[English] 日本語
Yorodumi
- PDB-3alq: Crystal structure of TNF-TNFR2 complex -

+
Open data


ID or keywords:

Loading...

-
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 bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis ...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 bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of fractalkine production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / aortic valve development / tumor necrosis factor receptor activity / positive regulation of leukocyte adhesion to arterial endothelial cell / negative regulation of extracellular matrix constituent secretion / positive regulation of vitamin D biosynthetic process / response to 3,3',5-triiodo-L-thyronine / response to macrophage colony-stimulating factor / positive regulation of protein transport / positive regulation of translational initiation by iron / positive regulation of apoptotic process involved in morphogenesis / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / regulation of T cell cytokine production / positive regulation of hair follicle development / response to gold nanoparticle / negative regulation of myelination / negative regulation of neuroinflammatory response / TNFs bind their physiological receptors / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / tumor necrosis factor binding / negative regulation of amyloid-beta clearance / positive regulation of interleukin-18 production / negative regulation of cardiac muscle hypertrophy / inflammatory response to wounding / death receptor agonist activity / positive regulation of action potential / positive regulation of myelination / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / regulation of neuroinflammatory response / toll-like receptor 3 signaling pathway / embryonic digestive tract development / negative regulation of D-glucose import / vascular endothelial growth factor production / leukocyte migration involved in inflammatory response / response to fructose / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / necroptotic signaling pathway / positive regulation of calcineurin-NFAT signaling cascade / leukocyte tethering or rolling / positive regulation of mononuclear cell migration / positive regulation of fever generation / negative regulation of myoblast differentiation / positive regulation of protein-containing complex disassembly / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of oxidative phosphorylation / cellular response to toxic substance / positive regulation of protein localization to cell surface / positive regulation of osteoclast differentiation / macrophage activation involved in immune response / tumor necrosis factor receptor binding / negative regulation of systemic arterial blood pressure / positive regulation of heterotypic cell-cell adhesion / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage derived foam cell differentiation / regulation of immunoglobulin production / positive regulation of hepatocyte proliferation / TNFR1-mediated ceramide production / positive regulation of programmed cell death / positive regulation of membrane protein ectodomain proteolysis / positive regulation of podosome assembly / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / regulation of canonical NF-kappaB signal transduction / regulation of fat cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / TNFR1-induced proapoptotic signaling / regulation of myelination / negative regulation of bicellular tight junction assembly / regulation of metabolic process / regulation of reactive oxygen species metabolic process / positive regulation of DNA biosynthetic process / response to L-glutamate / negative regulation of heart rate / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / response to isolation stress / regulation of synapse organization / negative regulation of fat cell differentiation
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. / 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. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more