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- PDB-5ygs: Human TNFRSF25 death domain -

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Basic information

Entry
Database: PDB / ID: 5ygs
TitleHuman TNFRSF25 death domain
ComponentsHuman TNRSF25 death domain
KeywordsAPOPTOSIS / TNFRSF25 / TL1A / NFkappaB
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Death domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.691 Å
AuthorsYin, X. / Jin, T.
CitationJournal: Febs J. / Year: 2019
Title: Crystal structure and activation mechanism of DR3 death domain.
Authors: Yin, X. / Li, W. / Ma, H. / Zeng, W. / Peng, C. / Li, Y. / Liu, M. / Chen, Q. / Zhou, R. / Jin, T.
History
DepositionSep 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_validate_close_contact / struct_conn
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human TNRSF25 death domain
B: Human TNRSF25 death domain
C: Human TNRSF25 death domain
D: Human TNRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,60728
Polymers204,6684
Non-polymers3,93924
Water181
1
A: Human TNRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1527
Polymers51,1671
Non-polymers9856
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Human TNRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2488
Polymers51,1671
Non-polymers1,0817
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Human TNRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0566
Polymers51,1671
Non-polymers8895
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Human TNRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1527
Polymers51,1671
Non-polymers9856
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.690, 153.550, 98.240
Angle α, β, γ (deg.)90.000, 90.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Human TNRSF25 death domain


Mass: 51166.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9*PLUS
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.6 M ammonium sulfate, sodium citrate 5.6, 10% glycerol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03292 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03292 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.48
ReflectionResolution: 2.691→98.25 Å / Num. obs: 59937 / % possible obs: 99.6 % / Redundancy: 7.335 % / Net I/σ(I): 18.53
Reflection shellResolution: 2.696→2.793 Å / Rmerge(I) obs: 1.12 / % possible all: 96.56

