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- PDB-6rmj: Crystal structure of human NGR-TNF -

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Basic information

Entry
Database: PDB / ID: 6rmj
TitleCrystal structure of human NGR-TNF
ComponentsTumor necrosis factor
KeywordsCYTOKINE / TNF ALPHA / TNFA / Immune system
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 / : ...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 / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of myosin-light-chain-phosphatase activity / positive regulation of hair follicle development / negative regulation of myelination / death receptor agonist activity / response to isolation stress / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / inflammatory response to wounding / cellular response to toxic substance / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of I-kappaB phosphorylation / sequestering of triglyceride / positive regulation of interleukin-18 production / positive regulation of action potential / TNF signaling / positive regulation of protein transport / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / positive regulation of superoxide dismutase activity / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of neuroinflammatory response / leukocyte tethering or rolling / positive regulation of synoviocyte proliferation / response to fructose / positive regulation of fever generation / positive regulation of mononuclear cell migration / negative regulation of myoblast differentiation / negative regulation of glucose import / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / macrophage activation involved in immune response / positive regulation of protein localization to cell surface / TNFR1-mediated ceramide production / negative regulation of oxidative phosphorylation / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / tumor necrosis factor receptor binding / negative regulation of systemic arterial blood pressure / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of programmed cell death / regulation of immunoglobulin production / positive regulation of hepatocyte proliferation / positive regulation of heterotypic cell-cell adhesion / positive regulation of protein-containing complex disassembly / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / regulation of fat cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / response to L-glutamate / cortical actin cytoskeleton organization / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / regulation of synapse organization / negative regulation of fat cell differentiation / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of interleukin-6 production / phagocytic cup / antiviral innate immune response / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / skeletal muscle contraction
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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsDegano, M. / Garau, G.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Mechanism of Action of the Tumor Vessel Targeting Agent NGR-hTNF: Role of Both NGR Peptide and hTNF in Cell Binding and Signaling.
Authors: Valentinis, B. / Porcellini, S. / Asperti, C. / Cota, M. / Zhou, D. / Di Matteo, P. / Garau, G. / Zucchelli, C. / Avanzi, N.R. / Rizzardi, G.P. / Degano, M. / Musco, G. / Traversari, C.
History
DepositionMay 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor
B: Tumor necrosis factor
C: Tumor necrosis factor


Theoretical massNumber of molelcules
Total (without water)53,8873
Polymers53,8873
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-31 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.011, 92.011, 116.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 31 or resid 36 through 105 or resid 111 through 157))
21(chain B and (resid 9 through 31 or resid 36 through 105 or resid 111 through 157))
31chain C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARG(chain A and (resid 9 through 31 or resid 36 through 105 or resid 111 through 157))AA9 - 3115 - 37
12LEULEUTHRTHR(chain A and (resid 9 through 31 or resid 36 through 105 or resid 111 through 157))AA36 - 10542 - 111
13ALAALALEULEU(chain A and (resid 9 through 31 or resid 36 through 105 or resid 111 through 157))AA111 - 157117 - 163
21SERSERARGARG(chain B and (resid 9 through 31 or resid 36 through 105 or resid 111 through 157))BB9 - 3115 - 37
22LEULEUTHRTHR(chain B and (resid 9 through 31 or resid 36 through 105 or resid 111 through 157))BB36 - 10542 - 111
23ALAALALEULEU(chain B and (resid 9 through 31 or resid 36 through 105 or resid 111 through 157))BB111 - 157117 - 163
31SERSERLEULEUchain CCC9 - 15715 - 163

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Components

#1: Protein Tumor necrosis factor / Cachectin / TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a


Mass: 17962.346 Da / Num. of mol.: 3 / Mutation: N-terminal fusion with CNGRCG peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNF, TNFA, TNFSF2 / Plasmid: pET27b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01375
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 50 mM MES, 2.8 M magnesium sulfate, 1 M NaCL, 2% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2007
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.65→49.33 Å / Num. obs: 15203 / % possible obs: 100 % / Redundancy: 15.9 % / Biso Wilson estimate: 78.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.035 / Rrim(I) all: 0.141 / Net I/σ(I): 15.6 / Num. measured all: 241457 / Scaling rejects: 352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.65-2.7816.33.563119730.4690.9053.678100
8.79-49.3312.30.05242.24980.9980.0150.05499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1-12.2829refinement
XDS20190315data reduction
Aimless0.7.4data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M2J

