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- PDB-3wd5: Crystal structure of TNFalpha in complex with Adalimumab Fab fragment -

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Basic information

Entry
Database: PDB / ID: 3wd5
TitleCrystal structure of TNFalpha in complex with Adalimumab Fab fragment
Components
  • Adalimumab Heavy Chain
  • Adalimumab Light Chain
  • Tumor necrosis factor
KeywordsIMMUNE SYSTEM / Antibody binding epitope
Function / homology
Function and homology information


negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / negative regulation of signaling receptor activity / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production ...negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / negative regulation of signaling receptor activity / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / response to macrophage colony-stimulating factor / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / response to 3,3',5-triiodo-L-thyronine / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / negative regulation of myelination / negative regulation of bicellular tight junction assembly / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / : / negative regulation of amyloid-beta clearance / response to isolation stress / positive regulation of action potential / inflammatory response to wounding / positive regulation of interleukin-18 production / death receptor agonist activity / positive regulation of protein transport / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / vascular endothelial growth factor production / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / response to fructose / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / leukocyte tethering or rolling / positive regulation of mononuclear cell migration / positive regulation of fever generation / negative regulation of myoblast differentiation / cellular response to toxic substance / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of D-glucose import / negative regulation of oxidative phosphorylation / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of protein-containing complex disassembly / negative regulation of systemic arterial blood pressure / positive regulation of heterotypic cell-cell adhesion / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage derived foam cell differentiation / regulation of immunoglobulin production / TNFR1-mediated ceramide production / positive regulation of programmed cell death / positive regulation of hepatocyte proliferation / positive regulation of membrane protein ectodomain proteolysis / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of podosome assembly / regulation of canonical NF-kappaB signal transduction / regulation of fat cell differentiation / TNFR1-induced proapoptotic signaling / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of metabolic process / regulation of reactive oxygen species metabolic process / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / response to L-glutamate / negative regulation of fat cell differentiation / regulation of synapse organization / Interleukin-10 signaling / negative regulation of endothelial cell proliferation / negative regulation of interleukin-6 production / negative regulation of blood vessel endothelial cell migration / humoral immune response / negative regulation of apoptotic signaling pathway / negative regulation of lipid storage / negative regulation of mitotic cell cycle / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of JUN kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell surface receptor signaling pathway via JAK-STAT / phagocytic cup / negative regulation of osteoblast differentiation / positive regulation of synaptic transmission
Similarity search - Function
Tumour necrosis factor 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 ...Tumour necrosis factor 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
Tumor necrosis factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
AuthorsHu, S. / Liang, S.Y. / Guo, Y.J. / Lou, Z.Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Comparison of the inhibition mechanisms of adalimumab and infliximab in treating tumor necrosis factor alpha-associated diseases from a molecular view
Authors: Hu, S. / Liang, S.Y. / Guo, H. / Zhang, D. / Li, H. / Wang, X. / Yang, W. / Qian, W. / Hou, S. / Wang, H. / Guo, Y.J. / Lou, Z.Y.
History
DepositionJun 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor
L: Adalimumab Light Chain
H: Adalimumab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)63,9353
Polymers63,9353
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.849, 161.849, 161.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

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Components

#1: Protein Tumor necrosis factor / TNFalpha


Mass: 17328.551 Da / Num. of mol.: 1 / Fragment: Tumor necrosis factor, soluble form
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFA / Production host: Escherichia coli (E. coli) / References: UniProt: P01375
#2: Antibody Adalimumab Light Chain


Mass: 23332.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Adalimumab Heavy Chain


Mass: 23273.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG400, 0.1M sodium acetate trihydrate, 0.1M cadmium chloride hydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→43.3 Å / Num. obs: 12943 / % possible obs: 100 % / Observed criterion σ(F): 5.1 / Observed criterion σ(I): 26.1 / Biso Wilson estimate: 49.23 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.101→43.256 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7814 / SU ML: 0.42 / σ(F): 1.34 / Phase error: 28.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.275 646 4.99 %RANDOM
Rwork0.1867 ---
obs0.1911 12943 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.82 Å2 / Biso mean: 48.0616 Å2 / Biso min: 15.79 Å2
Refinement stepCycle: LAST / Resolution: 3.101→43.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 0 0 34 4466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014536
X-RAY DIFFRACTIONf_angle_d1.4476168
X-RAY DIFFRACTIONf_chiral_restr0.113697
X-RAY DIFFRACTIONf_plane_restr0.006795
X-RAY DIFFRACTIONf_dihedral_angle_d17.8831630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.101-3.34040.34611330.211924222555
3.3404-3.67640.35761210.189924402561
3.6764-4.2080.25151380.170524292567
4.208-5.30010.23131240.155424622586
5.3001-43.26020.25851300.213125442674

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