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- PDB-1u5y: Crystal structure of murine APRIL, pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 1u5y
TitleCrystal structure of murine APRIL, pH 8.0
ComponentsTumor necrosis factor ligand superfamily member 13
KeywordsCytokine / HORMONE/GROWTH FACTOR / trimer / jelly-roll / TNFSF / 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: 2.3 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 / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)47,1153
Polymers47,1153
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-18 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.344, 81.166, 53.585
Angle α, β, γ (deg.)90.00, 111.79, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41A
51B
61D
71A
81B
91D
101A
111B
121D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASNASNAA105 - 1154 - 14
21LYSLYSASNASNBB105 - 1154 - 14
31LYSLYSASNASNDC105 - 1154 - 14
42ASPASPVALVALAA123 - 16522 - 64
52ASPASPVALVALBB123 - 16522 - 64
62ASPASPVALVALDC123 - 16522 - 64
73METMETARGARGAA169 - 18968 - 88
83METMETARGARGBB169 - 18968 - 88
93METMETARGARGDC169 - 18968 - 88
104ALAALALEULEUAA198 - 24197 - 140
114ALAALALEULEUBB198 - 24197 - 140
124ALAALALEULEUDC198 - 24197 - 140
DetailsThe asymmetric unit contains the biologically relevant trimer

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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.: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8.0, 1M LiCl, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 6, 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: 2.3→50 Å / Num. all: 23803 / Num. obs: 23803 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 2034 / Rsym value: 0.275 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: I23 structure of APRIL

Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.297 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.369 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26805 2210 10.7 %Thin Shells
Rwork0.20075 ---
all0.208 20737 --
obs0.20802 20737 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.653 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å20.92 Å2
2---2.02 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 0 81 3220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213212
X-RAY DIFFRACTIONr_bond_other_d0.0020.022959
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9374360
X-RAY DIFFRACTIONr_angle_other_deg0.78136824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7865400
X-RAY DIFFRACTIONr_chiral_restr0.0790.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023580
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02690
X-RAY DIFFRACTIONr_nbd_refined0.1910.2506
X-RAY DIFFRACTIONr_nbd_other0.2380.23514
X-RAY DIFFRACTIONr_nbtor_other0.0850.22143
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.24
X-RAY DIFFRACTIONr_mcbond_it2.6642.52002
X-RAY DIFFRACTIONr_mcangle_it4.06253224
X-RAY DIFFRACTIONr_scbond_it3.0682.51210
X-RAY DIFFRACTIONr_scangle_it4.61351136
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A679medium positional0.280.5
2B679medium positional0.350.5
3D679medium positional0.260.5
1A1110loose positional0.925
2B1110loose positional0.835
3D1110loose positional0.875
1A679medium thermal1.122
2B679medium thermal1.052
3D679medium thermal1.112
1A1110loose thermal3.0210
2B1110loose thermal3.0110
3D1110loose thermal2.5810
LS refinement shellResolution: 2.3→2.347 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.352 133 -
Rwork0.232 1081 -
obs-1081 93 %
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)
14.2543-0.11180.09583.9438-0.56892.7785-0.07550.1235-0.333-0.38090.15660.28930.3841-0.2113-0.08110.133-0.0389-0.06860.0601-0.00150.07921.8823-10.5969.5902
23.41981.7172-0.43925.9176-1.5952.02650.3036-0.5015-0.07610.8042-0.3742-0.268-0.12380.22780.07060.1736-0.0566-0.06120.1639-0.00220.034734.1973-2.05226.9825
31.48550.07990.46994.8101-0.18263.39030.12710.01490.21190.17430.1170.6413-0.2278-0.4008-0.24410.05540.03270.06960.08320.02950.200619.729412.010315.246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA105 - 2414 - 140
2X-RAY DIFFRACTION2BB105 - 2414 - 140
3X-RAY DIFFRACTION3DC105 - 2414 - 140

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