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- PDB-3k48: Crystal structure of APRIL bound to a peptide -

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Basic information

Entry
Database: PDB / ID: 3k48
TitleCrystal structure of APRIL bound to a peptide
Components
  • Tumor necrosis factor ligand superfamily member 13
  • peptide
KeywordsCYTOKINE / TNFSF / Cleavage on pair of basic residues / Disulfide bond / Glycoprotein / Immune response / Secreted
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHymowitz, S.G.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Multiple novel classes of APRIL-specific receptor-blocking peptides isolated by phage display.
Authors: Gordon, N.C. / Lien, S. / Johnson, J. / Wallweber, H.J. / Tran, T. / Currell, B. / Mathieu, M. / Quan, C. / Starovasnik, M.A. / Hymowitz, S.G. / Kelley, R.F.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
R: peptide
S: peptide
T: peptide


Theoretical massNumber of molelcules
Total (without water)53,2096
Polymers53,2096
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-46 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.811, 84.771, 55.562
Angle α, β, γ (deg.)90.00, 99.45, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
12R
22S
32T

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEUAA105 - 2414 - 140
21LYSLYSLEULEUBB105 - 2414 - 140
31LYSLYSLEULEUDC105 - 2414 - 140
12GLYGLYCYSCYSRD2 - 142 - 14
22GLYGLYCYSCYSSE2 - 142 - 14
32GLYGLYCYSCYSTF2 - 142 - 14

NCS ensembles :
ID
1
2

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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: residues 104-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: April, TNFSF 13, Tnfsf13 / Plasmid: pet-32A / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: Q9D777
#2: Protein/peptide peptide


Mass: 2031.253 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic peptide

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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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 2ul drops of protein (5 mg/mg. at pH 9.7) was added to 2 uL of 4M formate. Crystals formed immediately, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 11453 / Num. obs: 11453 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 50 Å2 / Rsym value: 0.108 / Net I/σ(I): 12.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1126 / Rsym value: 0.506 / % possible all: 98.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain A from pdb 1xu1

1xu1


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.87 / SU B: 38.59 / SU ML: 0.343 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 1143 10 %thin shells
Rwork0.20548 ---
obs0.21169 10257 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: 16.768 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-1.52 Å2
2---2.51 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 0 0 3613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213713
X-RAY DIFFRACTIONr_bond_other_d0.0040.022563
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9395042
X-RAY DIFFRACTIONr_angle_other_deg0.9533.0046159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82222170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04715604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5921536
X-RAY DIFFRACTIONr_chiral_restr0.0790.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02815
X-RAY DIFFRACTIONr_nbd_refined0.1970.2624
X-RAY DIFFRACTIONr_nbd_other0.1980.22669
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21684
X-RAY DIFFRACTIONr_nbtor_other0.0790.22131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.23
X-RAY DIFFRACTIONr_mcbond_it2.3452.52901
X-RAY DIFFRACTIONr_mcbond_other0.4942.5913
X-RAY DIFFRACTIONr_mcangle_it2.92953645
X-RAY DIFFRACTIONr_scbond_it1.7882.51720
X-RAY DIFFRACTIONr_scangle_it2.87251397
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1839medium positional0.550.5
12B1839medium positional0.460.5
13D1839medium positional0.50.5
21R206medium positional0.170.5
22S206medium positional0.120.5
23T206medium positional0.140.5
11A1839medium thermal0.52
12B1839medium thermal0.482
13D1839medium thermal0.492
21R206medium thermal0.42
22S206medium thermal0.322
23T206medium thermal0.32
LS refinement shellResolution: 2.8→2.857 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rwork0.268 675 -
Rfree-0 -
obs--99.41 %
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)
13.32790.3538-0.11482.4045-0.66741.9890.0115-0.33940.09180.2594-0.057-0.19550.08370.0160.0455-0.0441-0.0037-0.0119-0.0472-0.0209-0.06327.6862-1.213527.8663
22.03870.0241-0.19211.317-0.24863.54-0.18970.07740.1646-0.06360.03230.1283-0.2446-0.14710.1574-0.04040.0253-0.0356-0.094-0.00180.035915.033911.963913.742
32.9805-0.46210.13831.7970.19511.95570.06930.1088-0.1169-0.1622-0.02970.12710.21570.0018-0.0396-0.0030.0058-0.0167-0.0671-0.0209-0.067417.1933-10.70169.7295
48.2526-5.68083.779510.02236.034413.9338-0.4529-0.7111-0.00110.73260.9038-0.11290.7214-1.059-0.4509-0.03040.018-0.0214-0.10190.0364-0.106215.5525-20.423625.4938
50.14950.92310.71585.69864.41883.4265-0.4017-0.72490.73330.9038-0.19070.10560.1512-0.53220.59240.04860.0321-0.0209-0.0421-0.041-0.00218.23810.853435.8997
62.034-0.03951.01650.0008-0.01970.5080.34420.22760.068-0.2962-0.3590.8871-0.0751-0.57740.0147-0.03570.0153-0.10290.1616-0.0050.15630.43594.36828.3889
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 DIFFRACTION4R1 - 16
5X-RAY DIFFRACTION5S2 - 16
6X-RAY DIFFRACTION6T2 - 14

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