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- PDB-6fib: Structure of human 4-1BB ligand -

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Basic information

Entry
Database: PDB / ID: 6fib
TitleStructure of human 4-1BB ligand
Components
  • Tumor necrosis factor ligand superfamily member 9
  • Tumor necrosis factor ligand superfamily member 9,4-1BBL -CH/CL fusion
  • Tumor necrosis factor ligand superfamily member 9,Uncharacterized protein
KeywordsCYTOKINE / Signal anchor / TNF family
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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / cytokine activity / complement activation, classical pathway ...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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / cytokine activity / complement activation, classical pathway / antigen binding / cell-cell signaling / antibacterial humoral response / regulation of apoptotic process / blood microparticle / immune response / signaling receptor binding / extracellular space / extracellular exosome / 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 / Immunoglobulin V-Type ...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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Tumor necrosis factor ligand superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJoseph, C. / Claus, C. / Ferrara, C. / von Hirschheydt, T. / Prince, C. / Funk, D. / Klein, C. / Benz, J.
CitationJournal: Sci Transl Med / Year: 2019
Title: Tumor-targeted 4-1BB agonists for combination with T cell bispecific antibodies as off-the-shelf therapy.
Authors: Claus, C. / Ferrara, C. / Xu, W. / Sam, J. / Lang, S. / Uhlenbrock, F. / Albrecht, R. / Herter, S. / Schlenker, R. / Husser, T. / Diggelmann, S. / Challier, J. / Mossner, E. / Hosse, R.J. / ...Authors: Claus, C. / Ferrara, C. / Xu, W. / Sam, J. / Lang, S. / Uhlenbrock, F. / Albrecht, R. / Herter, S. / Schlenker, R. / Husser, T. / Diggelmann, S. / Challier, J. / Mossner, E. / Hosse, R.J. / Hofer, T. / Brunker, P. / Joseph, C. / Benz, J. / Ringler, P. / Stahlberg, H. / Lauer, M. / Perro, M. / Chen, S. / Kuttel, C. / Bhavani Mohan, P.L. / Nicolini, V. / Birk, M.C. / Ongaro, A. / Prince, C. / Gianotti, R. / Dugan, G. / Whitlow, C.T. / Solingapuram Sai, K.K. / Caudell, D.L. / Burgos-Rodriguez, A.G. / Cline, J.M. / Hettich, M. / Ceppi, M. / Giusti, A.M. / Crameri, F. / Driessen, W. / Morcos, P.N. / Freimoser-Grundschober, A. / Levitsky, V. / Amann, M. / Grau-Richards, S. / von Hirschheydt, T. / Tournaviti, S. / Molhoj, M. / Fauti, T. / Heinzelmann-Schwarz, V. / Teichgraber, V. / Colombetti, S. / Bacac, M. / Zippelius, A. / Klein, C. / Umana, P.
History
DepositionJan 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 9
B: Tumor necrosis factor ligand superfamily member 9,4-1BBL -CH/CL fusion
C: Tumor necrosis factor ligand superfamily member 9,Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)82,4973
Polymers82,4973
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-24 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.592, 119.592, 104.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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


Mass: 19439.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF9 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P41273
#2: Protein Tumor necrosis factor ligand superfamily member 9,4-1BBL -CH/CL fusion / 4-1BB ligand / 4-1BBL


Mass: 32892.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF9 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P41273
#3: Protein Tumor necrosis factor ligand superfamily member 9,Uncharacterized protein / 4-1BB ligand / 4-1BBL


Mass: 30164.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF9 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P41273, UniProt: A8K008
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris, pH 8.5, 20% PEG1000, 0.009M BaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99993 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 2.697→103.6 Å / Num. obs: 14507 / % possible obs: 91.4 % / Redundancy: 11.4 % / Biso Wilson estimate: 108.21 Å2 / CC1/2: 1 / Rsym value: 0.089 / Net I/σ(I): 21.6
Reflection shellResolution: 2.697→3.042 Å / Redundancy: 11 % / Num. unique obs: 725 / CC1/2: 0.703 / Rsym value: 1.403 / % possible all: 64.4

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x29

2x29


Resolution: 2.7→103.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.91 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.773 / SU Rfree Blow DPI: 0.325 / SU Rfree Cruickshank DPI: 0.336
RfactorNum. reflection% reflectionSelection details
Rfree0.221 696 4.8 %RANDOM
Rwork0.166 ---
obs0.169 14504 61.9 %-
Displacement parametersBiso mean: 86.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.0346 Å20 Å20 Å2
2--0.0346 Å20 Å2
3----0.0692 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.7→103.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 0 82 3347
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013330HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.294521HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1102SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes561HARMONIC5
X-RAY DIFFRACTIONt_it3330HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion21.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion412SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3553SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.91 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.38 -5.05 %
Rwork0.2622 282 -
all0.2677 297 -
obs--6.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.0393-0.7291-1.47984.1665-0.1474.14010.01420.19170.0006-0.0096-0.0505-0.3695-0.38180.21680.03630.0161-0.04690.0396-0.2312-0.0019-0.1875-54.868934.1846-4.9849
24.4053-0.77852.73473.7571-1.39447.2866-0.00740.0458-0.1397-0.460.0553-0.19420.62680.3064-0.0479-0.16110.0280.0953-0.2711-0.0045-0.2589-50.189416.697-18.9229
33.861.4967-0.81796.29750.05454.1212-0.0989-0.13570.15050.50620.0555-0.0028-0.12710.12410.0434-0.09280.1287-0.0211-0.22270.0634-0.1828-56.518212.88362.979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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