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- PDB-5cir: Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to ... -

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Basic information

Entry
Database: PDB / ID: 5cir
TitleCrystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)
Components
  • Tumor necrosis factor ligand superfamily member 10
  • Tumor necrosis factor receptor superfamily member 10A
KeywordsAPOPTOSIS / binding and specificity / ligand-receptor complex / TNF receptor family
Function / homology
Function and homology information


death receptor activity / TRAIL binding / TRAIL signaling / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / activation of NF-kappaB-inducing kinase activity / Caspase activation via Death Receptors in the presence of ligand / tumor necrosis factor receptor binding ...death receptor activity / TRAIL binding / TRAIL signaling / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / activation of NF-kappaB-inducing kinase activity / Caspase activation via Death Receptors in the presence of ligand / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Death Receptors and Ligands / RIPK1-mediated regulated necrosis / positive regulation of release of cytochrome c from mitochondria / plasma membrane raft / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / cytokine activity / Cell surface interactions at the vascular wall / cellular response to mechanical stimulus / cell-cell signaling / signaling receptor activity / protease binding / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / immune response / positive regulation of apoptotic process / membrane raft / signaling receptor binding / apoptotic process / cell surface / Golgi apparatus / signal transduction / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Tumour necrosis factor receptor 10 / Tumor necrosis factor receptor 10, N-terminal / Tumour necrosis factor receptor 10A/B, death domain / : / Tumour necrosis factor ligand 10/11 / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. ...Tumour necrosis factor receptor 10 / Tumor necrosis factor receptor 10, N-terminal / Tumour necrosis factor receptor 10A/B, death domain / : / Tumour necrosis factor ligand 10/11 / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / Jelly Rolls - #40 / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 10A / Tumor necrosis factor ligand superfamily member 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSheriff, S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: The structure of the death receptor 4-TNF-related apoptosis-inducing ligand (DR4-TRAIL) complex.
Authors: Ramamurthy, V. / Yamniuk, A.P. / Lawrence, E.J. / Yong, W. / Schneeweis, L.A. / Cheng, L. / Murdock, M. / Corbett, M.J. / Doyle, M.L. / Sheriff, S.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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
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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 10
B: Tumor necrosis factor ligand superfamily member 10
D: Tumor necrosis factor ligand superfamily member 10
E: Tumor necrosis factor receptor superfamily member 10A
F: Tumor necrosis factor receptor superfamily member 10A
G: Tumor necrosis factor receptor superfamily member 10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3058
Polymers94,2046
Non-polymers1012
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14900 Å2
ΔGint-54 kcal/mol
Surface area30440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.600, 87.600, 107.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixDetailsVector
1given(1), (1), (1)
2given(0.057355, 0.708067, 0.703812), (0.741502, 0.441835, -0.504932), (-0.668495, 0.550839, -0.499692)A to B44.94, -34.386, -12.311
3given(0.061362, 0.706339, 0.705209), (0.742935, 0.439508, -0.504857), (-0.666546, 0.554903, -0.497795)B to D44.897, -34.328, -12.292
4given(0.017137, 0.724811, 0.688735), (0.742818, 0.451858, -0.494009), (-0.669274, 0.520071, -0.530659)E to F45.066, -34.239, -12.575
5given(0.057723, 0.687378, 0.724002), (0.771874, 0.429206, -0.469033), (-0.633149, 0.585913, -0.505795)G to E45.658, -33.857, -13.153

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 10 / Apo-2 ligand / Apo-2L / TNF-related apoptosis-inducing ligand / Protein TRAIL


Mass: 19652.049 Da / Num. of mol.: 3 / Fragment: Residues 114-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF10, APO2L, TRAIL / Plasmid: pET28-NHis-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50591
#2: Protein Tumor necrosis factor receptor superfamily member 10A / Death receptor 4 / TNF-related apoptosis-inducing ligand receptor 1 / TRAIL-R1


Mass: 11749.284 Da / Num. of mol.: 3 / Fragment: Extracellular domain residues 125-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF10A, APO2, DR4, TRAILR1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Oragami B(DE3) / References: UniProt: O00220
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM MMT (1:2:2 ratio of DL-malic acid, MES, Tris base), pH 5.0, 22.2%(W/V) PEG 2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16742 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 71.79 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 20.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 6.4 / Rejects: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRAIL FROM 1D0G AND DR4 FROM 1DOG DR5

1d0g

1dog


Resolution: 3→27.6 Å / Cor.coef. Fo:Fc: 0.9265 / Cor.coef. Fo:Fc free: 0.8932 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.372
Details: Non-crystallographic symmetry was used in the form of Local Structure Similarity Restraints (LSSR) with automatic pruning of discrepant residues and with a TARGET_WEIGHT OF 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 1049 6.34 %RANDOM
Rwork0.1767 ---
obs0.1792 16541 99.89 %-
Displacement parametersBiso max: 135.15 Å2 / Biso mean: 42.22 Å2 / Biso min: 7.15 Å2
Baniso -1Baniso -2Baniso -3
1-4.728 Å20 Å20 Å2
2---8.4057 Å20 Å2
3---3.6777 Å2
Refine analyzeLuzzati coordinate error obs: 0.309 Å
Refinement stepCycle: final / Resolution: 3→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5601 0 2 8 5611
Biso mean--38.51 21.52 -
Num. residues----752
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1854SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes112HARMONIC2
X-RAY DIFFRACTIONt_gen_planes868HARMONIC5
X-RAY DIFFRACTIONt_it5752HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion776SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6230SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5752HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7806HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion19.72
LS refinement shellResolution: 3→3.21 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3035 206 7.04 %
Rwork0.2101 2722 -
all0.2166 2928 -
obs--99.89 %

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