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- PDB-1xu2: The crystal structure of APRIL bound to BCMA -

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Basic information

Entry
Database: PDB / ID: 1xu2
TitleThe crystal structure of APRIL bound to BCMA
Components
  • Tumor necrosis factor ligand superfamily member 13
  • Tumor necrosis factor receptor superfamily member 17
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 / lymphocyte homeostasis / positive regulation of isotype switching to IgA isotypes / TNFs bind their physiological receptors / germinal center formation / tumor necrosis factor receptor binding / regulation of immune response / endomembrane system ...HuR (ELAVL1) binds and stabilizes mRNA / positive regulation of germinal center formation / TNFs bind their physiological receptors / lymphocyte homeostasis / positive regulation of isotype switching to IgA isotypes / TNFs bind their physiological receptors / germinal center formation / tumor necrosis factor receptor binding / regulation of immune response / endomembrane system / immunoglobulin mediated immune response / tumor necrosis factor-mediated signaling pathway / cytokine activity / signaling receptor activity / adaptive immune response / receptor ligand activity / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular space / membrane / plasma membrane
Similarity search - Function
BCMA, TALL-1 binding / Tumour necrosis factor receptor 17 / BCMA, TALL-1 binding / Tumor necrosis factor receptor 13C/17 / : / 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. ...BCMA, TALL-1 binding / Tumour necrosis factor receptor 17 / BCMA, TALL-1 binding / Tumor necrosis factor receptor 13C/17 / : / 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 receptor superfamily member 17 / 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: 2.35 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 / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 17
S: Tumor necrosis factor receptor superfamily member 17
T: Tumor necrosis factor receptor superfamily member 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0837
Polymers62,0246
Non-polymers591
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-53 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.294, 114.294, 91.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe assymmetric unit contains the biologically relevant assembly of a trimer of APRIL bound to 3 copies of BCMA

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 13 / A proliferation-inducing ligand / APRIL / TNFSF13B or Tall-2


Mass: 15560.912 Da / Num. of mol.: 3 / Fragment: TNF domain of APRIL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf13, APRIL / Plasmid: pET32a (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: Q9D777
#2: Protein/peptide Tumor necrosis factor receptor superfamily member 17 / B-cell maturation protein / TNFFSF17


Mass: 5113.745 Da / Num. of mol.: 3 / Fragment: BCMA ECD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF17, BCM, BCMA / Plasmid: pZCT / Production host: Escherichia coli (E. coli) / References: UniProt: Q02223
#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.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: well solution: 0.1M MES, 5% Peg 8000, 10% Peg 1000, pH 5.0, 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: 2.35→50 Å / Num. all: 28292 / Num. obs: 28292 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.067 / Net I/σ(I): 11.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2831 / Rsym value: 0.425 / % 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 (1U5Z)

1u5z


Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.871 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.294 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21313 2856 10.1 %THIN SHELLS
Rwork0.17773 ---
all0.1815 28265 --
obs0.18151 25409 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.888 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å20 Å2
2---0.11 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 1 36 4119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214187
X-RAY DIFFRACTIONr_bond_other_d0.0020.023760
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9465686
X-RAY DIFFRACTIONr_angle_other_deg0.76238723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0645513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024636
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02883
X-RAY DIFFRACTIONr_nbd_refined0.180.2589
X-RAY DIFFRACTIONr_nbd_other0.2290.24165
X-RAY DIFFRACTIONr_nbtor_other0.0830.22776
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.25
X-RAY DIFFRACTIONr_mcbond_it2.5752.52585
X-RAY DIFFRACTIONr_mcangle_it4.08454189
X-RAY DIFFRACTIONr_scbond_it3.0772.51602
X-RAY DIFFRACTIONr_scangle_it4.71151497
LS refinement shellResolution: 2.35→2.398 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rwork0.195 1680 -
Rfree-0 -
obs--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)
13.1461-0.12520.91152.7331-0.22722.56380.1006-0.2092-0.3960.06270.02980.20270.2755-0.2148-0.13050.1011-0.0141-0.03410.10910.10240.158311.45184.03274.6368
22.66950.40750.95532.6706-0.16673.82960.0179-0.31330.23350.3207-0.04490.4227-0.2728-0.22420.0270.0730.04420.09140.16150.05330.16556.1167105.94839.182
32.98610.13240.99743.6954-0.83932.95770.08270.1931-0.0274-0.0713-0.0891-0.45320.10060.29880.00640.05010.01710.0550.12740.08140.113626.0421100.8884-1.3595
44.81491.58435.9669.52164.693714.35110.2382-0.0941-0.6291-0.45350.17030.79240.8782-0.5263-0.40850.2739-0.1393-0.16880.29090.14140.3931-7.663683.1563-9.5482
59.218-3.99941.405210.6111-0.437411.1624-0.02510.31730.2861-0.66380.07711.4078-0.5072-1.1028-0.0520.25060.0712-0.11360.30330.16260.4320.9554117.8873-10.0897
69.85754.1672-1.69256.2674-4.141721.7778-0.47911.758-0.3046-1.65340.6037-0.68570.49780.0757-0.12450.5681-0.06910.1130.5537-0.09160.171222.390294.1774-23.5163
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA105 - 2412 - 138
2X-RAY DIFFRACTION2BB105 - 2412 - 138
3X-RAY DIFFRACTION3DC105 - 2412 - 138
4X-RAY DIFFRACTION4RD8 - 434 - 39
5X-RAY DIFFRACTION5SE6 - 422 - 38
6X-RAY DIFFRACTION6TF8 - 424 - 38

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