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- PDB-3alq: Crystal structure of TNF-TNFR2 complex -

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Basic information

Entry
Database: PDB / ID: 3alq
TitleCrystal structure of TNF-TNFR2 complex
Components
  • Tumor necrosis factor
  • Tumor necrosis factor receptor superfamily member 1B
KeywordsCYTOKINE/CYTOKINE RECEPTOR / LIGAND-RECEPTOR COMPLEX / CYTOKINE / CYTOKINE-CYTOKINE RECEPTOR complex
Function / homology
Function and homology information


glial cell-neuron signaling / regulation of cytokine production involved in immune response / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / negative regulation of L-glutamate import across plasma membrane / negative regulation of alkaline phosphatase activity / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium ...glial cell-neuron signaling / regulation of cytokine production involved in immune response / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / negative regulation of L-glutamate import across plasma membrane / negative regulation of alkaline phosphatase activity / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / varicosity / positive regulation of fractalkine production / positive regulation of vitamin D biosynthetic process / aortic valve development / tumor necrosis factor receptor activity / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of translational initiation by iron / response to 3,3',5-triiodo-L-thyronine / negative regulation of extracellular matrix constituent secretion / response to macrophage colony-stimulating factor / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / positive regulation of apoptotic process involved in morphogenesis / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of I-kappaB phosphorylation / regulation of T cell cytokine production / positive regulation of hair follicle development / negative regulation of myelination / : / negative regulation of neuroinflammatory response / negative regulation of bicellular tight junction assembly / TNFs bind their physiological receptors / negative regulation of cytokine production involved in immune response / response to isolation stress / negative regulation of amyloid-beta clearance / negative regulation of vascular wound healing / tumor necrosis factor binding / inflammatory response to wounding / positive regulation of calcidiol 1-monooxygenase activity / triglyceride storage / positive regulation of myelination / positive regulation of interleukin-18 production / positive regulation of action potential / death receptor agonist activity / positive regulation of protein transport / TNF signaling / negative regulation of cardiac muscle hypertrophy / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / leukocyte migration involved in inflammatory response / embryonic digestive tract development / regulation of neuroinflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / response to fructose / cellular response to toxic substance / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / leukocyte tethering or rolling / positive regulation of mononuclear cell migration / negative regulation of myoblast differentiation / positive regulation of fever generation / endothelial cell apoptotic process / regulation of establishment of endothelial barrier / negative regulation of D-glucose import / negative regulation of oxidative phosphorylation / macrophage activation involved in immune response / positive regulation of protein localization to cell surface / TNFR1-mediated ceramide production / positive regulation of protein-containing complex disassembly / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / negative regulation of systemic arterial blood pressure / tumor necrosis factor receptor binding / positive regulation of heterotypic cell-cell adhesion / regulation of immunoglobulin production / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of hepatocyte proliferation / positive regulation of programmed cell death / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / regulation of metabolic process / regulation of canonical NF-kappaB signal transduction / regulation of fat cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / regulation of myelination / cortical actin cytoskeleton organization / positive regulation of DNA biosynthetic process
Similarity search - Function
Tumour necrosis factor receptor 1B / Tumor necrosis factor receptor 1B, N-terminal / : / Tumour necrosis factor alpha / 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. ...Tumour necrosis factor receptor 1B / Tumor necrosis factor receptor 1B, N-terminal / : / Tumour necrosis factor alpha / 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. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Tumor necrosis factor / Tumor necrosis factor receptor superfamily member 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMukai, Y. / Nakamura, T. / Yamagata, Y. / Tsutsumi, Y.
CitationJournal: Sci.Signal. / Year: 2010
Title: Solution of the Structure of the TNF-TNFR2 Complex
Authors: Mukai, Y. / Nakamura, T. / Yoshikawa, M. / Yoshioka, Y. / Tsunoda, S.I. / Nakagawa, S. / Yamagata, Y. / Tsutsumi, Y.
History
DepositionAug 6, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: 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
B: Tumor necrosis factor
C: Tumor necrosis factor
D: Tumor necrosis factor
E: Tumor necrosis factor
F: Tumor necrosis factor
R: Tumor necrosis factor receptor superfamily member 1B
S: Tumor necrosis factor receptor superfamily member 1B
T: Tumor necrosis factor receptor superfamily member 1B
U: Tumor necrosis factor receptor superfamily member 1B
V: Tumor necrosis factor receptor superfamily member 1B
W: Tumor necrosis factor receptor superfamily member 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,74118
Polymers216,38812
Non-polymers3546
Water19811
1
A: Tumor necrosis factor
B: Tumor necrosis factor
C: Tumor necrosis factor
R: Tumor necrosis factor receptor superfamily member 1B
S: Tumor necrosis factor receptor superfamily member 1B
T: Tumor necrosis factor receptor superfamily member 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3719
Polymers108,1946
Non-polymers1773
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14240 Å2
ΔGint-58 kcal/mol
Surface area41620 Å2
MethodPISA
2
D: Tumor necrosis factor
E: Tumor necrosis factor
F: Tumor necrosis factor
U: Tumor necrosis factor receptor superfamily member 1B
V: Tumor necrosis factor receptor superfamily member 1B
W: Tumor necrosis factor receptor superfamily member 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3719
Polymers108,1946
Non-polymers1773
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14280 Å2
ΔGint-58 kcal/mol
Surface area41460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.470, 117.356, 246.835
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 / TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a / Cachectin


