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- PDB-5nt2: Complex of influenza A NS1 with TRIM25 coiled coil domain -

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Basic information

Entry
Database: PDB / ID: 5nt2
TitleComplex of influenza A NS1 with TRIM25 coiled coil domain
Components
  • E3 ubiquitin/ISG15 ligase TRIM25
  • Non-structural protein 1
KeywordsLIGASE / Viral protein/host protein/E3 ligase/TRIM protein
Function / homology
Function and homology information


: / Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / RIG-I binding / symbiont-mediated suppression of host mRNA processing / regulation of viral entry into host cell / suppression of viral release by host / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling ...: / Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / RIG-I binding / symbiont-mediated suppression of host mRNA processing / regulation of viral entry into host cell / suppression of viral release by host / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / negative regulation of viral entry into host cell / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / NS1 Mediated Effects on Host Pathways / protein serine/threonine kinase inhibitor activity / response to vitamin D / RSV-host interactions / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / ERAD pathway / protein monoubiquitination / ligase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / antiviral innate immune response / TRAF6 mediated NF-kB activation / Viral mRNA Translation / viral release from host cell / protein K48-linked ubiquitination / cellular response to leukemia inhibitory factor / Evasion by RSV of host interferon responses / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / RING-type E3 ubiquitin transferase / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / ISG15 antiviral mechanism / positive regulation of DNA-binding transcription factor activity / cytoplasmic stress granule / response to estrogen / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / Interferon gamma signaling / ubiquitin protein ligase activity / Ovarian tumor domain proteases / positive regulation of NF-kappaB transcription factor activity / TRAF3-dependent IRF activation pathway / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / response to oxidative stress / host cell cytoplasm / transcription coactivator activity / nuclear body / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / virus-mediated perturbation of host defense response / innate immune response / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
TRIM25, PRY/SPRY domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY ...TRIM25, PRY/SPRY domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / S15/NS1, RNA-binding / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Non-structural protein 1 / E3 ubiquitin/ISG15 ligase TRIM25
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.259 Å
AuthorsKoliopoulos, M.G. / Rittinger, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001142 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition.
Authors: Koliopoulos, M.G. / Lethier, M. / van der Veen, A.G. / Haubrich, K. / Hennig, J. / Kowalinski, E. / Stevens, R.V. / Martin, S.R. / Reis E Sousa, C. / Cusack, S. / Rittinger, K.
History
DepositionApr 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Non-structural protein 1
C: Non-structural protein 1
D: Non-structural protein 1
E: Non-structural protein 1
I: E3 ubiquitin/ISG15 ligase TRIM25
A: E3 ubiquitin/ISG15 ligase TRIM25
V: E3 ubiquitin/ISG15 ligase TRIM25
N: E3 ubiquitin/ISG15 ligase TRIM25


Theoretical massNumber of molelcules
Total (without water)191,5188
Polymers191,5188
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS analysis shows that full-length NS1 is a dimer., gel filtration, SEC-MALLS analysis shows that TRIM25 coiled-coil is dimeric. Additional structural data show that ...Evidence: gel filtration, SEC-MALLS analysis shows that full-length NS1 is a dimer., gel filtration, SEC-MALLS analysis shows that TRIM25 coiled-coil is dimeric. Additional structural data show that it is an antiparallel dimer (see 4LTB in PDB).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32560 Å2
ΔGint-203 kcal/mol
Surface area69220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.257, 76.296, 92.072
Angle α, β, γ (deg.)100.04, 93.71, 111.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Non-structural protein 1 / NS1 / NS1A


Mass: 25867.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: P03496
#2: Protein
E3 ubiquitin/ISG15 ligase TRIM25 / Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / ...Estrogen-responsive finger protein / RING finger protein 147 / RING-type E3 ubiquitin transferase / RING-type E3 ubiquitin transferase TRIM25 / Tripartite motif-containing protein 25 / Ubiquitin/ISG15-conjugating enzyme TRIM25 / Zinc finger protein 147


Mass: 22011.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM25, EFP, RNF147, ZNF147 / Production host: Escherichia coli (E. coli)
References: UniProt: Q14258, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases), RING-type E3 ubiquitin transferase

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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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM sodium citrate pH 6.5, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.259→61.51 Å / Num. obs: 12516 / % possible obs: 98.6 % / Redundancy: 2.6 % / CC1/2: 0.985 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.14 / Net I/σ(I): 5.7
Reflection shellResolution: 4.26→4.33 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 630 / CC1/2: 0.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LTB

