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- PDB-4mxw: Structure of heterotrimeric lymphotoxin LTa1b2 bound to lymphotox... -

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Basic information

Entry
Database: PDB / ID: 4mxw
TitleStructure of heterotrimeric lymphotoxin LTa1b2 bound to lymphotoxin beta receptor LTbR and anti-LTa Fab
Components
  • Lymphotoxin-alpha
  • Lymphotoxin-beta
  • Tumor necrosis factor receptor superfamily member 3
  • anti-Lymphotoxin alpha antibody heavy chain
  • anti-Lymphotoxin alpha antibody light chain
KeywordsCYTOKINE/IMMUNE SYSTEM / TNF / Tumor Necrosis Factor / TNFR Receptor / lymphotoxin beta receptor / lymphotoxin alpha / Lymphoid development / Tumor immunity / Auto-immunity / CYTOKINE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


hematopoietic or lymphoid organ development / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of humoral immune response mediated by circulating immunoglobulin / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / myeloid dendritic cell differentiation / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / skin development / humoral immune response ...hematopoietic or lymphoid organ development / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of humoral immune response mediated by circulating immunoglobulin / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / myeloid dendritic cell differentiation / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / skin development / humoral immune response / positive regulation of glial cell proliferation / lymph node development / negative regulation of fibroblast proliferation / positive regulation of interleukin-12 production / response to nutrient / cytokine activity / TNFR2 non-canonical NF-kB pathway / positive regulation of JNK cascade / cellular response to mechanical stimulus / positive regulation of type II interferon production / cell-cell signaling / response to lipopolysaccharide / gene expression / response to hypoxia / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-positive bacterium / immune response / response to xenobiotic stimulus / signaling receptor binding / apoptotic process / ubiquitin protein ligase binding / Golgi apparatus / signal transduction / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Lymphotoxin-beta / Tumour necrosis factor receptor 3 / Tumour necrosis factor receptor 3, N-terminal / Lymphotoxin-alpha / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. ...Lymphotoxin-beta / Tumour necrosis factor receptor 3 / Tumour necrosis factor receptor 3, N-terminal / Lymphotoxin-alpha / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNF(Tumour Necrosis Factor) family / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / Jelly Rolls - #40 / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Ribbon / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lymphotoxin-alpha / Tumor necrosis factor receptor superfamily member 3 / Lymphotoxin-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSudhamsu, J. / Yin, J.P. / Hymowitz, S.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Dimerization of LT beta R by LT alpha 1 beta 2 is necessary and sufficient for signal transduction.
Authors: Sudhamsu, J. / Yin, J. / Chiang, E.Y. / Starovasnik, M.A. / Grogan, J.L. / Hymowitz, S.G.
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: Tumor necrosis factor receptor superfamily member 3
X: Lymphotoxin-alpha
Y: Lymphotoxin-beta
Z: Lymphotoxin-beta
A: Lymphotoxin-alpha
B: Lymphotoxin-beta
D: Lymphotoxin-beta
R: Tumor necrosis factor receptor superfamily member 3
W: anti-Lymphotoxin alpha antibody heavy chain
H: anti-Lymphotoxin alpha antibody heavy chain
V: anti-Lymphotoxin alpha antibody light chain
L: anti-Lymphotoxin alpha antibody light chain


Theoretical massNumber of molelcules
Total (without water)259,33112
Polymers259,33112
Non-polymers00
Water00
1
S: Tumor necrosis factor receptor superfamily member 3
X: Lymphotoxin-alpha
Y: Lymphotoxin-beta
Z: Lymphotoxin-beta
W: anti-Lymphotoxin alpha antibody heavy chain
V: anti-Lymphotoxin alpha antibody light chain


Theoretical massNumber of molelcules
Total (without water)129,6666
Polymers129,6666
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lymphotoxin-alpha
B: Lymphotoxin-beta
D: Lymphotoxin-beta
R: Tumor necrosis factor receptor superfamily member 3
H: anti-Lymphotoxin alpha antibody heavy chain
L: anti-Lymphotoxin alpha antibody light chain


Theoretical massNumber of molelcules
Total (without water)129,6666
Polymers129,6666
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.201, 52.428, 253.241
Angle α, β, γ (deg.)90.00, 101.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 3 / Lymphotoxin-beta receptor / Tumor necrosis factor C receptor / Tumor necrosis factor receptor 2- ...Lymphotoxin-beta receptor / Tumor necrosis factor C receptor / Tumor necrosis factor receptor 2-related protein / Tumor necrosis factor receptor type III / TNF-RIII / TNFR-III


Mass: 21367.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTBR, D12S370, TNFCR, TNFR3, TNFRSF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P36941
#2: Protein Lymphotoxin-alpha / LT-alpha / TNF-beta / Tumor necrosis factor ligand superfamily member 1


Mass: 17313.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTA, TNFB, TNFSF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01374
#3: Protein
Lymphotoxin-beta / LT-beta / Tumor necrosis factor C / TNF-C / Tumor necrosis factor ligand superfamily member 3


Mass: 22514.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTB, TNFC, TNFSF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q06643
#4: Antibody anti-Lymphotoxin alpha antibody heavy chain / anti-LT-alpha antibody heavy chain


Mass: 22890.713 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody anti-Lymphotoxin alpha antibody light chain / anti-LT-alpha antibody light chain


Mass: 23065.541 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 15% PEG6000, 0.1 M sodium citrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.6→49.701 Å / Num. all: 32265 / Num. obs: 32265 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 %
Reflection shellHighest resolution: 3.6 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TNR AND 1FVE

1tnr

1fve


Resolution: 3.6→49.701 Å / SU ML: 0.55 / σ(F): 2 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1614 5 %RANDOM
Rwork0.2307 ---
obs0.234 32265 99.33 %-
all-32265 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→49.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14217 0 0 0 14217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01314611
X-RAY DIFFRACTIONf_angle_d1.58119851
X-RAY DIFFRACTIONf_dihedral_angle_d15.0375191
X-RAY DIFFRACTIONf_chiral_restr0.0622211
X-RAY DIFFRACTIONf_plane_restr0.0092565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.7060.40661340.31242541X-RAY DIFFRACTION99
3.706-3.82560.36031320.29372514X-RAY DIFFRACTION100
3.8256-3.96220.32161320.27422516X-RAY DIFFRACTION99
3.9622-4.12080.31631360.25392549X-RAY DIFFRACTION100
4.1208-4.30820.29651340.21412551X-RAY DIFFRACTION100
4.3082-4.53520.2131320.19872520X-RAY DIFFRACTION100
4.5352-4.81920.29431350.19232552X-RAY DIFFRACTION100
4.8192-5.19090.28011340.19322558X-RAY DIFFRACTION100
5.1909-5.71260.26091350.2052567X-RAY DIFFRACTION100
5.7126-6.53760.35211360.22212573X-RAY DIFFRACTION99
6.5376-8.23070.2981360.23882564X-RAY DIFFRACTION99
8.2307-49.70540.27761380.23882646X-RAY DIFFRACTION97

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