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- PDB-1ext: EXTRACELLULAR DOMAIN OF THE 55KDA TUMOR NECROSIS FACTOR RECEPTOR.... -

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Basic information

Entry
Database: PDB / ID: 1ext
TitleEXTRACELLULAR DOMAIN OF THE 55KDA TUMOR NECROSIS FACTOR RECEPTOR. CRYSTALLIZED AT PH3.7 IN P 21 21 21.
ComponentsTUMOR NECROSIS FACTOR RECEPTORTNF receptor superfamily
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 / tumor necrosis factor binding ...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 / tumor necrosis factor binding / TNFs bind their physiological receptors / negative regulation of cardiac muscle hypertrophy / TNF signaling / TNFR1-mediated ceramide production / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-induced proapoptotic signaling / positive regulation of execution phase of apoptosis / prostaglandin metabolic process / Interleukin-10 signaling / 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 / negative regulation of inflammatory response / positive regulation of inflammatory response / cytokine-mediated signaling pathway / 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. / TNFR/NGFR cysteine-rich region ...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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNaismith, J.H. / Sprang, S.R.
Citation
Journal: Structure / Year: 1996
Title: Structures of the extracellular domain of the type I tumor necrosis factor receptor.
Authors: Naismith, J.H. / Devine, T.Q. / Kohno, T. / Sprang, S.R.
#1: 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.
#2: 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.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Crystal Structure of the Soluble Human 55 Kd Tnf Receptor-Human Tnf Beta Complex: Implications for Tnf Receptor Activation
Authors: Banner, D.W. / D'Arcy, A. / Janes, W. / Gentz, R. / Schoenfeld, H.J. / Broger, C. / Loetscher, H. / Lesslauer, W.
History
DepositionJul 3, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,9846
Polymers36,6722
Non-polymers3124
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-51 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.810, 83.060, 67.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TUMOR NECROSIS FACTOR RECEPTOR / TNF receptor superfamily


Mass: 18335.830 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: THE CONSTRUCT CONTAINS RESIDUES 12 TO 172 OF THE MATURE SEQUENCE OF THE ENTIRE RECEPTOR. RESIDUE 11 IS MUTATED TO MET AS A RESULT OF THE EXPRESSION SYSTEM
Production host: Escherichia coli (E. coli) / References: UniProt: P19438
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 3.03 Å3/Da / Density % sol: 58 %
Crystal growpH: 3.7 / Details: CRYSTALLIZED AT PH3.7 IN P 21 21 21.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 293 K / 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 formulaDetails
10.5 mg/mlprotein1drop
350 mMsodium formate1drop
41 M1dropMgSO4
51.7 M1reservoirMgSO4
6100 mMsodium formate1reservoir
2PBS1drop0.025ml

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.992
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionNum. obs: 36977 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.85→1.93 Å / % possible all: 77
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 11 Å / Num. obs: 37300

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NCF

1ncf


Resolution: 1.85→8 Å / Cross valid method: FREE R / σ(F): 0
Details: ATOMS WITH ZERO OCCUPANCY ARE STEREOCHEMICALLY MODELED (68 OUT OF 2162) AND WERE NOT LOCATED IN EXPERIMENTAL MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3685 10 %RANDOM
Rwork0.203 ---
obs0.203 36977 --
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 16 400 2888
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.683
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.29
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.519
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.29
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.519

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