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- PDB-4zch: Single-chain human APRIL-BAFF-BAFF Heterotrimer -

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Basic information

Entry
Database: PDB / ID: 4zch
TitleSingle-chain human APRIL-BAFF-BAFF Heterotrimer
ComponentsTumor necrosis factor ligand superfamily member 13,Tumor necrosis factor ligand superfamily member 13B,Tumor necrosis factor ligand superfamily member 13B
KeywordsCYTOKINE / B-cell activating factor / A proliferation-inducing ligand / TNF superfamily / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


positive regulation of germinal center formation / HuR (ELAVL1) binds and stabilizes mRNA / B cell costimulation / positive regulation of isotype switching to IgA isotypes / 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 ...positive regulation of germinal center formation / HuR (ELAVL1) binds and stabilizes mRNA / B cell costimulation / positive regulation of isotype switching to IgA isotypes / 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 / regulation of mRNA stability / T cell costimulation / cytokine activity / TNFR2 non-canonical NF-kB pathway / receptor ligand activity / immune response / intracellular membrane-bounded organelle / focal adhesion / signaling receptor binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Tumor necrosis factor ligand superfamily member 13 / Tumor necrosis factor ligand superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsLammens, A. / Jiang, X. / Maskos, K. / Schneider, P.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Institute of Arthritis Research Switzerland
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Stoichiometry of Heteromeric BAFF and APRIL Cytokines Dictates Their Receptor Binding and Signaling Properties.
Authors: Schuepbach-Mallepell, S. / Das, D. / Willen, L. / Vigolo, M. / Tardivel, A. / Lebon, L. / Kowalczyk-Quintas, C. / Nys, J. / Smulski, C. / Zheng, T.S. / Maskos, K. / Lammens, A. / Jiang, X. / ...Authors: Schuepbach-Mallepell, S. / Das, D. / Willen, L. / Vigolo, M. / Tardivel, A. / Lebon, L. / Kowalczyk-Quintas, C. / Nys, J. / Smulski, C. / Zheng, T.S. / Maskos, K. / Lammens, A. / Jiang, X. / Hess, H. / Tan, S.L. / Schneider, P.
History
DepositionApr 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jul 8, 2015Group: Database references
Revision 1.3Apr 3, 2019Group: Advisory / Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.5Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 13,Tumor necrosis factor ligand superfamily member 13B,Tumor necrosis factor ligand superfamily member 13B
B: Tumor necrosis factor ligand superfamily member 13,Tumor necrosis factor ligand superfamily member 13B,Tumor necrosis factor ligand superfamily member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5853
Polymers97,4632
Non-polymers1221
Water6,107339
1
A: Tumor necrosis factor ligand superfamily member 13,Tumor necrosis factor ligand superfamily member 13B,Tumor necrosis factor ligand superfamily member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8542
Polymers48,7311
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tumor necrosis factor ligand superfamily member 13,Tumor necrosis factor ligand superfamily member 13B,Tumor necrosis factor ligand superfamily member 13B


Theoretical massNumber of molelcules
Total (without water)48,7311
Polymers48,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.041, 117.865, 295.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 13,Tumor necrosis factor ligand superfamily member 13B,Tumor necrosis factor ligand superfamily member 13B / A proliferation-inducing ligand / APRIL / TNF- and APOL-related leukocyte expressed ligand 2 / TALL- ...A proliferation-inducing ligand / APRIL / TNF- and APOL-related leukocyte expressed ligand 2 / TALL-2 / TNF-related death ligand 1 / TRDL-1 / 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 / 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


Mass: 48731.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The compound is a single chain APRIL-BAFF-BAFF heterotrimer from the construct of His-FLAG-TEV-GS-hAPRIL (aa111-250, T126A)-GGGGS-hBAFF(aa140-285)-GGGGS-hBAFF(aa140-285) with cleaved tags.
Source: (gene. exp.) Homo sapiens (human)
Gene: TNFSF13, APRIL, TALL2, ZTNF2, UNQ383/PRO715, TNFSF13B, BAFF, BLYS, TALL1, TNFSF20, ZTNF4, UNQ401/PRO738
Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O75888, UniProt: Q9Y275
#2: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: RESERVOIR SOLUTION : 14% PEG6000 , 1M LiCL , TRIS-HCL pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.43→147.76 Å / Num. obs: 36901 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.46
Reflection shellResolution: 2.43→2.68 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.505 / Rejects: 0 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q5X and 1KD7

