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- PDB-4g3y: Crystal structure of TNF-alpha in complex with Infliximab Fab fragment -

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Basic information

Entry
Database: PDB / ID: 4g3y
TitleCrystal structure of TNF-alpha in complex with Infliximab Fab fragment
Components
  • Tumor necrosis factor
  • infliximab Fab H
  • infliximab Fab L
KeywordsIMMUNE SYSTEM / TNF / Infliximab
Function / homology
Function and homology information


negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / positive regulation of vitamin D biosynthetic process ...negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / positive regulation of vitamin D biosynthetic process / response to macrophage colony-stimulating factor / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of translational initiation by iron / response to 3,3',5-triiodo-L-thyronine / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / positive regulation of interleukin-18 production / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / epithelial cell proliferation involved in salivary gland morphogenesis / positive regulation of hair follicle development / : / death receptor agonist activity / negative regulation of myelination / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / response to isolation stress / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / inflammatory response to wounding / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of action potential / sequestering of triglyceride / positive regulation of I-kappaB phosphorylation / TNF signaling / positive regulation of protein transport / toll-like receptor 3 signaling pathway / embryonic digestive tract development / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / regulation of immunoglobulin production / positive regulation of calcineurin-NFAT signaling cascade / response to fructose / positive regulation of neuroinflammatory response / cellular response to toxic substance / positive regulation of mononuclear cell migration / leukocyte tethering or rolling / positive regulation of synoviocyte proliferation / positive regulation of fever generation / negative regulation of myoblast differentiation / negative regulation of D-glucose import / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / macrophage activation involved in immune response / negative regulation of oxidative phosphorylation / positive regulation of protein localization to cell surface / TNFR1-mediated ceramide production / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of cytokine production involved in inflammatory response / regulation of metabolic process / negative regulation of systemic arterial blood pressure / positive regulation of heterotypic cell-cell adhesion / positive regulation of protein-containing complex disassembly / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of programmed cell death / positive regulation of podosome assembly / positive regulation of hepatocyte proliferation / regulation of canonical NF-kappaB signal transduction / positive regulation of membrane protein ectodomain proteolysis / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of fat cell differentiation / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / response to L-glutamate / cortical actin cytoskeleton organization / negative regulation of heart rate / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / positive regulation of DNA biosynthetic process / regulation of synapse organization / negative regulation of fat cell differentiation / : / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / negative regulation of blood vessel endothelial cell migration / humoral immune response / negative regulation of apoptotic signaling pathway / skeletal muscle contraction / phagocytic cup / negative regulation of lipid storage / negative regulation of mitotic cell cycle / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway via death domain receptors
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: 2.6 Å
AuthorsLiang, S.Y. / Dai, J.X. / Guo, Y.J. / Lou, Z.Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural basis for treating tumor necrosis factor alpha (TNFalpha)-associated diseases with the therapeutic antibody infliximab
Authors: Liang, S.Y. / Dai, J.X. / Hou, S. / Su, L. / Zhang, D. / Guo, H. / Hu, S. / Wang, H. / Rao, Z. / Guo, Y.J. / Lou, Z.Y.
History
DepositionJul 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Oct 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: infliximab Fab L
H: infliximab Fab H
C: Tumor necrosis factor


Theoretical massNumber of molelcules
Total (without water)65,1883
Polymers65,1883
Non-polymers00
Water2,414134
1
L: infliximab Fab L
H: infliximab Fab H
C: Tumor necrosis factor

L: infliximab Fab L
H: infliximab Fab H
C: Tumor necrosis factor

L: infliximab Fab L
H: infliximab Fab H
C: Tumor necrosis factor


Theoretical massNumber of molelcules
Total (without water)195,5639
Polymers195,5639
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-31 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.663, 153.663, 99.279
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Antibody infliximab Fab L


Mass: 23460.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody infliximab Fab H


Mass: 24356.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Tumor necrosis factor / TNF-alpha


Mass: 17370.658 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR CHAIN L, H DO NOT CURRENTLY EXIST.

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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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.0M Na/K phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 27113 / Num. obs: 27025 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→21.535 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8317 / SU ML: 0.33 / σ(F): 0.08 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 1278 5.03 %random
Rwork0.189 ---
all0.1985 27025 --
obs0.1914 25400 94.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.583 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 102.76 Å2 / Biso mean: 38.9057 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.6239 Å20 Å20 Å2
2---1.6239 Å2-0 Å2
3---3.2478 Å2
Refinement stepCycle: LAST / Resolution: 2.6→21.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4465 0 0 134 4599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084576
X-RAY DIFFRACTIONf_angle_d1.2236214
X-RAY DIFFRACTIONf_chiral_restr0.079695
X-RAY DIFFRACTIONf_plane_restr0.005800
X-RAY DIFFRACTIONf_dihedral_angle_d16.5881647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.7040.31491220.24852366248882
2.704-2.82680.30811220.24522483260588
2.8268-2.97550.29421460.2482627277393
2.9755-3.16130.31081610.23082725288695
3.1613-3.40460.26141470.21522719286697
3.4046-3.74560.23891350.18712787292298
3.7456-4.28380.19251610.15562779294098
4.2838-5.38320.16561410.13162808294999
5.3832-21.53560.20871430.17112828297199

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