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- PDB-5ygp: Human TNFRSF25 death domain mutant-D412E -

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Basic information

Entry
Database: PDB / ID: 5ygp
TitleHuman TNFRSF25 death domain mutant-D412E
ComponentsTNFRSF25 death domain
KeywordsAPOPTOSIS / TNFRSF25 / TL1A / death domain / 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-maltose / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsYin, X. / Jin, T.C.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Structure of human TNFRSF25 death domain mutant-D412E at 2.0 Angstroms resolution
Authors: Yin, X.Y. / Jin, T.C.
History
DepositionSep 25, 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _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: TNFRSF25 death domain
B: TNFRSF25 death domain
C: TNFRSF25 death domain
D: TNFRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,76615
Polymers204,7244
Non-polymers2,04211
Water1,18966
1
A: TNFRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7154
Polymers51,1811
Non-polymers5343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TNFRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8125
Polymers51,1811
Non-polymers6304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TNFRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6193
Polymers51,1811
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TNFRSF25 death domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6193
Polymers51,1811
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.620, 155.020, 74.030
Angle α, β, γ (deg.)90.000, 90.180, 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
TNFRSF25 death domain


Mass: 51181.016 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 / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Description: the entry contains Friedel pairs in I_Plus/Minus columns
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulfate, sodium citrate 5.6, 10% glycerol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.43
ReflectionResolution: 2.09→46.99 Å / Num. obs: 126843 / % possible obs: 98 % / Redundancy: 3.3 % / Net I/σ(I): 10.57
Reflection shellResolution: 2.092→2.167 Å / Rmerge(I) obs: 0.5573 / % possible all: 91.22

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Processing

Software
NameVersionClassification
PHENIXv1.12-2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H7Q

