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- PDB-1u5x: Crystal structure of murine APRIL at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 1u5x
TitleCrystal structure of murine APRIL at pH 5.0
ComponentsTumor necrosis factor ligand superfamily member 13
KeywordsCYTOKINE / HORMONE/GROWTH FACTOR / TNFSF / jelly-roll / trimer / 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
Tumor necrosis factor ligand superfamily member 13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Apr 3, 2024Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)15,7051
Polymers15,7051
Non-polymers00
Water77543
1
A: Tumor necrosis factor ligand superfamily member 13

A: Tumor necrosis factor ligand superfamily member 13

A: Tumor necrosis factor ligand superfamily member 13


Theoretical massNumber of molelcules
Total (without water)47,1153
Polymers47,1153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area4930 Å2
ΔGint-19 kcal/mol
Surface area15130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.779, 90.779, 90.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsThe biologically relevant trimer is formed by the 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 5
Details: 0.1 M Citric Acid, 1.0 M LiCL, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 7, 2004 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 11701 / Num. obs: 11701 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.042 / Net I/σ(I): 30.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 5 / Num. unique all: 1162 / Rsym value: 0.442 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.07refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APRIL at pH 8.5

Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.704 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.162 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 1136 9.7 %RANDOM
Rwork0.21375 ---
all0.2179 11701 --
obs0.21799 11697 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.636 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 0 43 1037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211025
X-RAY DIFFRACTIONr_bond_other_d0.0020.02968
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9381391
X-RAY DIFFRACTIONr_angle_other_deg0.82832222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.58421.42942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21615163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9411510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021129
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02223
X-RAY DIFFRACTIONr_nbd_refined0.2030.2149
X-RAY DIFFRACTIONr_nbd_other0.2570.21056
X-RAY DIFFRACTIONr_nbtor_other0.0850.2619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.28
X-RAY DIFFRACTIONr_mcbond_it2.575643
X-RAY DIFFRACTIONr_mcangle_it3.60461034
X-RAY DIFFRACTIONr_scbond_it3.8526382
X-RAY DIFFRACTIONr_scangle_it5.5598357
LS refinement shellResolution: 1.8→1.838 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.458 70 -
Rwork0.376 627 -
obs-1136 100 %
Refinement TLS params.Method: refined / Origin x: 17.4225 Å / Origin y: 13.7804 Å / Origin z: 59.4666 Å
111213212223313233
T0.1164 Å20.0033 Å2-0.0532 Å2-0.0259 Å2-0.0322 Å2--0.0609 Å2
L4.2488 °2-0.5897 °2-0.5612 °2-2.5135 °20.3975 °2--4.9307 °2
S-0.0373 Å °0.2567 Å °-0.3726 Å °-0.3268 Å °-0.0324 Å °0.3005 Å °0.5213 Å °-0.0681 Å °0.0697 Å °

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