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- PDB-6mge: Structure of human 4-1BBL -

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Basic information

Entry
Database: PDB / ID: 6mge
TitleStructure of human 4-1BBL
ComponentsTumor necrosis factor ligand superfamily member 9
KeywordsIMMUNE SYSTEM / Signaling / TNF ligand / Trimer / 4-1BBL / CD137L
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
PHOSPHATE ION / Tumor necrosis factor ligand superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsKimberlin, C.R. / Chin, S.M. / Roe-Zurz, Z. / Xu, A. / Yang, Y.
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the 4-1BB/4-1BBL complex and distinct binding and functional properties of utomilumab and urelumab.
Authors: Chin, S.M. / Kimberlin, C.R. / Roe-Zurz, Z. / Zhang, P. / Xu, A. / Liao-Chan, S. / Sen, D. / Nager, A.R. / Oakdale, N.S. / Brown, C. / Wang, F. / Yang, Y. / Lindquist, K. / Yeung, Y.A. / ...Authors: Chin, S.M. / Kimberlin, C.R. / Roe-Zurz, Z. / Zhang, P. / Xu, A. / Liao-Chan, S. / Sen, D. / Nager, A.R. / Oakdale, N.S. / Brown, C. / Wang, F. / Yang, Y. / Lindquist, K. / Yeung, Y.A. / Salek-Ardakani, S. / Chaparro-Riggers, J.
History
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
B: Tumor necrosis factor ligand superfamily member 9
C: Tumor necrosis factor ligand superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3809
Polymers65,8133
Non-polymers5676
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-57 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.910, 118.910, 105.494
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 21937.758 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF9 / Plasmid: pFastBac / Cell line (production host): HighFive / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P41273
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 8% w/v PEG 8000, 100mM Tris 8.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.95→46.95 Å / Num. obs: 17937 / % possible obs: 99.77 % / Redundancy: 10.3 % / CC1/2: 0.997 / Net I/σ(I): 13.25
Reflection shellResolution: 2.95→3.056 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1796 / CC1/2: 0.34 / % possible all: 99.05

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
Aimless0.5.32data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x29

2x29


Resolution: 2.95→46.947 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.65
RfactorNum. reflection% reflection
Rfree0.2465 925 5.17 %
Rwork0.1943 --
obs0.1971 17900 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.61 Å2 / Biso mean: 95.5112 Å2 / Biso min: 50.37 Å2
Refinement stepCycle: final / Resolution: 2.95→46.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 31 16 3345
Biso mean--154.66 76.34 -
Num. residues----453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033393
X-RAY DIFFRACTIONf_angle_d0.6124631
X-RAY DIFFRACTIONf_chiral_restr0.038542
X-RAY DIFFRACTIONf_plane_restr0.003592
X-RAY DIFFRACTIONf_dihedral_angle_d2.8291938
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9502-3.10580.39461380.33272396253499
3.1058-3.30030.41331170.305624322549100
3.3003-3.5550.28511340.235324042538100
3.555-3.91260.27531180.191924332551100
3.9126-4.47840.20061330.163324212554100
4.4784-5.64080.21311420.154524332575100
5.6408-46.95270.23591430.193924562599100
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)
12.42341.7579-0.95064.52820.74682.8959-0.10720.3002-0.2119-0.02780.0734-0.0961-0.0540.05190.07740.5133-0.0219-0.07240.73130.01760.5581-20.584161.7614-8.3609
25.197-1.7995-1.39373.40931.08143.2772-0.0032-0.1460.12320.20750.06950.0139-0.25630.1998-0.10360.7456-0.0887-0.01790.7987-0.0170.6375-3.124874.05110.6577
32.8110.37362.70022.8772-0.96376.10410.0453-0.4251-0.15980.4072-0.06430.11510.1529-0.430.01010.664-0.03990.06680.7439-0.06450.6572-20.749268.582414.3207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA89 - 242
2X-RAY DIFFRACTION2chain BB90 - 244
3X-RAY DIFFRACTION3chain CC90 - 242

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