5h7q


Resolution: 2.09→46.99 Å / Cross valid method: FREE R-VALUE
Details: the entry contains Friedel pairs in I_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 3853 1.6 %random selection
Rwork0.2178 ---
obs-126833 94.3863 %-
Refinement stepCycle: LAST / Resolution: 2.09→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14064 0 127 66 14257
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)
11.7207-0.1442-0.03770.76580.09320.4954-0.2491-0.14990.4198-0.0240.3223-0.0113-0.19730.062-0.12160.23850.0462-0.07190.5097-0.01560.446234.60829.7973112.9911
20.505-0.1268-0.44260.413-0.18861.36780.00190.03670.0432-0.08960.09420.11260.1375-0.0519-0.10340.2045-0.0212-0.07040.3433-0.05390.353944.401616.849499.1447
30.3832-0.25070.33330.69840.69691.80220.03270.02280.098-0.08030.0127-0.0667-0.04910.1750.00640.17340.015-0.02180.4433-0.05580.396964.212415.6441118.1005
40.3832-0.20170.25770.3495-0.21210.4375-0.0068-0.21490.22210.00950.10410.14840.01450.0594-0.05820.20390.031-0.05020.3784-0.08070.359348.866717.8752131.8829
50.75060.25210.01370.62360.0010.4728-0.0843-0.2236-0.304-0.02370.0917-0.20990.07950.12890.06040.2140.05610.02480.4420.03260.462959.3096-22.8803130.6847
60.37980.03330.35370.91340.17150.3578-0.07780.1273-0.10870.02030.1460.16450.0115-0.09310.03130.18480.0675-0.00950.3758-0.00240.358838.3531-24.6678129.3001
70.4832-0.00920.22951.03810.12270.4197-0.0432-0.1588-0.04610.11630.04610.1550.0940.04780.04380.2290.07470.0090.46490.06560.337731.8079-15.7427140.6566
80.67670.16350.51660.50860.1480.554-0.03410.0287-0.26090.05190.0623-0.02040.11070.03040.09080.19080.06560.01420.34470.01990.432743.0103-29.7411131.164
90.97890.29240.3610.8491-0.02730.1599-0.051-0.25-0.1330.12540.17790.1180.1017-0.01540.17360.18910.06770.03270.4240.06210.37737.2686-17.0825137.7024
102.20590.75080.06860.97920.39940.2007-0.013-0.3593-0.09480.1158-0.02930.0624-0.08370.22880.05060.27710.04510.01080.4852-0.08460.297247.17660.8595144.0634
110.43250.2642-0.09060.7322-0.21460.07780.0017-0.1577-0.0992-0.0131-0.1278-0.062-0.07640.0017-0.00220.15420.0347-0.02080.4638-0.01850.284563.3672-0.2916131.3364
122.0094-0.0840.48381.17490.01241.68610.13220.1149-0.11840.0651-0.0456-0.08280.40330.22780.00050.23160.052-0.02920.3915-0.07440.39220.9876-30.1388111.5418
130.6677-0.28180.16830.3406-0.15980.74720.01020.07620.0203-0.0735-0.0195-0.0326-0.01380.022-0.02250.21280.04780.03290.3360.00750.363110.7113-16.392103.8183
140.777-0.2109-0.34390.53930.07521.40680.03130.0568-0.0158-0.0321-0.05-0.01660.098-0.20130.02410.27460.0164-0.01040.40210.01410.3081-3.8249-12.514695.995
150.4892-0.23870.48550.6194-0.43771.03520.01960.1767-0.0499-0.1996-0.0743-0.22370.06840.2211-0.06620.22590.04320.07920.4164-0.00090.358914.4829-20.554997.5974
160.1533-0.0685-0.26570.30540.28570.7211-0.06270.16770.0681-0.1820.01150.07290.15660.0529-0.05670.29150.00850.03110.44220.04250.33970.639-14.4768100.2057
170.3688-0.2373-0.4250.5252-0.38751.9687-0.02450.3017-0.19140.0604-0.06640.09790.169-0.0443-0.10640.13260.01660.00680.5595-0.00450.4249-11.5575-15.2367118.1458
180.66780.09790.03360.7289-0.14810.7113-0.071-0.1206-0.20560.0780.0719-0.0675-0.0344-0.03820.00280.15930.04250.01860.49390.03830.33823.9373-17.3094132.0861
191.53210.40380.01120.86820.50260.45760.04110.02550.61650.0542-0.00020.2533-0.0222-0.0958-0.08340.22070.095-0.02530.4652-0.06290.5336-9.298928.7646128.6191
200.88370.31910.18070.7219-0.17150.4601-0.18750.07370.1518-0.10630.0496-0.04440.1080.05560.09960.15810.0391-0.02550.47650.00950.35130.051915.2575125.2762
210.4569-0.2097-0.20540.6937-0.25210.3311-0.0355-0.25130.48630.12530.1652-0.3022-0.373-0.0414-0.10860.25610.0907-0.07510.5947-0.15270.629421.48330.6292140.8051
220.66610.018-0.15410.572-0.2330.151-0.1592-0.43930.19950.2320.1688-0.1365-0.0453-0.1269-0.03440.26410.1378-0.11140.6386-0.19990.478520.16417.6322142.2706
230.8705-0.0071-0.35220.55050.05430.2994-0.07580.08670.6997-0.0120.15190.0078-0.08870.0262-0.01660.2040.078-0.03940.4567-0.01980.63578.257329.7984127.7199
240.62570.0998-0.03931.20010.10210.1012-0.0295-0.38070.4056-0.0005-0.01420.01220.08440.05610.06790.16630.0716-0.03560.4815-0.06280.387815.220917.358137.7219
251.41390.83320.04050.95720.04720.3252-0.1167-0.5757-0.01420.0197-0.0472-0.13950.0054-0.0082-0.01260.15290.0516-0.02410.73110.0570.3215.1826-0.5094144.0627
260.48220.0790.0760.69960.25490.0881-0.0098-0.0534-0.05940.0854-0.00810.14770.0339-0.03430.0340.15610.04050.00430.4903-0.00280.3389-11.02740.5261130.8689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 51 )A4 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 357 )A52 - 357
3X-RAY DIFFRACTION3chain 'A' and (resid 358 through 398 )A358 - 398
4X-RAY DIFFRACTION4chain 'A' and (resid 399 through 456 )A399 - 456
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 73 )B4 - 73
6X-RAY DIFFRACTION6chain 'B' and (resid 74 through 143 )B74 - 143
7X-RAY DIFFRACTION7chain 'B' and (resid 144 through 201 )B144 - 201
8X-RAY DIFFRACTION8chain 'B' and (resid 202 through 315 )B202 - 315
9X-RAY DIFFRACTION9chain 'B' and (resid 316 through 357 )B316 - 357
10X-RAY DIFFRACTION10chain 'B' and (resid 358 through 398 )B358 - 398
11X-RAY DIFFRACTION11chain 'B' and (resid 399 through 456 )B399 - 456
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 43 )C6 - 43
13X-RAY DIFFRACTION13chain 'C' and (resid 44 through 142 )C44 - 142
14X-RAY DIFFRACTION14chain 'C' and (resid 143 through 201 )C143 - 201
15X-RAY DIFFRACTION15chain 'C' and (resid 202 through 315 )C202 - 315
16X-RAY DIFFRACTION16chain 'C' and (resid 316 through 357 )C316 - 357
17X-RAY DIFFRACTION17chain 'C' and (resid 358 through 398 )C358 - 398
18X-RAY DIFFRACTION18chain 'C' and (resid 399 through 457 )C399 - 457
19X-RAY DIFFRACTION19chain 'D' and (resid 4 through 43 )D4 - 43
20X-RAY DIFFRACTION20chain 'D' and (resid 44 through 106 )D44 - 106
21X-RAY DIFFRACTION21chain 'D' and (resid 107 through 162 )D107 - 162
22X-RAY DIFFRACTION22chain 'D' and (resid 163 through 219 )D163 - 219
23X-RAY DIFFRACTION23chain 'D' and (resid 220 through 315 )D220 - 315
24X-RAY DIFFRACTION24chain 'D' and (resid 316 through 357 )D316 - 357
25X-RAY DIFFRACTION25chain 'D' and (resid 358 through 398 )D358 - 398
26X-RAY DIFFRACTION26chain 'D' and (resid 399 through 457 )D399 - 457

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