and promotes processing of NF-kappaB2.
Authors: Kayagaki, N. / Yan, M. / Seshasayee, D. / Wang, H. / Lee, W. / French, D.M. / Grewal, I.S. / Cochran, A.G. / Gordon, N.C. / Yin, J. / Starovasnik, M.A. / Dixit, V.M.
History
DepositionSep 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THIS IS PART OF AN OPTIMIZED BETA-HAIRPIN SCAFFOLD, (SEE RUSSELL, BLANDL, SKELTON, & ...SEQUENCE THIS IS PART OF AN OPTIMIZED BETA-HAIRPIN SCAFFOLD, (SEE RUSSELL, BLANDL, SKELTON, & COCHRAN, "STABILITY OF CYCLIC BETA-HAIRPINS: ASYMMETRIC CONTRIBUTIONS FROM SIDE CHAINS OF A HYDROGEN-BONDED CROSS-STRAND RESIDUE PAIR", J. AMER. CHEM. SOC., IN PRESS.)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BLyS Receptor 3


Theoretical massNumber of molelcules
Total (without water)1,5941
Polymers1,5941
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 / 80structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide BLyS Receptor 3 / Tumor necrosis factor receptor superfamily member 13C / B cell-activating factor receptor / BAFF ...Tumor necrosis factor receptor superfamily member 13C / B cell-activating factor receptor / BAFF receptor / BAFF-R / BLys receptor 3


Mass: 1593.918 Da / Num. of mol.: 1 / Fragment: BR3 loop (residues 26-31) / Source method: obtained synthetically
Details: The Peptide was synthesized chemically with acetylated N-terminus and amidated C-terminus
References: UniProt: Q96RJ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
152COSY-35

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Sample preparation

Details
Solution-IDContentsSolvent system
12.9 mM bhpBR3 peptide92% H2O, 8% D2O, 0.1 mM DSS, pH 4.5
22.9 mM bhpBR3 peptide100% D2O, 0.1 mM DSS, pH 4.5
Sample conditionsIonic strength: no added salt / pH: 4.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.37.4.2Brukercollection
Felix98Accelrysdata analysis
DGII98Accelrysstructure solution
Discover98Accelrysrefinement
RefinementMethod: hybrid distance geometry, simulated annealing, restrained molecular dynamics.
Software ordinal: 1
Details: Complete 1H resonance assignments were obtained using standard 2D homonuclear NMR methods. Distance restraints were derived from analysis of a 2D NOESY spectrum (250ms mixing time); HN-Ha ...Details: Complete 1H resonance assignments were obtained using standard 2D homonuclear NMR methods. Distance restraints were derived from analysis of a 2D NOESY spectrum (250ms mixing time); HN-Ha coupling constants were obtained from analysis of a DQF-COSY spectrum acquired in water; and HaHb values were obtained from analysis of a COSY-35 spectrum acquired in D2O. Structures were calculated from a total of 119 NOE-derived (including 46 long-range) distance restraints and 16 dihedral angle restraints. Structures satisfy the experimental data very well with no distance or dihedral angle violations greater than 0.1 angstrom or 1 degree, respectively.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

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