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- PDB-6d3n: Crystal structure of h4-1BB ligand -

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Basic information

Entry
Database: PDB / ID: 6d3n
TitleCrystal structure of h4-1BB ligand
ComponentsTumor necrosis factor ligand superfamily member 9
KeywordsSIGNALING PROTEIN / TNF / bell shape fold
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / regulation of apoptotic process / immune response ...tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / regulation of apoptotic process / immune response / signaling receptor binding / extracellular space / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 9 / 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 / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls ...Tumor necrosis factor ligand superfamily member 9 / 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 / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAruna, B. / Zajonc, D.M. / Doukov, T.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal structures of the human 4-1BB receptor bound to its ligand 4-1BBL reveal covalent receptor dimerization as a potential signaling amplifier.
Authors: Bitra, A. / Doukov, T. / Croft, M. / Zajonc, D.M.
History
DepositionApr 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,4102
Polymers18,3181
Non-polymers921
Water18010
1
A: Tumor necrosis factor ligand superfamily member 9
hetero molecules

A: Tumor necrosis factor ligand superfamily member 9
hetero molecules

A: Tumor necrosis factor ligand superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2306
Polymers54,9533
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area4140 Å2
ΔGint-22 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.167, 73.167, 162.814
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 9 / 4-1BB ligand / 4-1BBL


Mass: 18317.826 Da / Num. of mol.: 1 / Fragment: residues 80-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF9
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P41273
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.085M tri- Na citrate, pH 5.6, 25.5% PEG 4000 0.17M Amm acetate 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→59.05 Å / Num. obs: 4818 / % possible obs: 99.6 % / Redundancy: 9.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.033 / Rrim(I) all: 0.101 / Net I/σ(I): 11.6 / Num. measured all: 44504 / Scaling rejects: 117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.838.40.8596300.9270.3030.91399.4
8.96-59.057.90.0721570.9930.0280.07898.5

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Processing

Software
NameVersionClassification
SCALA0.6.3data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CPR

6cpr


Resolution: 2.7→59.05 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.755 / SU ML: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.124 / ESU R Free: 0.342
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 475 9.9 %RANDOM
Rwork0.2076 ---
obs0.2119 4340 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 169.63 Å2 / Biso mean: 77.154 Å2 / Biso min: 46.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 2.7→59.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 6 10 1017
Biso mean--118.37 86.74 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191024
X-RAY DIFFRACTIONr_bond_other_d0.0020.02963
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9661393
X-RAY DIFFRACTIONr_angle_other_deg0.85332196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.595133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99922.97337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48615143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.062155
X-RAY DIFFRACTIONr_chiral_restr0.0740.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 31 -
Rwork0.321 318 -
all-349 -
obs--99.15 %

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