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- PDB-4mxv: Structure of Lymphotoxin alpha bound to anti-LTa Fab -

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Basic information

Entry
Database: PDB / ID: 4mxv
TitleStructure of Lymphotoxin alpha bound to anti-LTa Fab
Components
  • Lymphotoxin-alpha
  • 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


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 / tumor necrosis factor receptor binding / humoral immune response / lymph node development / negative regulation of fibroblast proliferation / positive regulation of glial cell proliferation / response to nutrient ...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 / tumor necrosis factor receptor binding / humoral immune response / lymph node development / negative regulation of fibroblast proliferation / positive regulation of glial cell proliferation / response to nutrient / cytokine activity / TNFR2 non-canonical NF-kB pathway / positive regulation of type II interferon production / cell-cell signaling / response to lipopolysaccharide / response to hypoxia / defense response to Gram-positive bacterium / positive regulation of apoptotic process / response to xenobiotic stimulus / signaling receptor binding / apoptotic process / signal transduction / extracellular space / plasma membrane
Similarity search - Function
Lymphotoxin-alpha / Tumour necrosis factor / 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 ...Lymphotoxin-alpha / Tumour necrosis factor / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYin, 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 1.4Oct 9, 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
A: Lymphotoxin-alpha
B: Lymphotoxin-alpha
D: Lymphotoxin-alpha
E: anti-Lymphotoxin alpha antibody light chain
F: anti-Lymphotoxin alpha antibody heavy chain
L: anti-Lymphotoxin alpha antibody light chain
H: anti-Lymphotoxin alpha antibody heavy chain
X: anti-Lymphotoxin alpha antibody light chain
Y: anti-Lymphotoxin alpha antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)189,8099
Polymers189,8099
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.847, 209.847, 130.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Lymphotoxin-alpha / LT-alpha / TNF-beta / Tumor necrosis factor ligand superfamily member 1


Mass: 17313.338 Da / Num. of mol.: 3
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
#2: Antibody anti-Lymphotoxin alpha antibody light chain / anti-LT-alpha antibody light chain


Mass: 23065.541 Da / Num. of mol.: 3 / 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)
#3: Antibody anti-Lymphotoxin alpha antibody heavy chain / anti-LT-alpha antibody heavy chain


Mass: 22890.713 Da / Num. of mol.: 3 / 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: 3.77 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG6000, 2 M sodium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2007
RadiationMonochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 46756 / Num. obs: 46756 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.2-3.311100
3.31-3.451100
3.45-4.031100
4.03-5.471100
5.47-6.891100
6.89-50199.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TNR AND 1FVE

1tnr

1fve


Resolution: 3.2→29.796 Å / SU ML: 0.37 / σ(F): 2 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2796 5.98 %RANDOM
Rwork0.1774 ---
obs0.1807 46756 96.76 %-
all-46756 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→29.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12881 0 0 0 12881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113236
X-RAY DIFFRACTIONf_angle_d1.30318013
X-RAY DIFFRACTIONf_dihedral_angle_d14.7594670
X-RAY DIFFRACTIONf_chiral_restr0.0832007
X-RAY DIFFRACTIONf_plane_restr0.0062296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.25530.34555020.27961648X-RAY DIFFRACTION90
3.2553-3.314400.26652188X-RAY DIFFRACTION92
3.3144-3.37800.24152213X-RAY DIFFRACTION92
3.378-3.446900.22452257X-RAY DIFFRACTION95
3.4469-3.52170.2494390.21031851X-RAY DIFFRACTION96
3.5217-3.603500.20472271X-RAY DIFFRACTION96
3.6035-3.693500.20122276X-RAY DIFFRACTION96
3.6935-3.79310.26623810.20631922X-RAY DIFFRACTION97
3.7931-3.904500.1772330X-RAY DIFFRACTION97
3.9045-4.030300.16562350X-RAY DIFFRACTION98
4.0303-4.17390.2233220.16512011X-RAY DIFFRACTION98
4.1739-4.340600.14572395X-RAY DIFFRACTION99
4.3406-4.53750.1882780.13742069X-RAY DIFFRACTION98
4.5375-4.775800.13242390X-RAY DIFFRACTION99
4.7758-5.07360.18912470.13442125X-RAY DIFFRACTION98
5.0736-5.46310.175130.14742391X-RAY DIFFRACTION98
5.4631-6.00890.20721900.16612219X-RAY DIFFRACTION98
6.0089-6.86910.2631320.1762300X-RAY DIFFRACTION99
6.8691-8.61940.21391870.17752271X-RAY DIFFRACTION99
8.6194-29.79760.22641150.19652483X-RAY DIFFRACTION99

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