[English] 日本語
Yorodumi
- PDB-1xu2: The crystal structure of APRIL bound to BCMA -

+
Open data


ID or keywords:

Loading...

-
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 / immunoglobulin mediated immune response ...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 / immunoglobulin mediated immune response / endomembrane system / 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. / Jelly Rolls - #40 ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more