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- PDB-1tnr: CRYSTAL STRUCTURE OF THE SOLUBLE HUMAN 55 KD TNF RECEPTOR-HUMAN T... -

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Basic information

Entry
Database: PDB / ID: 1tnr
TitleCRYSTAL STRUCTURE OF THE SOLUBLE HUMAN 55 KD TNF RECEPTOR-HUMAN TNF-BETA COMPLEX: IMPLICATIONS FOR TNF RECEPTOR ACTIVATION
Components
  • TUMOR NECROSIS FACTOR BETA
  • TUMOR NECROSIS FACTOR RECEPTOR P55
KeywordsCOMPLEX(LYMPHOKINE/RECEPTOR) / COMPLEX(LYMPHOKINE-RECEPTOR) / COMPLEX(LYMPHOKINE-RECEPTOR) complex
Function / homology
Function and homology information


positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / positive regulation of lipid metabolic process / aortic valve development / positive regulation of chronic inflammatory response to antigenic stimulus / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / regulation of membrane lipid metabolic process ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / positive regulation of lipid metabolic process / aortic valve development / positive regulation of chronic inflammatory response to antigenic stimulus / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / regulation of membrane lipid metabolic process / positive regulation of humoral immune response mediated by circulating immunoglobulin / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / tumor necrosis factor binding / negative regulation of cardiac muscle hypertrophy / TNF signaling / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / TNFR1-mediated ceramide production / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / prostaglandin metabolic process / Interleukin-10 signaling / humoral immune response / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / cell surface receptor signaling pathway via JAK-STAT / lymph node development / negative regulation of fibroblast proliferation / response to nutrient / cytokine activity / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / negative regulation of inflammatory response / positive regulation of type II interferon production / cytokine-mediated signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of inflammatory response / cell-cell signaling / signaling receptor activity / response to lipopolysaccharide / transcription by RNA polymerase II / response to hypoxia / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / receptor complex / defense response to Gram-positive bacterium / defense response to bacterium / immune response / membrane raft / response to xenobiotic stimulus / inflammatory response / signaling receptor binding / Golgi membrane / apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Lymphotoxin-alpha / Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumour necrosis factor / 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. ...Lymphotoxin-alpha / Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / : / Tumour necrosis factor / 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
Lymphotoxin-alpha / Tumor necrosis factor receptor superfamily member 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.85 Å
AuthorsBanner, D.W.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and preliminary crystallographic analysis of a TNF-beta-55 kDa TNF receptor complex.
Authors: D'Arcy, A. / Banner, D.W. / Janes, W. / Winkler, F.K. / Loetscher, H. / Schonfeld, H.J. / Zulauf, M. / Gentz, R. / Lesslauer, W.
History
DepositionMay 9, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR BETA
R: TUMOR NECROSIS FACTOR RECEPTOR P55


Theoretical massNumber of molelcules
Total (without water)31,6402
Polymers31,6402
Non-polymers00
Water82946
1
A: TUMOR NECROSIS FACTOR BETA
R: TUMOR NECROSIS FACTOR RECEPTOR P55

A: TUMOR NECROSIS FACTOR BETA
R: TUMOR NECROSIS FACTOR RECEPTOR P55

A: TUMOR NECROSIS FACTOR BETA
R: TUMOR NECROSIS FACTOR RECEPTOR P55


Theoretical massNumber of molelcules
Total (without water)94,9196
Polymers94,9196
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12540 Å2
ΔGint-52 kcal/mol
Surface area40120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.640, 145.640, 145.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein TUMOR NECROSIS FACTOR BETA


Mass: 15872.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01374
#2: Protein TUMOR NECROSIS FACTOR RECEPTOR P55


Mass: 15766.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: SF9 cells / References: UniProt: P19438
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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

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Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.75 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %PEG40001reservoir
2200-400 mM1reservoirMgCl
32 %beta-octyl glucoside1reservoir
4100 mMsodium cacodylate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.83 Å / Num. obs: 13270 / % possible obs: 99.7 % / Num. measured all: 43171 / Rmerge(I) obs: 0.078

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.85→50 Å / σ(F): 2
Details: THE RECEPTOR REGIONS R 15 - R 29 AND R 144 - R 153, I.E. THE N- AND C-TERMINAL ENDS OF THE RECEPTOR, MUST BE REGARDED AS TENTATIVE. THERE IS WEAK ELECTRON DENSITY FOR THE THREE CARBOHYDRATE ...Details: THE RECEPTOR REGIONS R 15 - R 29 AND R 144 - R 153, I.E. THE N- AND C-TERMINAL ENDS OF THE RECEPTOR, MUST BE REGARDED AS TENTATIVE. THERE IS WEAK ELECTRON DENSITY FOR THE THREE CARBOHYDRATE CHAINS ATTACHED TO ASPARAGINES R 25, R 116 AND R 122. THESE POSITIONS HAVE BEEN MARKED WITH WATER MOLECULES 45, 42 AND 43, RESPECTIVELY. ASPARTIC ACID A 50 ADOPTS THE UNUSUAL EPSILON CONFORMATION ON BINDING THE RECEPTOR. THE PEPTIDE PLANES A 40 - A 41 AND R 100 - R 101 MAY HAVE THE WRONG ORIENTATION.
RfactorNum. reflection
Rwork0.16 -
obs0.16 11513
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 0 46 2254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.8

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