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- PDB-1u5z: The Crystal structure of murine APRIL, pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 1u5z
TitleThe Crystal structure of murine APRIL, pH 8.5
ComponentsTumor necrosis factor ligand superfamily member 13
KeywordsCytokine / HORMONE/GROWTH FACTOR / TNFSF / trimer / jelly-roll / HORMONE-GROWTH FACTOR 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 / germinal center formation / tumor necrosis factor receptor binding / regulation of immune response / immunoglobulin mediated immune response / cytokine activity / receptor ligand activity ...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 / germinal center formation / tumor necrosis factor receptor binding / regulation of immune response / immunoglobulin mediated immune response / cytokine activity / receptor ligand activity / external side of plasma membrane / positive regulation of cell population proliferation / extracellular space
Similarity search - Function
Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / 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
NICKEL (II) ION / Tumor necrosis factor ligand superfamily member 13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWallweber, H.J. / Compaan, D.M. / Starovasnik, M.A. / Hymowitz, S.G.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Crystal Structure of A Proliferation-inducing Ligand, APRIL.
Authors: Wallweber, H.J. / Compaan, D.M. / Starovasnik, M.A. / Hymowitz, S.G.
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / 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_special_symmetry / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7642
Polymers15,7051
Non-polymers591
Water32418
1
A: Tumor necrosis factor ligand superfamily member 13
hetero molecules

A: Tumor necrosis factor ligand superfamily member 13
hetero molecules

A: Tumor necrosis factor ligand superfamily member 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2916
Polymers47,1153
Non-polymers1763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5480 Å2
ΔGint-76 kcal/mol
Surface area15650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.166, 92.166, 92.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1-

HOH

DetailsThe biologically relevant trimer is generated by a crystallographic 3-fold

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Components

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


Mass: 15705.042 Da / Num. of mol.: 1 / 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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / 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: 2.1 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.5 M KSCN, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 26, 2003
RadiationMonochromator: double crystals Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 5238 / Num. obs: 5238 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 60 Å2 / Rsym value: 0.043 / Net I/σ(I): 15.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 510 / Rsym value: 0.461 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.07refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: truncated model of BAFF (pdb entry 1OSG)

1osg


Resolution: 2.4→29.11 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.034 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.654 / ESU R Free: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.26452 506 9.7 %Random
Rwork0.21866 ---
all0.2232 5231 --
obs0.2232 5231 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.341 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 1 18 1007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211009
X-RAY DIFFRACTIONr_bond_other_d0.0020.02938
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9351367
X-RAY DIFFRACTIONr_angle_other_deg0.70632160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.82422.14342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16215162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.361158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02216
X-RAY DIFFRACTIONr_nbd_refined0.1860.2151
X-RAY DIFFRACTIONr_nbd_other0.2340.21021
X-RAY DIFFRACTIONr_nbtor_other0.0820.2614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2880.216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.25
X-RAY DIFFRACTIONr_mcbond_it1.8015631
X-RAY DIFFRACTIONr_mcangle_it2.7661010
X-RAY DIFFRACTIONr_scbond_it2.4186378
X-RAY DIFFRACTIONr_scangle_it3.7468357
LS refinement shellResolution: 2.4→2.45 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.303 31 -
Rwork0.227 266 -
obs-266 100 %
Refinement TLS params.Method: refined / Origin x: 78.86 Å / Origin y: 61.184 Å / Origin z: 64.125 Å
111213212223313233
T0.0971 Å20.0483 Å20.0504 Å2-0.0705 Å2-0.067 Å2--0.2085 Å2
L7.4656 °2-0.6856 °20.8217 °2-4.2619 °2-1.0219 °2--7.587 °2
S0.0921 Å °0.3582 Å °-0.8896 Å °-0.3802 Å °0.0747 Å °-0.4547 Å °0.6784 Å °0.635 Å °-0.1668 Å °

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