5m2j


Resolution: 2.65→49.33 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.39
RfactorNum. reflection% reflection
Rfree0.2525 718 4.74 %
Rwork0.2091 --
obs0.2111 15138 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 246.56 Å2 / Biso mean: 98.2006 Å2 / Biso min: 47.12 Å2
Refinement stepCycle: final / Resolution: 2.65→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 0 26 3449
Biso mean---63.46 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033500
X-RAY DIFFRACTIONf_angle_d0.6264764
X-RAY DIFFRACTIONf_chiral_restr0.048534
X-RAY DIFFRACTIONf_plane_restr0.003620
X-RAY DIFFRACTIONf_dihedral_angle_d10.642106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2548X-RAY DIFFRACTION8.146TORSIONAL
12B2548X-RAY DIFFRACTION8.146TORSIONAL
13C2548X-RAY DIFFRACTION8.146TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6501-2.85470.40381440.358928222966
2.8547-3.1420.35881320.301128152947
3.142-3.59650.27261480.240728392987
3.5965-4.53070.24331470.188428883035
4.5307-49.33910.21441470.178930563203
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.58962.03621.45399.15843.1862.21040.01190.71860.5047-0.65920.1447-0.4895-1.06340.9837-0.16320.757-0.22990.10980.7672-0.03590.87316.885576.9032115.569
28.44622.89874.25273.94081.49329.16470.1604-0.32030.57930.0881-0.1785-0.626-0.35311.20450.06310.4695-0.12690.00420.5943-0.1520.715110.243270.2308119.8103
38.0891-4.46126.07852.67-3.79945.5131.58420.5203-1.7329-3.2647-0.4080.87252.3436-0.6201-1.01771.27640.0118-0.21210.60360.02170.9545-8.522251.8661108.8126
49.02395.46732.06865.55690.84555.76150.16780.5279-0.59940.23450.0604-1.27990.45931.0581-0.04870.6750.1138-0.0440.7414-0.02570.810712.163259.2854119.6719
59.09274.62421.45455.38244.86445.87220.81920.4585-1.54410.3347-0.48212.381-0.0878-1.8378-0.10451.0501-0.162-0.14751.2308-0.15571.4622-17.084953.3322108.6983
60.95890.9013-0.13754.46490.59064.2946-0.16830.26950.2131-0.28570.2349-0.4915-0.39340.52440.02890.4438-0.12180.03980.741-0.08640.63924.016266.6861118.7205
74.6359-5.0745-0.45438.8527-2.22293.92240.1422-0.1598-0.53240.06950.517-1.01250.6990.8097-0.60650.90150.0261-0.1720.8948-0.10010.68828.928754.1312136.4118
85.5424-0.17431.37759.2046-1.84447.88380.0364-0.19570.18480.9965-0.13-0.92320.73331.65550.06540.73530.0308-0.19111.1529-0.06940.774611.567857.8915141.9611
96.38594.4657-0.14738.22980.32485.49560.110.04-0.42390.12510.2615-0.22010.8689-0.2015-0.35550.66120.0065-0.06410.62640.12670.6015-5.100954.6226130.6391
103.79762.41331.91287.5793-0.84714.96960.0987-0.70720.45241.27230.09240.0982-0.15670.4305-0.15190.91350.00630.01530.9829-0.13990.7965-5.209460.0162143.9354
117.028.1464.82999.60235.76445.73890.2009-0.00260.1037-0.7764-0.35281.80061.6876-0.31220.56371.4186-0.1496-0.34121.48550.02311.0334-15.694545.0265118.4928
126.55452.00452.47367.75213.81838.64480.236-0.2496-0.18660.501-0.1513-0.45840.48430.3461-0.07330.5348-0.03270.00040.58510.01790.49680.503957.5052134.9953
132.06030.2364-2.16726.16980.4424.6591-0.4335-1.22820.49140.93210.31160.3817-0.4210.1780.25880.99540.03690.00060.9036-0.12490.8697-11.872577.2935138.213
144.7914.06781.01184.5079-0.25444.48060.2327-0.34071.13620.89520.04-0.438-1.52880.6362-0.33781.0001-0.14310.00830.8081-0.21220.8597-7.421984.4593137.9387
153.49360.63221.39942.9963-1.33567.51980.4024-1.07030.49071.1365-0.40310.54890.4175-0.06830.09210.46670.0832-0.01990.5479-0.14980.6419-6.233472.2164130.9904
162.02252.2165-1.92333.7539-3.24782.9209-1.12830.2507-2.0685-1.50890.53360.40630.8113-1.60530.54860.9256-0.1685-0.0931.1564-0.09241.4956-23.556161.412118.9711
175.07282.6442-1.63079.1532-2.98413.8486-0.12080.2105-0.1302-0.52950.3073-0.1763-0.14280.067-0.27040.54250.01840.03870.6067-0.00470.5762-11.919273.0081121.2828
185.16273.2539-0.91963.7939-2.64364.33510.44190.19640.16461.23960.21190.2515-0.3555-0.2367-0.63430.541-0.01210.0040.6734-0.07260.7433-6.097969.8747127.1657
193.96364.45953.74726.03955.33589.57690.5114-0.31431.20340.79930.1554-0.0056-1.23780.4877-0.6740.9658-0.01890.03850.5288-0.14290.895-6.516385.2475128.9116
202.9941-1.01483.20723.0849-0.49326.48240.0479-0.72130.18570.33040.00330.8402-0.2117-1.0116-0.06310.7122-0.00130.13950.7511-0.16330.8228-12.630170.558132.9666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 38 )A9 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 67 )A39 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 75 )A68 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 98 )A76 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 112 )A99 - 112
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 157 )A113 - 157
7X-RAY DIFFRACTION7chain 'B' and (resid 9 through 27 )B9 - 27
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 53 )B28 - 53
9X-RAY DIFFRACTION9chain 'B' and (resid 54 through 75 )B54 - 75
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 98 )B76 - 98
11X-RAY DIFFRACTION11chain 'B' and (resid 99 through 113 )B99 - 113
12X-RAY DIFFRACTION12chain 'B' and (resid 114 through 157 )B114 - 157
13X-RAY DIFFRACTION13chain 'C' and (resid 9 through 27 )C9 - 27
14X-RAY DIFFRACTION14chain 'C' and (resid 28 through 53 )C28 - 53
15X-RAY DIFFRACTION15chain 'C' and (resid 54 through 66 )C54 - 66
16X-RAY DIFFRACTION16chain 'C' and (resid 67 through 75 )C67 - 75
17X-RAY DIFFRACTION17chain 'C' and (resid 76 through 113 )C76 - 113
18X-RAY DIFFRACTION18chain 'C' and (resid 114 through 126 )C114 - 126
19X-RAY DIFFRACTION19chain 'C' and (resid 127 through 136 )C127 - 136
20X-RAY DIFFRACTION20chain 'C' and (resid 137 through 157 )C137 - 157

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