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- PDB-1xu1: The crystal structure of APRIL bound to TACI -

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Basic information

Entry
Database: PDB / ID: 1xu1
TitleThe crystal structure of APRIL bound to TACI
Components
  • Tumor necrosis factor ligand superfamily member 13
  • Tumor necrosis factor receptor superfamily member 13B
KeywordsCYTOKINE / HORMONE/GROWTH FACTOR receptor / TNFSF / CRD / receptor / jelly-roll / cysteine-rich / HORMONE-GROWTH FACTOR receptor COMPLEX
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / positive regulation of germinal center formation / TNFs bind their physiological receptors / positive regulation of isotype switching to IgA isotypes / TNFs bind their physiological receptors / germinal center formation / tumor necrosis factor receptor binding / negative regulation of B cell proliferation / B cell homeostasis / regulation of immune response ...HuR (ELAVL1) binds and stabilizes mRNA / positive regulation of germinal center formation / TNFs bind their physiological receptors / positive regulation of isotype switching to IgA isotypes / TNFs bind their physiological receptors / germinal center formation / tumor necrosis factor receptor binding / negative regulation of B cell proliferation / B cell homeostasis / regulation of immune response / immunoglobulin mediated immune response / hematopoietic progenitor cell differentiation / cytokine activity / signaling receptor activity / adaptive immune response / receptor ligand activity / cell surface receptor signaling pathway / external side of plasma membrane / positive regulation of cell population proliferation / extracellular space / plasma membrane
Similarity search - Function
TACI, cysteine-rich domain / Tumour necrosis factor receptor 13B / TACI, cysteine-rich domain / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 ...TACI, cysteine-rich domain / Tumour necrosis factor receptor 13B / TACI, cysteine-rich domain / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region signature. / 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
NICKEL (II) ION / Tumor necrosis factor receptor superfamily member 13B / Tumor necrosis factor ligand superfamily member 13
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHymowitz, S.G. / Patel, D.R. / Wallweber, H.J.A. / Runyon, S. / Yan, M. / Yin, J. / Shriver, S.K. / Gordon, N.C. / Pan, B. / Skelton, N.J. ...Hymowitz, S.G. / Patel, D.R. / Wallweber, H.J.A. / Runyon, S. / Yan, M. / Yin, J. / Shriver, S.K. / Gordon, N.C. / Pan, B. / Skelton, N.J. / Kelley, R.F. / Starovasnik, M.A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structures of APRIL-receptor complexes: Like BCMA, TACI employs only a single cysteine-rich domain for high-affinity ligand binding
Authors: Hymowitz, S.G. / Patel, D.R. / Wallweber, H.J.A. / Runyon, S. / Yan, M. / Yin, J. / Shriver, S.K. / Gordon, N.C. / Pan, B. / Skelton, N.J. / Kelley, R.F. / Starovasnik, M.A.
History
DepositionOct 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 23, 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: Tumor necrosis factor ligand superfamily member 13
D: Tumor necrosis factor ligand superfamily member 13
R: Tumor necrosis factor receptor superfamily member 13B
S: Tumor necrosis factor receptor superfamily member 13B
T: Tumor necrosis factor receptor superfamily member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4107
Polymers61,3526
Non-polymers591
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.339, 91.839, 102.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe assymmetric unit contains the biologically relevant assembly of a trimer of APRIL bound to 3 copies of TACI

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 13 / A proliferation-inducing ligand / APRIL / TNFSF13 / TALL-2


Mass: 15560.912 Da / Num. of mol.: 3 / Fragment: TNF domain of murine APRIL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf13, APRIL / Plasmid: pet-32a (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: Q9D777
#2: Protein/peptide Tumor necrosis factor receptor superfamily member 13B / Transmembrane activator and CAML interactor / TNFRSF13B


Mass: 4889.686 Da / Num. of mol.: 3 / Fragment: TACI CRD2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF13B, TACI / Plasmid: pET32a (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: O14836
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: well solution: 70% MPD, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9804 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 14, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 44579 / Num. obs: 44579 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.086 / Net I/σ(I): 7.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4416 / Rsym value: 0.347 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APRIL alone, pdbcode 1U5Z

1u5z


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.458 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic plus TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.142 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20317 4449 10 %THIN SHELLS
Rwork0.16724 ---
all0.1709 44518 --
obs0.17087 40069 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.37 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 0 1 130 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214248
X-RAY DIFFRACTIONr_bond_other_d0.0020.023824
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9435744
X-RAY DIFFRACTIONr_angle_other_deg0.73938872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024700
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02915
X-RAY DIFFRACTIONr_nbd_refined0.1770.2558
X-RAY DIFFRACTIONr_nbd_other0.2440.24174
X-RAY DIFFRACTIONr_nbtor_other0.0810.22724
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0570.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.22
X-RAY DIFFRACTIONr_mcbond_it2.5582.52599
X-RAY DIFFRACTIONr_mcangle_it4.20354191
X-RAY DIFFRACTIONr_scbond_it3.4232.51649
X-RAY DIFFRACTIONr_scangle_it5.26651553
LS refinement shellResolution: 1.9→1.94 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.206 244 -
Rwork0.17 2318 -
obs-4416 100 %
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)
11.0007-0.11390.11190.8469-0.35451.03380.01940.0564-0.1639-0.09220.04010.02850.1407-0.0234-0.05950.0601-0.0171-0.01610.0156-0.01690.050110.3589-9.697622.7869
21.074-0.05060.27041.55220.04741.78880.00430.09290.1025-0.07560.0052-0.1328-0.16350.1757-0.00950.0262-0.02010.01030.03780.0060.040120.712510.921219.6245
31.41530.16150.54661.3993-0.2662.0180.0085-0.10380.05760.00950.01780.2303-0.1039-0.2699-0.02630.02880.03240.00240.0485-0.01480.0676-0.85610.12427.7306
43.9522-2.61810.88573.4718-0.3782.5252-0.1034-0.2337-0.29360.12320.0452-0.430.39440.44880.05820.16060.0375-0.04410.13240.00670.215628.0782-14.350638.1989
52.69692.09352.89043.7454-0.05656.8817-0.0971-0.28870.44990.5003-0.258-0.1705-0.78670.21310.3550.2729-0.0829-0.05550.1475-0.02660.161425.727421.153540.579
60.7283-0.15650.78140.7620.821110.6199-0.021-0.2302-0.0780.1936-0.09930.15780.1127-0.88220.12030.08670.02380.01550.1915-0.00720.0944-0.08832.293452.1092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A105 - 241
2X-RAY DIFFRACTION2B105 - 241
3X-RAY DIFFRACTION3D105 - 241
4X-RAY DIFFRACTION4R68 - 105
5X-RAY DIFFRACTION5S71 - 106
6X-RAY DIFFRACTION6T71 - 109

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