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- PDB-3v56: Re-refinement of PDB entry 1OSG - Complex between BAFF and a BR3 ... -

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Basic information

Entry
Database: PDB / ID: 3v56
TitleRe-refinement of PDB entry 1OSG - Complex between BAFF and a BR3 derived peptide presented in a beta-hairpin scaffold - reveals an additonal copy of the peptide.
Components
  • BR3 derived peptive
  • 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 / signaling receptor activity / adaptive immune response / receptor ligand activity / external side of plasma membrane / signaling receptor binding / intracellular membrane-bounded organelle / focal adhesion / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
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 / Tumor necrosis factor (TNF) homology domain (THD) profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls ...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 / Tumor necrosis factor (TNF) homology domain (THD) profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 13C / Tumor necrosis factor ligand superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / RE-REFINEMENT / Resolution: 3 Å
AuthorsSmart, O.S. / Womack, T.O. / Flensburg, C. / Keller, P. / Sharff, A. / Paciorek, W. / Vonrhein, C. / Bricogne, G.
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. / F Kelley, R. / Cochran, A.G. / Yan, M. / Dixit, V.M. / Fairbrother, W.J. / Starovasnik, M.A.
History
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 13, 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 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 3V56 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA OF R1OSGTSF ...THIS ENTRY 3V56 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA OF R1OSGTSF DETERMINED BY THE AUTHORS OF THE PDB ENTRY 1OSG: N.C.GORDON,B.PAN,S.G.HYMOWITZ,J.P.YIN,R.F.KELLEY, A.G.COCHRAN,M.YAN,V.M.DIXIT,W.J.FAIRBROTHER,M.A.STAROVASNIK

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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 peptive
H: BR3 derived peptive
I: BR3 derived peptive
J: BR3 derived peptive
K: BR3 derived peptive
L: BR3 derived peptive
Z: BR3 derived peptive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,83015
Polymers147,63813
Non-polymers1922
Water32418
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 peptive
H: BR3 derived peptive
I: BR3 derived peptive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1187
Polymers73,0226
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-50 kcal/mol
Surface area18150 Å2
MethodPISA
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 peptive
K: BR3 derived peptive
L: BR3 derived peptive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1187
Polymers73,0226
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-49 kcal/mol
Surface area18200 Å2
MethodPISA
3
Z: BR3 derived peptive


Theoretical massNumber of molelcules
Total (without water)1,5941
Polymers1,5941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
DetailsThe biologically relevant assembly of BAFF is a trimer. The crystallographic asymmetric unit contains two trimers. Each individual BAFF trimer binds 3 copies of BR3 peptide. An additional copy of the BR3 peptide was located in this re-refinement at a crystal contact (modeled as the Z chain). The additional BR3 peptide is not biologically relevant.

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Components

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


Mass: 22746.762 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TNFSF13B, BAFF, BLYS, TALL1, TNFSF20, ZTNF4, UNQ401/PRO738
Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y275
#2: Protein/peptide
BR3 derived peptive


Mass: 1593.918 Da / Num. of mol.: 7 / Source method: obtained synthetically / References: UniProt: Q96RJ3*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.27 Å3/Da / Density % sol: 45.91 % / Description: AUTHOR USED THE SF DATA FROM THE ENTRY 1OSG.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
AMoREphasing
BUSTER2.13.0refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: RE-REFINEMENT
Starting model: 1OSG with water molecules and ions removed.