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Processing

Software
NameVersionClassification
PHENIXv1.12-2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 2.691→98.25 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 3023 5 %random selection
Rwork0.1898 ---
obs-59934 99.63 %-
Refinement stepCycle: LAST / Resolution: 2.691→98.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14189 0 236 1 14426
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)
16.19010.36556.29322.119-0.11676.51130.0299-1.0553-0.34980.6408-0.05380.10730.04270.18690.03880.6504-0.0671-0.05960.74470.12110.303218.8283-3.494263.8608
20.7294-0.9517-0.39593.27611.33722.05980.0942-0.1190.0463-0.0956-0.0315-0.12560.00990.1933-0.05650.36220.0644-0.0620.63190.07020.373121.34277.402751.8565
32.36720.0167-0.7690.96710.24970.3192-0.16570.3199-0.4257-0.0837-0.11990.1676-0.7593-0.60520.23390.78980.1576-0.24720.6502-0.00330.50523.7182-6.024630.2432
45.382-3.5377-5.2212.60922.96066.5692-0.14070.0013-0.276-1.7232-0.24670.6516-1.03890.68120.48471.01430.0964-0.21370.5509-0.0240.488814.021518.82434.5663
51.1148-1.18040.13131.5902-0.77521.44720.20610.6377-0.93170.1425-0.22090.6075-0.61570.21560.00870.74570.0682-0.40620.8956-0.06830.9356-1.0913-1.023134.2241
64.321-2.38810.58081.42460.38144.8793-0.08150.0023-0.8364-0.98910.17371.28120.28880.6819-0.10550.7430.0761-0.31430.4730.02010.65729.3857-12.745639.743
71.1263-0.3044-0.73250.9728-0.44090.9256-0.0289-0.1191-0.0468-0.12740.1837-0.3150.04780.1872-0.13180.75780.1095-0.05990.76090.00420.216821.0184.150348.2057
80.7451-0.39010.25733.5094-0.05820.35260.12450.059-0.0306-0.2926-0.11650.30990.05690.0196-0.01050.41060.0343-0.05520.54970.03560.246613.997514.720252.3636
93.7679-1.06232.45624.692-0.58282.0544-0.59580.21830.1278-1.21860.23990.4075-0.687-0.05190.37630.7409-0.1329-0.19140.6338-0.07220.499734.249955.428732.76
103.12161.2506-0.23842.19420.0541.2119-0.11780.4591-0.5643-0.56320.143-0.16670.0179-0.1783-0.04480.47-0.0391-0.01360.4587-0.10510.362235.325140.309839.7283
112.1452-0.0625-0.4021.9286-0.85312.5554-0.1037-0.2535-0.24320.1073-0.2243-0.4727-0.11210.4990.34580.37660.0433-0.13160.49480.00870.70757.968641.060653.4892
127.6333.41080.30152.3327-1.48373.4729-0.27330.6421-0.3998-0.4779-0.0879-1.52950.12560.44610.34150.50070.05170.10610.5301-0.03880.86160.229749.42939.7385
132.66171.0506-0.03382.1202-0.02440.6562-0.14360.0342-0.2212-0.17190.0886-0.255-0.11980.00330.05810.41070.0032-0.08630.4201-0.07240.330633.675640.898847.8556
141.53020.01-0.9743.0633-0.34410.779-0.00830.33230.1615-0.0930.1327-0.0325-0.66370.0866-0.15780.8396-0.1575-0.05170.88450.02570.27520.466446.3966-1.2857
153.01391.0942-1.48242.74010.8671.56970.446-0.42470.7057-1.0765-0.30760.0221-0.7698-0.0879-0.13970.9661-0.04580.00420.85880.04430.7292.695659.656727.3175
162.04720.2312-0.7630.94391.27892.54140.2032-0.15960.39620.1680.0330.3264-0.6511-0.3481-0.23071.0746-0.05670.08780.7360.02590.46126.571448.599518.7072
170.558-0.2098-0.39752.0553-0.05132.60950.09150.05710.08260.2928-0.13780.0883-0.5029-0.04550.05060.5822-0.13460.01920.7187-0.01820.275315.234536.82363.3141
187.82790.1024-5.11056.9-3.07894.6954-0.6730.5591-0.83440.26920.0899-0.61860.1432-0.1930.51980.504-0.01050.03330.5993-0.12750.461434.2509-5.282123.5023
190.6452-0.42340.93231.1797-0.83092.69840.22670.13510.0095-0.0620.268-0.11240.12620.1986-0.45130.5480.04250.11280.7085-0.09530.391632.29470.087812.1484
200.8657-0.44870.10890.7878-0.69671.43520.05030.28710.24910.1626-0.3152-0.4923-0.11050.63150.2410.44-0.08920.08820.93110.12940.722150.539912.10527.5637
212.5146-0.0341-0.6713.1384-1.46533.4355-0.2322-0.0119-0.12920.3845-0.3331-0.9887-0.10750.46710.43670.4157-0.0748-0.01690.70310.0660.701450.08344.713317.1989
222.5676-0.22770.38760.8482-0.35890.5553-0.10480.1732-0.0748-0.23510.0331-0.24440.00580.16740.05540.4908-0.12630.12520.7122-0.09040.38728.86259.28990.6857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 43 )A2 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 119 )A44 - 119
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 162 )A120 - 162
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 186 )A163 - 186
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 219 )A187 - 219
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 246 )A220 - 246
7X-RAY DIFFRACTION7chain 'A' and (resid 247 through 283 )A247 - 283
8X-RAY DIFFRACTION8chain 'A' and (resid 284 through 457 )A284 - 457
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 43 )B1 - 43
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 119 )B44 - 119
11X-RAY DIFFRACTION11chain 'B' and (resid 120 through 219 )B120 - 219
12X-RAY DIFFRACTION12chain 'B' and (resid 220 through 246 )B220 - 246
13X-RAY DIFFRACTION13chain 'B' and (resid 247 through 456 )B247 - 456
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 119 )C1 - 119
15X-RAY DIFFRACTION15chain 'C' and (resid 120 through 152 )C120 - 152
16X-RAY DIFFRACTION16chain 'C' and (resid 153 through 246 )C153 - 246
17X-RAY DIFFRACTION17chain 'C' and (resid 247 through 457 )C247 - 457
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 32 )D1 - 32
19X-RAY DIFFRACTION19chain 'D' and (resid 33 through 73 )D33 - 73
20X-RAY DIFFRACTION20chain 'D' and (resid 74 through 201 )D74 - 201
21X-RAY DIFFRACTION21chain 'D' and (resid 202 through 315 )D202 - 315
22X-RAY DIFFRACTION22chain 'D' and (resid 316 through 458 )D316 - 458

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