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- PDB-5wjf: Crystal structure of murine 4-1BB from HEK293T cells in P21212 sp... -

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Basic information

Entry
Database: PDB / ID: 5wjf
TitleCrystal structure of murine 4-1BB from HEK293T cells in P21212 space group
ComponentsTumor necrosis factor receptor superfamily member 9
KeywordsIMMUNE SYSTEM / Tumor necrosis factor / apoptosis
Function / homology
Function and homology information


TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / signaling receptor activity / regulation of cell population proliferation / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process
Similarity search - Function
Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZajonc, D.M. / Doukov, T. / Bitra, A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal structure of murine 4-1BB and its interaction with 4-1BBL support a role for galectin-9 in 4-1BB signaling.
Authors: Bitra, A. / Doukov, T. / Wang, J. / Picarda, G. / Benedict, C.A. / Croft, M. / Zajonc, D.M.
History
DepositionJul 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 9
B: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9167
Polymers31,2882
Non-polymers6295
Water1,40578
1
A: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9894
Polymers15,6441
Non-polymers3453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9273
Polymers15,6441
Non-polymers2832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.050, 67.760, 87.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / T-cell antigen 4-1BB


Mass: 15643.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfrsf9, Cd137, Ila, Ly63
Production host: Mammalian expression vector pcDNA3-N-HA-LIC (others)
References: UniProt: P20334
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M bicine and 30% W/V PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 2 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2016
RadiationMonochromator: Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.49→17.9 Å / Num. obs: 26227 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 70.055 % / Biso Wilson estimate: 57.135 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.156 / Χ2: 0.994 / Net I/σ(I): 33.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.5539.4152.3571.517270.5922.38888.5
2.55-2.6268.8551.6463.319310.9661.658100
2.62-2.770.9451.3154.3318390.9771.324100
2.7-2.7870.381.0195.6617880.9891.02699.9
2.78-2.8766.4740.8696.7217440.9890.87699.8
2.87-2.9773.3070.57810.3417020.9950.582100
2.97-3.0872.9510.44613.7116470.9970.449100
3.08-3.2171.6220.35317.4115570.9970.355100
3.21-3.3567.3770.25922.8615180.9990.261100
3.35-3.5275.7430.19232.0214140.9990.19399.9
3.52-3.7175.2540.14842.0413640.9990.149100
3.71-3.9373.9950.12252.6812980.9990.123100
3.93-4.268.3330.08864.55121810.089100
4.2-4.5478.4320.0876.63112310.08100
4.54-4.9777.5830.07980.89105310.079100
4.97-5.5675.1320.07980.0893810.079100
5.56-6.4272.030.08481.1983310.084100
6.42-7.8678.8010.06997.270010.069100
7.86-11.1271.4460.06103.2154210.061100
11.12-17.976.2750.043130.9129110.04397.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
BUCCANEERmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.6→17.9 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.878 / SU B: 10.297 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.587 / ESU R Free: 0.349
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 1200 10.1 %RANDOM
Rwork0.2218 ---
obs0.2282 10728 95.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.21 Å2 / Biso mean: 57.379 Å2 / Biso min: 33.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2--3.02 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 2.6→17.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 40 78 2117
Biso mean--89.65 56.51 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192100
X-RAY DIFFRACTIONr_bond_other_d0.0020.021837
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9662846
X-RAY DIFFRACTIONr_angle_other_deg0.83534274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71224.09188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25515325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2761514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
LS refinement shellResolution: 2.6→2.666 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 78 -
Rwork0.273 698 -
all-776 -
obs--87.88 %

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