1osg


Resolution: 3→29.85 Å / Cor.coef. Fo:Fc: 0.9445 / Cor.coef. Fo:Fc free: 0.9201 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber EH99
Details: 1. X-ray weight: 14.83. 2. Void correction : ON. 3. Similarity, NCS representation : RESTRAINT LSSR, Target restraints: NONE, Target structure : NULL. 4. Molecules SO4 A 499, SO4 D 499, HOH ...Details: 1. X-ray weight: 14.83. 2. Void correction : ON. 3. Similarity, NCS representation : RESTRAINT LSSR, Target restraints: NONE, Target structure : NULL. 4. Molecules SO4 A 499, SO4 D 499, HOH A 500, HOH D 500 are modeled into density on NCS 3 fold axes where map interpretation is difficult, and so should be treated with caution. 5. Due to radiation damage or only partial oxidation residues CYS 232 and CYS 245 in the A, B, C, D, E and F chains form only a partial disulfide bond. The disulfide bond is modeled as the A alternate whereas the B alternate represents the reduced CYS residues.
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 2536 9.64 %RANDOM
Rwork0.1617 ---
all0.1654 26393 --
obs0.1654 26306 99.67 %-
Displacement parametersBiso mean: 50.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.478 Å20 Å20 Å2
2--1.478 Å20 Å2
3----2.9561 Å2
Refine analyzeLuzzati coordinate error obs: 0.339 Å
Refinement stepCycle: LAST / Resolution: 3→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7406 0 10 18 7434
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017595HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.210339HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2520SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes189HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1088HARMONIC5
X-RAY DIFFRACTIONt_it7595HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion19.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1002SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance12HARMONIC1
X-RAY DIFFRACTIONt_utility_angle12HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8381SEMIHARMONIC4
LS refinement shellResolution: 3→3.12 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2849 308 10.36 %
Rwork0.209 2665 -
all0.2165 2973 -
obs--99.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1063-0.95820.22432.3334-0.3462.2385-0.2172-0.05670.11620.50910.1543-0.1268-0.29890.03280.06290.0887-0.0088-0.0711-0.14170.0309-0.127276.98219.4174-5.3574
21.58180.17930.48592.14750.0262.1172-0.07730.31290.0002-0.15980.0009-0.10030.30980.11380.0764-0.0014-0.05210.0032-0.0482-0.0161-0.114777.22385.4476-23.8906
31.69960.14570.24552.19020.84932.1678-0.08710.36960.1928-0.2631-0.09230.0956-0.3806-0.14610.17950.0197-0.0166-0.0774-0.05750.1261-0.132370.783727.5423-26.3224
42.7909-0.3906-0.33163.0579-0.23872.42350.203-0.34570.15670.6533-0.0943-0.0814-0.4737-0.1903-0.10870.1557-0.00890.0533-0.2188-0.015-0.178377.3637-2.357623.6635
50.610.17260.15052.40530.42012.02950.2454-0.1444-0.18810.778-0.2141-0.01150.2782-0.2442-0.03120.1125-0.09350.016-0.11760.1039-0.132571.6579-24.578326.5059
61.17750.37350.36373.4437-0.78152.31170.0060.0513-0.1591-0.09730.1034-0.08370.0542-0.0743-0.10940.01450.03380.0468-0.12850.0309-0.09377.5137-16.29615.3864
75.5217-4.94046.53520.5488-2.01016.83770.0232-0.1892-0.3221-0.1856-0.0543-1.02840.07710.75280.0311-0.12960.1023-0.2133-0.06960.070.174197.202512.2883-5.2573
8-2.23610.1516-2.2226.1831-1.8686.22460.0540.51150.0132-0.6878-0.083-0.7584-0.42610.25840.0290.0323-0.24330.11860.34990.0424-0.388690.770612.789-38.9737
9-0.0076-2.46935.39879.42951.09471.5175-0.0706-0.43910.71910.48610.1169-0.5362-0.48440.4024-0.04620.1173-0.1509-0.3866-0.28260.12780.155786.599940.6107-20.1043
10-1.16760.12914.58413.0556-3.76665.7299-0.0912-0.5657-0.26990.45760.0354-0.71710.16450.50810.05580.5716-0.0403-0.34670.00680.0565-0.44291.0778-9.063739.0814
11-0.6863-0.742-5.273111.70271.14220.0521-0.18260.5319-0.2898-0.27490.1174-0.28360.53710.61770.06520.38410.0431-0.1439-0.2710.0611-0.110187.9735-37.154420.2413
121.54666.5025-0.75186.9937-4.662710.3443-0.0720.14510.2202-0.07740.215-0.7546-0.39480.7325-0.1429-0.0611-0.14730.2538-0.18640.00670.22497.2764-8.31365.5517
130.4355-2.1667-1.72717.3952-4.94781.14890.1034-0.03630.03450.0819-0.26540.20910.0941-0.07040.16210.1631-0.0219-0.0401-0.33370.32290.175384.51-45.662625.5181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A142 - 502
2X-RAY DIFFRACTION2{ B|* }B142 - 504
3X-RAY DIFFRACTION3{ C|* }C142 - 502
4X-RAY DIFFRACTION4{ D|* }D142 - 502
5X-RAY DIFFRACTION5{ E|* }E142 - 502
6X-RAY DIFFRACTION6{ F|* }F142 - 506
7X-RAY DIFFRACTION7{ G|* }G22 - 35
8X-RAY DIFFRACTION8{ H|* }H23 - 35
9X-RAY DIFFRACTION9{ I|* }I23 - 35
10X-RAY DIFFRACTION10{ J|* }J23 - 35
11X-RAY DIFFRACTION11{ K|* }K23 - 35
12X-RAY DIFFRACTION12{ L|* }L23 - 35
13X-RAY DIFFRACTION13{ Z|* }Z23 - 35

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