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- PDB-9cu8: Crystal Structure of TNFR2 TNFR2_mb1 Complex -

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Basic information

Entry
Database: PDB / ID: 9cu8
TitleCrystal Structure of TNFR2 TNFR2_mb1 Complex
Components
  • TNFR2_mb1
  • Tumor necrosis factor receptor superfamily member 1B
KeywordsDE NOVO PROTEIN / TNFR2 / antagonists and agonists / TNFR1
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 / aortic valve development / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / regulation of T cell cytokine production ...glial cell-neuron signaling / regulation of cytokine production involved in immune response / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / aortic valve development / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / regulation of T cell cytokine production / negative regulation of neuroinflammatory response / TNFs bind their physiological receptors / tumor necrosis factor binding / negative regulation of cardiac muscle hypertrophy / positive regulation of myelination / regulation of neuroinflammatory response / positive regulation of membrane protein ectodomain proteolysis / regulation of myelination / Interleukin-10 signaling / regulation of T cell proliferation / positive regulation of oligodendrocyte differentiation / specific granule membrane / tumor necrosis factor-mediated signaling pathway / extrinsic apoptotic signaling pathway / TNFR2 non-canonical NF-kB pathway / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / inflammatory response / membrane raft / ubiquitin protein ligase binding / Neutrophil degranulation / extracellular region / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 1B / Tumor necrosis factor receptor 1B, N-terminal / : / 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
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 1B
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBera, A.K. / Glogl, M. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2024
Title: Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists.
Authors: Glogl, M. / Krishnakumar, A. / Ragotte, R.J. / Goreshnik, I. / Coventry, B. / Bera, A.K. / Kang, A. / Joyce, E. / Ahn, G. / Huang, B. / Yang, W. / Chen, W. / Sanchez, M.G. / Koepnick, B. / Baker, D.
History
DepositionJul 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNFR2_mb1
B: Tumor necrosis factor receptor superfamily member 1B


Theoretical massNumber of molelcules
Total (without water)32,0802
Polymers32,0802
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-8 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.071, 74.621, 104.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein TNFR2_mb1


Mass: 11504.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Tumor necrosis factor receptor superfamily member 1B / Tumor necrosis factor receptor 2 / TNF-R2 / Tumor necrosis factor receptor type II / TNF-RII / TNFR- ...Tumor necrosis factor receptor 2 / TNF-R2 / Tumor necrosis factor receptor type II / TNF-RII / TNFR-II / p75 / p80 TNF-alpha receptor


Mass: 20575.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF1B, TNFBR, TNFR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P20333
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.0M Imidazole; MES monohydrate (acid) pH 6.5, 0.12 M Monosaccharides, 40% v/v PEG 500 MME; 20% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 1.96→29.16 Å / Num. obs: 20443 / % possible obs: 99.7 % / Redundancy: 11 % / Biso Wilson estimate: 26.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.1
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1409 / CC1/2: 0.88 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→29.16 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 1998 9.8 %
Rwork0.183 --
obs0.1869 20386 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 0 187 2339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.799
X-RAY DIFFRACTIONf_dihedral_angle_d17.725838
X-RAY DIFFRACTIONf_chiral_restr0.047353
X-RAY DIFFRACTIONf_plane_restr0.008394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.28081340.21991229X-RAY DIFFRACTION96
2.01-2.060.29311400.1971298X-RAY DIFFRACTION100
2.06-2.130.22911390.19171278X-RAY DIFFRACTION100
2.13-2.190.2391420.18521311X-RAY DIFFRACTION100
2.19-2.270.27221390.1781269X-RAY DIFFRACTION100
2.27-2.360.25951410.19211309X-RAY DIFFRACTION100
2.36-2.470.2331430.18321315X-RAY DIFFRACTION100
2.47-2.60.27621410.1881288X-RAY DIFFRACTION100
2.6-2.760.2191440.19261324X-RAY DIFFRACTION100
2.76-2.980.25971430.19631314X-RAY DIFFRACTION100
2.98-3.280.24541420.18781318X-RAY DIFFRACTION100
3.28-3.750.20231460.17451337X-RAY DIFFRACTION100
3.75-4.720.1671470.15021355X-RAY DIFFRACTION100
4.72-29.160.20451570.19861443X-RAY DIFFRACTION100

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