Mass: 17279.377 Da / Num. of mol.: 6 / Fragment: soluble form / Mutation: K11M, K65S, K90P, K98R, K112N, K128P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNF, TNFA, TNFSF2 / Plasmid: PYAS (MODIFIED FROM PUC18) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01375
#2: Protein
Tumor necrosis factor receptor superfamily member 1B / Tumor necrosis factor receptor 2 / TNF-R2 / Tumor necrosis factor-binding protein 2 / TBPII / TBP-2


Mass: 18785.223 Da / Num. of mol.: 6 / Fragment: residues in UNP 33-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFBR, TNFR2, TNFRSF1B / Plasmid: PYAS (MODIFIED FROM PUC18) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20333
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 45945 / % possible obs: 98.9 % / Rmerge(I) obs: 0.183 / Net I/σ(I): 10.75
Reflection shellResolution: 2.95→3.06 Å / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.51 / Num. unique all: 4075 / % possible all: 89.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX1.5_2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2e7a

2e7a


Resolution: 3→49.96 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 4438 10.09 %RANDOM
Rwork0.2129 ---
obs0.2199 43981 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.479 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-23.5824 Å2-0 Å2-0 Å2
2---9.5132 Å2-0 Å2
3----14.0692 Å2
Refinement stepCycle: LAST / Resolution: 3→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13910 0 6 11 13927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414288
X-RAY DIFFRACTIONf_angle_d0.75919505
X-RAY DIFFRACTIONf_dihedral_angle_d15.0785135
X-RAY DIFFRACTIONf_chiral_restr0.052169
X-RAY DIFFRACTIONf_plane_restr0.0032562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.03420.32721270.27521192X-RAY DIFFRACTION92
3.0342-3.06990.3551460.28841237X-RAY DIFFRACTION95
3.0699-3.10730.34651710.26481294X-RAY DIFFRACTION98
3.1073-3.14660.36751540.26321260X-RAY DIFFRACTION99
3.1466-3.1880.33061320.26061298X-RAY DIFFRACTION100
3.188-3.23170.29981430.25231341X-RAY DIFFRACTION100
3.2317-3.27780.32981410.23411293X-RAY DIFFRACTION100
3.2778-3.32680.32971460.23741282X-RAY DIFFRACTION100
3.3268-3.37870.32571610.23041326X-RAY DIFFRACTION100
3.3787-3.43410.29191260.22711283X-RAY DIFFRACTION100
3.4341-3.49330.28481600.2241313X-RAY DIFFRACTION100
3.4933-3.55680.30331530.21111339X-RAY DIFFRACTION100
3.5568-3.62520.29671350.19881273X-RAY DIFFRACTION100
3.6252-3.69920.25691380.21121344X-RAY DIFFRACTION100
3.6992-3.77960.26931290.19581326X-RAY DIFFRACTION100
3.7796-3.86750.24231460.18791327X-RAY DIFFRACTION100
3.8675-3.96420.25571460.18851331X-RAY DIFFRACTION100
3.9642-4.07130.26461540.18251286X-RAY DIFFRACTION100
4.0713-4.1910.24821360.17611345X-RAY DIFFRACTION100
4.191-4.32630.23231530.17571323X-RAY DIFFRACTION100
4.3263-4.48080.20291330.16551339X-RAY DIFFRACTION100
4.4808-4.66010.23621710.15561317X-RAY DIFFRACTION100
4.6601-4.8720.2271510.15931308X-RAY DIFFRACTION100
4.872-5.12860.25881490.18531340X-RAY DIFFRACTION100
5.1286-5.44960.2591640.19811320X-RAY DIFFRACTION100
5.4496-5.86970.32371750.21191325X-RAY DIFFRACTION100
5.8697-6.45930.25251570.22711331X-RAY DIFFRACTION100
6.4593-7.39140.29121430.22531395X-RAY DIFFRACTION100
7.3914-9.30250.29171470.21691385X-RAY DIFFRACTION100
9.3025-49.96680.29331510.23831470X-RAY DIFFRACTION100

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