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- PDB-4ht1: Human TWEAK in complex with the Fab fragment of a neutralizing an... -

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Basic information

Entry
Database: PDB / ID: 4ht1
TitleHuman TWEAK in complex with the Fab fragment of a neutralizing antibody
Components
  • (chimeric antibody Fab) x 2
  • Tumor necrosis factor ligand superfamily member 12
KeywordsIMMUNE SYSTEM / antibody Fab / TNF homology domain / cytokine / Tweak receptor / membrane bound / extracellular THD domain
Function / homology
Function and homology information


TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / endothelial cell migration / extrinsic apoptotic signaling pathway / positive regulation of endothelial cell proliferation / cytokine activity / TNFR2 non-canonical NF-kB pathway / positive regulation of angiogenesis / positive regulation of protein catabolic process ...TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / endothelial cell migration / extrinsic apoptotic signaling pathway / positive regulation of endothelial cell proliferation / cytokine activity / TNFR2 non-canonical NF-kB pathway / positive regulation of angiogenesis / positive regulation of protein catabolic process / angiogenesis / cell differentiation / receptor ligand activity / immune response / signaling receptor binding / apoptotic process / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / plasma membrane
Similarity search - Function
: / 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 ...: / 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 ligand superfamily member 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsLammens, A.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structure of Human TWEAK in Complex with the Fab Fragment of a Neutralizing Antibody Reveals Insights into Receptor Binding.
Authors: Lammens, A. / Baehner, M. / Kohnert, U. / Niewoehner, J. / von Proff, L. / Schraeml, M. / Lammens, K. / Hopfner, K.P.
History
DepositionOct 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Oct 30, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

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Assembly

Deposited unit
T: Tumor necrosis factor ligand superfamily member 12
H: chimeric antibody Fab
L: chimeric antibody Fab


Theoretical massNumber of molelcules
Total (without water)64,8023
Polymers64,8023
Non-polymers00
Water1,802100
1
T: Tumor necrosis factor ligand superfamily member 12
H: chimeric antibody Fab
L: chimeric antibody Fab

T: Tumor necrosis factor ligand superfamily member 12
H: chimeric antibody Fab
L: chimeric antibody Fab

T: Tumor necrosis factor ligand superfamily member 12
H: chimeric antibody Fab
L: chimeric antibody Fab


Theoretical massNumber of molelcules
Total (without water)194,4059
Polymers194,4059
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
Unit cell
Length a, b, c (Å)101.630, 101.630, 57.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 12 / APO3 ligand / TNF-related weak inducer of apoptosis / TWEAK / Tumor necrosis factor ligand ...APO3 ligand / TNF-related weak inducer of apoptosis / TWEAK / Tumor necrosis factor ligand superfamily member 12 / membrane form / Tumor necrosis factor ligand superfamily member 12 / secreted form


Mass: 17095.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43508
#2: Antibody chimeric antibody Fab


Mass: 24084.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: chimeric antibody / Source: (natural) Oryctolagus cuniculus (rabbit)
#3: Antibody chimeric antibody Fab


Mass: 23621.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: chimeric antibody / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% Ethanol, 10% PEG6000, 100 mM Sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.933 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.4
ReflectionResolution: 2.498→29.338 Å / Num. all: 22932 / Num. obs: 22932 / % possible obs: 99.5 % / Observed criterion σ(F): 84796 / Observed criterion σ(I): 84796

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.498→29.338 Å / σ(F): 2.17 / Phase error: 40.78 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2111 2296 10.01 %
Rwork0.1834 --
obs0.1879 22932 99.53 %
all-22932 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1128 Å20 Å2-0 Å2
2--0.1128 Å2-0 Å2
3----0.5803 Å2
Refinement stepCycle: LAST / Resolution: 2.498→29.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 0 100 4365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134379
X-RAY DIFFRACTIONf_angle_d1.6255955
X-RAY DIFFRACTIONf_dihedral_angle_d16.9341542
X-RAY DIFFRACTIONf_chiral_restr0.103672
X-RAY DIFFRACTIONf_plane_restr0.011759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4981-2.55240.34221310.27611170X-RAY DIFFRACTION86
2.5524-2.61170.33011490.27081344X-RAY DIFFRACTION90
2.6117-2.6770.29831410.25641272X-RAY DIFFRACTION90
2.677-2.74930.29171470.2481320X-RAY DIFFRACTION90
2.7493-2.83020.26061410.24041269X-RAY DIFFRACTION90
2.8302-2.92140.24111430.22651293X-RAY DIFFRACTION90
2.9214-3.02570.26171470.22861318X-RAY DIFFRACTION90
3.0257-3.14670.21771440.1981293X-RAY DIFFRACTION90
3.1467-3.28980.21341420.19281278X-RAY DIFFRACTION90
3.2898-3.46290.22651450.17821311X-RAY DIFFRACTION90
3.4629-3.67950.2051420.16641280X-RAY DIFFRACTION90
3.6795-3.96290.16651440.16061292X-RAY DIFFRACTION90
3.9629-4.36050.16151460.14251314X-RAY DIFFRACTION90
4.3605-4.98860.14731420.12881282X-RAY DIFFRACTION90
4.9886-6.27440.18431450.15851301X-RAY DIFFRACTION90
6.2744-28.80670.19021450.15871300X-RAY DIFFRACTION89

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