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- PDB-1ncf: A NEW PARADIGM FOR TUMOR NECROSIS FACTOR SIGNALLING -

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Basic information

Entry
Database: PDB / ID: 1ncf
TitleA NEW PARADIGM FOR TUMOR NECROSIS FACTOR SIGNALLING
ComponentsTUMOR NECROSIS FACTOR RECEPTOR
KeywordsSIGNALLING PROTEIN / BINDING PROTEIN / CYTOKINE
Function / homology
Function and homology information


positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / TNFs bind their physiological receptors ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / TNFs bind their physiological receptors / tumor necrosis factor binding / negative regulation of cardiac muscle hypertrophy / TNF signaling / regulation of establishment of endothelial barrier / TNFR1-mediated ceramide production / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-induced proapoptotic signaling / prostaglandin metabolic process / Interleukin-10 signaling / positive regulation of execution phase of apoptosis / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / Regulation of TNFR1 signaling / cytokine-mediated signaling pathway / negative regulation of inflammatory response / positive regulation of inflammatory response / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of canonical NF-kappaB signal transduction / transcription by RNA polymerase II / receptor complex / defense response to bacterium / inflammatory response / membrane raft / Golgi membrane / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. ...Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsNaismith, J.H. / Sprang, S.R.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystallographic evidence for dimerization of unliganded tumor necrosis factor receptor.
Authors: Naismith, J.H. / Devine, T.Q. / Brandhuber, B.J. / Sprang, S.R.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Two Crystal Forms of the Extracellular Domain of Type I Tumor Necrosis Factor Receptor
Authors: Rodseth, L.E. / Brandhuber, B. / Devine, T.Q. / Eck, M.J. / Hale, K. / Naismith, J.H. / Sprang, S.R.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Crystal Structure of the Soluble Human 55 Kd Tnf Receptor-Human Tnfb Complex: Implication for Tnf Receptor Activation
Authors: Banner, D.W. / Arcy, A. / Janes, W. / Gentz, R. / Schoenfield, H. / Broger, C. / Loetscher, H. / Lesslauer, W.
History
DepositionOct 12, 1994Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR RECEPTOR
B: TUMOR NECROSIS FACTOR RECEPTOR


Theoretical massNumber of molelcules
Total (without water)36,6722
Polymers36,6722
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-5 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.000, 69.000, 185.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.745, 0.008, 0.667), (0.02, -0.999, 0.035), (0.667, 0.04, 0.744)14.567, 27.107, -6.043
2given(-0.746, -0.029, 0.665), (0.045, -0.999, 0.007), (0.664, 0.035, 0.747)14.683, 27.245, -5.932
3given(-0.814, -0.073, 0.576), (0.147, -0.986, 0.083), (0.562, 0.153, 0.813)19.59, 22.201, -7.719
4given(-0.862, 0.043, 0.505), (0.102, -0.961, 0.255), (0.496, 0.272, 0.825)23.919, 11.131, -7.606
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD M1 A 15 .. A 52 B 15 .. B 52 0.214 THE NCS TRANSFORMATION BETWEEN DOMAIN 1 OF THE TWO MONOMERS IN THE ASYMMETRIC UNIT. M2 A 55 .. A 96 B 55 .. B 96 0.314 THE NCS TRANSFORMATION BETWEEN DOMAIN 2 OF THE TWO MONOMERS IN THE ASYMMETRIC UNIT. M3 A 98 .. A 137 B 98 .. B 137 0.348 THE NCS TRANSFORMATION BETWEEN DOMAIN 3 OF THE TWO MONOMERS IN THE ASYMMETRIC UNIT. M4 A 139 .. A 150 B 139 .. B 150 0.743 THE NCS TRANSFORMATION BETWEEN DOMAIN 4 OF THE TWO MONOMERS IN THE ASYMMETRIC UNIT. S1 B 13 .. B 156 ? 13 .. ? 156 THIS GENERATES A MOLECULE WHICH MAY FORM AN ALTERNATIVE DIMER TO THE ONE DESCRIBED BY THE COORDINATES. SYMMETRY1 1 -1.000000 0.000000 0.000000 34.50000 SYMMETRY2 1 0.000000 1.000000 0.000000 -34.50000 SYMMETRY3 1 0.000000 0.000000 -1.000000 46.30000

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Components

#1: Protein TUMOR NECROSIS FACTOR RECEPTOR / TYPE I RECEPTOR / STNFR1


Mass: 18335.830 Da / Num. of mol.: 2 / Mutation: R11M
Source method: isolated from a genetically manipulated source
Details: THE CONSTRUCT CONTAINS RESIDUES 12 - 172 OF THE MATURE RECEPTOR SEQUENCE
Source: (gene. exp.) Homo sapiens (human)
Description: RESIDUE 11 IS MUTATED TO MET AS A RESULT OF THE EXPRESSION SYSTEM
Production host: Escherichia coli (E. coli) / References: UniProt: P19438
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSOURCE 1 THE CONSTRUCT CONTAINS RESIDUES 12 - 172 OF THE MATURE SEQUENCE OF THE ENTIRE RECEPTOR. ...SOURCE 1 THE CONSTRUCT CONTAINS RESIDUES 12 - 172 OF THE MATURE SEQUENCE OF THE ENTIRE RECEPTOR. RESIDUE 11 IS MUTATED TO MET AS A RESULT OF THE EXPRESSION SYSTEM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.06 %
Crystal grow
*PLUS
Temperature: 293 K / pH: 8.5 / Method: vapor diffusion, sitting drop / Details: Rodseth, L.E., (1994) J.Mol.Biol., 239, 332.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.6 mg/mlprotein1drop
225 %(v/v)MPD1drop
350 mMTris-HCl1drop
40.1 %(w/v)beta-octylglucoside1drop
5100 mM1dropNaCl
6250 mMammonium acetate1drop
754 %MPD1reservoir
8100 mMTris-HCl1reservoir
9500 mMammonium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 24198 / % possible obs: 100 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. obs: 21874 / Redundancy: 6.5 % / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Mean I/σ(I) obs: 5.2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.25→6 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.249 -10 %
Rwork0.193 --
obs0.193 19343 93 %
Displacement parametersBiso mean: 31.58 Å2
Refinement stepCycle: LAST / Resolution: 2.25→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 0 260 2422
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.605
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.02
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it2.52.5
Refinement
*PLUS
Rfactor all: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.02

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