1q5x

1kd7


Resolution: 2.43→32.61 Å / Cor.coef. Fo:Fc: 0.9454 / Cor.coef. Fo:Fc free: 0.9176 / SU R Cruickshank DPI: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.411 / SU Rfree Blow DPI: 0.25 / SU Rfree Cruickshank DPI: 0.25
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 1111 3.01 %RANDOM
Rwork0.1771 ---
obs0.1788 36894 96.72 %-
Displacement parametersBiso max: 132.35 Å2 / Biso mean: 48.37 Å2 / Biso min: 12.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.923 Å20 Å20 Å2
2---2.6576 Å20 Å2
3---5.5805 Å2
Refine analyzeLuzzati coordinate error obs: 0.334 Å
Refinement stepCycle: final / Resolution: 2.43→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6644 0 8 339 6991
Biso mean--79.15 47.91 -
Num. residues----841
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2367SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes974HARMONIC5
X-RAY DIFFRACTIONt_it6797HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion873SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7336SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6797HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9194HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion19.5
LS refinement shellResolution: 2.43→2.5 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3682 87 2.88 %
Rwork0.2712 2929 -
all0.2742 3016 -
obs--96.72 %
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)
11.8003-0.8758-0.22433.9022-0.11594.078-0.0284-0.1558-0.26710.31070.00970.2280.5453-0.62720.0187-0.2253-0.15710.0173-0.02860.0405-0.0876-10.672827.309561.3683
21.13550.5297-0.07714.0941-1.39092.8982-0.03450.11320.0708-0.15090.05780.15970.0406-0.4485-0.0233-0.0974-0.0755-0.0069-0.0255-0.0205-0.0237-3.050330.33839.2703
303.8298-1.77445.3116-2.72121.42020.0015-0.1629-0.06860.0998-0.0035-0.0580.059-0.18050.0020.0167-0.0708-0.0136-0.04340.09930.105711.203440.603431.9199
41.29970.4092-0.46311.0930.49792.8078-0.09860.0242-0.0996-0.18070.0698-0.06370.276-0.16490.0287-0.0969-0.0423-0.0211-0.09960.01430.05121.566627.633843.9856
51.44990.2182-0.55832.25280.26193.4413-0.0278-0.17270.06920.0920.1128-0.2606-0.1090.2432-0.085-0.0992-0.0437-0.0228-0.0426-0.02380.019811.165540.119558.3562
61.86970.48422.62710.0426-1.9122.70710.04330.11710.08830.1249-0.2033-0.154-0.25120.16190.1601-0.0074-0.08240.0272-0.0175-0.04810.037310.902447.630275.2222
71.56370.1492-0.91731.99281.49773.7063-0.0275-0.18990.00850.20890.1451-0.24380.15040.1683-0.1176-0.105-0.0011-0.0593-0.05650.0263-0.00429.178233.270759.7748
82.0321-0.48920.71043.5859-0.13744.593-0.01240.32140.2161-0.351-0.1537-0.4998-0.74130.55350.16610.0847-0.08250.0856-0.1990.072-0.1756-0.03719.143312.9924
93.67090.086-0.55132.81550.36383.7668-0.0281-0.0339-0.0820.07650.0764-0.1399-0.10020.1668-0.0483-0.0618-0.0249-0.0098-0.10920.0475-0.0217-1.4353-0.108834.4642
101.98743.8355-3.97320-3.94631.82760.00640.0263-0.10230.0065-0.05070.08460.2136-0.18630.04430.003-0.05070.0624-0.02650.04080.0755-12.3408-14.139741.2798
111.54260.56150.88392.4754-0.65142.96450.10730.1755-0.1375-0.1966-0.0487-0.31460.0330.3635-0.0586-0.11070.02420.0129-0.08590.04070.00010.5416-4.371829.2771
122.2446-0.38850.73573.7523-1.4386.85880.20110.0561-0.2666-0.69130.09910.47720.962-0.3333-0.30030.0906-0.0681-0.1387-0.2806-0.003-0.1686-13.1419-12.337815.0163
1300.6373-2.427901.62141.0948-0.026-0.0451-0.1535-0.02130.06550.11750.0888-0.1346-0.03940.1620.0344-0.1819-0.0283-0.0257-0.1126-20.0644-10.8655-2.0951
140.32271.15880.79123.3172-1.20365.45450.07780.0647-0.1096-0.8302-0.0211-0.23810.62180.3315-0.05680.13960.05450.0021-0.2009-0.0101-0.1895-6.0912-10.530613.3922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|8 - A|142 }A8 - 142
2X-RAY DIFFRACTION2{ A|150 - A|221 }A150 - 221
3X-RAY DIFFRACTION3{ A|222 - A|235 }A222 - 235
4X-RAY DIFFRACTION4{ A|236 - A|294 }A236 - 294
5X-RAY DIFFRACTION5{ A|301 - A|372 }A301 - 372
6X-RAY DIFFRACTION6{ A|373 - A|386 }A373 - 386
7X-RAY DIFFRACTION7{ A|387 - A|444 }A387 - 444
8X-RAY DIFFRACTION8{ B|7 - B|142 }B7 - 142
9X-RAY DIFFRACTION9{ B|151 - B|221 }B151 - 221
10X-RAY DIFFRACTION10{ B|222 - B|235 }B222 - 235
11X-RAY DIFFRACTION11{ B|236 - B|294 }B236 - 294
12X-RAY DIFFRACTION12{ B|300 - B|372 }B300 - 372
13X-RAY DIFFRACTION13{ B|373 - B|386 }B373 - 386
14X-RAY DIFFRACTION14{ B|387 - B|444 }B387 - 444

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