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Basic information

Entry
Database: PDB / ID: 4en0
TitleCrystal structure of light
ComponentsTumor necrosis factor ligand superfamily member 14
KeywordsCYTOKINE / STRUCTURAL GENOMICS / PSI-BIOLOGY / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / IMMUNITY / TNF SUPERFAMILY / HVEM / DCR3 / N-GLYCOSYLATION / MEMBRANE / SECRETED PROTEIN / ATOMS-TO-ANIMALS: THE IMMUNE FUNCTION NETWORK / IFN / Jelly-roll Fold / Bind TNF receptor HVEM and LTbR / LTbR
Function / homology
Function and homology information


TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell chemotaxis / T cell chemotaxis / tumor necrosis factor receptor binding / positive regulation of myoblast fusion / T cell homeostasis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of myoblast differentiation / T cell proliferation ...TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell chemotaxis / T cell chemotaxis / tumor necrosis factor receptor binding / positive regulation of myoblast fusion / T cell homeostasis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of myoblast differentiation / T cell proliferation / T cell costimulation / T cell activation / cytokine activity / TNFR2 non-canonical NF-kB pathway / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / immune response / signaling receptor binding / apoptotic process / signal transduction / extracellular space / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor / 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 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsZhan, C. / Liu, W. / Patskovsky, Y. / Ramagopal, U.A. / Bonanno, J.B. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: Structure / Year: 2014
Title: Mechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly.
Authors: Liu, W. / Zhan, C. / Cheng, H. / Kumar, P.R. / Bonanno, J.B. / Nathenson, S.G. / Almo, S.C.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMay 9, 2012ID: 3UGN
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 14
B: Tumor necrosis factor ligand superfamily member 14
C: Tumor necrosis factor ligand superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7076
Polymers55,2983
Non-polymers4083
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-32 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.699, 99.981, 124.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 14 / Herpes virus entry mediator ligand / HVEM-L / Herpesvirus entry mediator ligand / Tumor necrosis ...Herpes virus entry mediator ligand / HVEM-L / Herpesvirus entry mediator ligand / Tumor necrosis factor ligand superfamily member 14 / membrane form / Tumor necrosis factor ligand superfamily member 14 / soluble form


Mass: 18432.820 Da / Num. of mol.: 3 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HVEML, LIGHT, TNFSF14, UNQ391/PRO726 / Plasmid: PMT/BIP/V5-HIS / Production host: DROSOPHILA (fruit flies) / References: UniProt: O43557
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / 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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DIFFERENCE BETWEEN SEQUENCE AND UNP REFERENCE REFLECTS NATURAL VARIATION

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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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.26M NAH2PO4, 0.14M K2HPO4 AND 0.2M NDSB-211, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 18664 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 51.83 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.09 / Net I/σ(I): 7.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QE3

2qe3


Resolution: 2.59→46.122 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2861 956 5.13 %RANDOM
Rwork0.2337 ---
obs0.2363 18647 99.48 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.859 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.6607 Å20 Å20 Å2
2--4.668 Å20 Å2
3---11.9927 Å2
Refinement stepCycle: LAST / Resolution: 2.59→46.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 25 12 3329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033404
X-RAY DIFFRACTIONf_angle_d0.7884622
X-RAY DIFFRACTIONf_dihedral_angle_d14.1831195
X-RAY DIFFRACTIONf_chiral_restr0.048514
X-RAY DIFFRACTIONf_plane_restr0.003586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5902-2.72680.40961400.35032427X-RAY DIFFRACTION97
2.7268-2.89760.35841180.31552518X-RAY DIFFRACTION100
2.8976-3.12130.32081490.27422496X-RAY DIFFRACTION100
3.1213-3.43530.30761560.24612490X-RAY DIFFRACTION100
3.4353-3.93210.24591190.21832538X-RAY DIFFRACTION100
3.9321-4.95320.23261300.18022558X-RAY DIFFRACTION100
4.9532-46.12910.29041440.23492664X-RAY DIFFRACTION100
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)
11.34690.36450.4161.81340.02622.6269-0.29880.3920.356-0.70860.46620.5145-0.04840.37760.00980.3478-0.262-0.17890.61190.25060.3783-14.912828.013313.7225
21.62781.9108-0.5353.07790.31923.8-0.168-0.3164-0.27290.49050.45080.2940.13090.3807-0.19980.38980.09280.02950.54350.22670.3186-16.339714.672831.0576
32.2274-0.5761-0.54791.6089-0.01472.4257-0.2710.33830.2492-0.42510.11591.04460.207-0.1658-0.07040.2566-0.1972-0.23680.45540.31070.8162-31.660314.120115.8158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 93:240)
2X-RAY DIFFRACTION2chain 'B' and (resseq 92:240)
3X-RAY DIFFRACTION3chain 'C' and (resseq 92:240)

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