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- PDB-1osg: Complex between BAFF and a BR3 derived peptide presented in a bet... -

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Basic information

Entry
Database: PDB / ID: 1osg
TitleComplex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold
Components
  • BR3 derived PEPTIDE
  • Tumor necrosis factor ligand superfamily member 13B
KeywordsIMMUNE SYSTEM / jelly-roll / beta hairpin / protein-peptide complex
Function / homology
Function and homology information


positive regulation of germinal center formation / B cell costimulation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / germinal center formation / tumor necrosis factor receptor binding / skin development / B cell proliferation / B cell homeostasis ...positive regulation of germinal center formation / B cell costimulation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / germinal center formation / tumor necrosis factor receptor binding / skin development / B cell proliferation / B cell homeostasis / T cell proliferation / positive regulation of T cell proliferation / positive regulation of B cell proliferation / tumor necrosis factor-mediated signaling pathway / T cell costimulation / cytokine activity / TNFR2 non-canonical NF-kB pathway / receptor ligand activity / intracellular membrane-bounded organelle / focal adhesion / signaling receptor binding / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGordon, N.C. / Pan, B. / Hymowitz, S.G. / Yin, J.P. / Kelley, R.F. / Cochran, A.G. / Yan, M. / Dixit, V.M. / Fairbrother, W.J. / Starovasnik, M.A.
CitationJournal: Biochemistry / Year: 2003
Title: BAFF/BLyS receptor 3 comprises a minimal TNF receptor-like module that encodes a highly focused ligand-binding site
Authors: Gordon, N.C. / Pan, B. / Hymowitz, S.G. / Yin, J.P. / Kelley, R.F. / Cochran, A.G. / Yan, M. / Dixit, V.M. / Fairbrother, W.J. / Starovasnik, M.A.
History
DepositionMar 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
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.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999an appropriate sequence database reference was not available for the BR3 derived PEPTIDE at the ...an appropriate sequence database reference was not available for the BR3 derived PEPTIDE at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 13B
B: Tumor necrosis factor ligand superfamily member 13B
C: Tumor necrosis factor ligand superfamily member 13B
D: Tumor necrosis factor ligand superfamily member 13B
E: Tumor necrosis factor ligand superfamily member 13B
F: Tumor necrosis factor ligand superfamily member 13B
G: BR3 derived PEPTIDE
J: BR3 derived PEPTIDE
H: BR3 derived PEPTIDE
I: BR3 derived PEPTIDE
K: BR3 derived PEPTIDE
L: BR3 derived PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,99716
Polymers145,90012
Non-polymers974
Water36020
1
A: Tumor necrosis factor ligand superfamily member 13B
B: Tumor necrosis factor ligand superfamily member 13B
C: Tumor necrosis factor ligand superfamily member 13B
G: BR3 derived PEPTIDE
H: BR3 derived PEPTIDE
I: BR3 derived PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9998
Polymers72,9506
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Tumor necrosis factor ligand superfamily member 13B
E: Tumor necrosis factor ligand superfamily member 13B
F: Tumor necrosis factor ligand superfamily member 13B
J: BR3 derived PEPTIDE
K: BR3 derived PEPTIDE
L: BR3 derived PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9998
Polymers72,9506
Non-polymers492
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.633, 121.633, 157.214
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F
12G
22H
32I
42J
52K
62L

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALARGARGAA142 - 21465 - 137
211VALVALARGARGBB142 - 21465 - 137
311VALVALARGARGCC142 - 21465 - 137
411VALVALARGARGDD142 - 21465 - 137
511VALVALARGARGEE142 - 21465 - 137
611VALVALARGARGFF142 - 21465 - 137
721VALVALLEULEUAA227 - 285150 - 208
821VALVALLEULEUBB227 - 285150 - 208
921VALVALLEULEUCC227 - 285150 - 208
1021VALVALLEULEUDD227 - 285150 - 208
1121VALVALLEULEUEE227 - 285150 - 208
1221VALVALLEULEUFF227 - 285150 - 208
112CYSCYSCYSCYSGG23 - 341 - 12
212CYSCYSCYSCYSHI23 - 341 - 12
312CYSCYSCYSCYSIJ23 - 341 - 12
412CYSCYSCYSCYSJH23 - 341 - 12
512CYSCYSCYSCYSKK23 - 341 - 12
612CYSCYSCYSCYSLL23 - 341 - 12

NCS ensembles :
ID
1
2
DetailsThe biologically relevant assembly of BAFF is a trimer. The crystallographic asymetric unit contains 2 trimers. / The biologically relevant unit of BR3 is a monomer. Three monomers bind to each ligand trimer

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Components

#1: Protein
Tumor necrosis factor ligand superfamily member 13B / TNF-and APOL- related leukocyte expressed ligand 1 / TALL-1 / B lymphocyte stimulator / BLyS / B ...TNF-and APOL- related leukocyte expressed ligand 1 / TALL-1 / B lymphocyte stimulator / BLyS / B cell-activating factor / BAFF / Dendritic cell- derived TNF-like molecule


Mass: 22746.762 Da / Num. of mol.: 6 / Fragment: TNF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAFF / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 (DE3) / References: UniProt: Q9Y275
#2: Protein/peptide
BR3 derived PEPTIDE


Mass: 1569.873 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: This peptide was chemically synthesized.
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.18 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20% PEG 3350, 1.0 M LiCl, 0.1M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlprotein1drop
250 mMTris1droppH8.0
3500 mM1dropNaCl
40.1 Msodium cacodylate1reservoirpH6.7
519-21 %PEG33501reservoir
60.7-1.1 M1reservoirLiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 26356 / Num. obs: 26356 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.081 / Net I/σ(I): 10.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2630 / Rsym value: 0.41 / % possible all: 98.8
Reflection
*PLUS
Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 41 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KXG with the waters removed

1kxg


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.836 / SU B: 17.975 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28633 2536 9.6 %random
Rwork0.21288 ---
obs0.21992 23768 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.339 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7507 0 4 20 7531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217686
X-RAY DIFFRACTIONr_bond_other_d0.0020.026946
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.96210414
X-RAY DIFFRACTIONr_angle_other_deg0.775316200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021534
X-RAY DIFFRACTIONr_nbd_refined0.1970.21309
X-RAY DIFFRACTIONr_nbd_other0.2340.28004
X-RAY DIFFRACTIONr_nbtor_other0.0880.25331
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0230.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9312.54644
X-RAY DIFFRACTIONr_mcangle_it1.67837493
X-RAY DIFFRACTIONr_scbond_it1.0423.53036
X-RAY DIFFRACTIONr_scangle_it1.72242909
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2017medium positional0.480.5
12B2017medium positional0.580.5
13C2017medium positional0.480.5
14D2017medium positional0.570.5
15E2017medium positional0.520.5
16F2017medium positional0.470.5
21G198medium positional0.660.5
22H198medium positional0.760.5
23I198medium positional0.880.5
24J198medium positional0.750.5
25K198medium positional0.670.5
26L198medium positional0.820.5
11A2017medium thermal0.382
12B2017medium thermal0.362
13C2017medium thermal0.382
14D2017medium thermal0.442
15E2017medium thermal0.412
16F2017medium thermal0.452
21G198medium thermal0.292
22H198medium thermal0.232
23I198medium thermal0.292
24J198medium thermal0.252
25K198medium thermal0.322
26L198medium thermal0.292
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 308 -
Rwork0.24 1609 -
obs--98.8 %
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.36

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