4ltb


Resolution: 4.259→61.684 Å / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 38.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3088 635 5.1 %
Rwork0.2702 --
obs0.2721 12451 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.259→61.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10516 0 0 0 10516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410633
X-RAY DIFFRACTIONf_angle_d0.814298
X-RAY DIFFRACTIONf_dihedral_angle_d12.9076705
X-RAY DIFFRACTIONf_chiral_restr0.0451678
X-RAY DIFFRACTIONf_plane_restr0.0051834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2585-4.58730.39431280.30972341X-RAY DIFFRACTION97
4.5873-5.04870.30691340.29752355X-RAY DIFFRACTION98
5.0487-5.77880.37191240.32452377X-RAY DIFFRACTION99
5.7788-7.27880.40851260.34262396X-RAY DIFFRACTION99
7.2788-61.69070.22131230.20042347X-RAY DIFFRACTION98
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)
16.32522.838-4.06467.80844.09318.43251.50640.46181.9186-0.054-1.1066-0.641-0.7840.5151-0.11531.70290.3645-0.26021.3278-0.35681.6546-136.6101-75.8288-197.6639
21.96071.5648-0.39514.96725.23755.81781.5373-4.30631.53831.2681.94120.5509-0.23560.70950.87142.20730.54870.33042.39370.57840.3712-150.0506-76.7036-210.8737
37.3227-0.0759-0.23152.81312.0976.99220.14141.4032-2.1823-0.5447-0.68550.99111.1438-1.4199-0.13641.80240.1083-0.37521.19710.35930.894-145.0457-85.0576-214.1167
47.57180.6272-0.10385.39411.51278.60890.1153-1.9804-0.71440.81230.5651-2.4040.7367-0.3229-0.23421.20920.4275-0.28461.3608-0.14471.2888-131.0545-83.2523-201.3731
54.36680.4689-2.64694.07580.54427.3246-1.69580.53680.27520.37460.80750.76270.46352.6412-0.00291.21180.03570.18850.88110.08490.9333-139.448-80.1826-204.363
66.0275-0.73190.86023.73163.46777.8374-0.148-0.63541.92040.52950.4318-1.65-0.0987-0.26060.17361.3770.5066-0.181.8835-0.22331.4581-142.0312-77.4693-209.7861
75.6473-2.0888-1.44221.08730.96490.9033-2.4663-1.0161-0.48970.41540.0239-0.43951.0996-0.38770.25741.84810.46690.05430.9099-0.34961.3646-142.9369-93.1775-198.3719
85.8151.2753-2.57875.60293.09077.03550.3593-0.7366-0.86030.94050.1952-3.24491.86372.68850.47651.80910.09280.33870.57630.50961.7136-136.1873-88.3846-213.0649
95.5197-1.1633-1.3973.891-1.37633.2249-0.30211.19481.36880.57581.0449-0.1846-0.80850.5488-0.21351.00510.08830.11711.2671-0.10191.2336-133.261-78.3855-217.0923
104.63612.8047-2.07935.43171.29672.7752-1.5696-0.28-0.3414-0.01070.9133-0.5-0.27813.1539-0.27661.15210.0074-0.33951.2505-0.12021.533-126.3161-81.8527-204.492
118.9438-3.454-2.03576.4919-0.66065.1326-0.9015-1.0249-2.88771.27823.05960.64141.89051.1658-0.01861.61050.06950.47832.0554-0.59950.9021-102.5399-36.5781-78.8204
125.20983.13262.30794.78861.28995.2568-1.70980.28930.3827-1.19151.1342.0237-2.57090.1562-0.44991.20760.37640.26511.42170.02521.7581-107.0707-23.0074-67.016
132.011-2.3319-3.28692.2789-1.29853.2154-0.93340.00531.78270.7683-0.30880.1582-0.88110.3845-1.4729-1.18460.05393.19742.07490.3666-0.455-93.5674-20.2828-64.3732
142.89681.45992.64413.3560.93085.0659-3.39670.6668-0.472-0.65281.4451-0.2927-0.94381.8833-1.8771-0.05471.02771.75751.8345-1.0799-0.975-98.6333-25.6719-62.0294
151.64652.7040.76777.0761-2.59926.3062-1.02561.8195-1.206-2.0951-0.3659-0.97820.7154-1.1171-0.691.31880.5091-0.02891.7844-0.59591.5231-93.6625-37.9821-75.2851
162.11910.59592.03795.52250.35126.5964-0.307-0.8221-1.1857-0.506-0.1916-0.41121.51812.236-0.46771.22190.33960.20341.4174-0.01390.7401-101.5647-30.6278-69.5343
173.7377-4.5949-1.3626.23631.86110.5301-0.9943-0.0201-0.6794-0.7444-1.5849-0.517-0.23573.5081-0.441.57230.0865-0.09312.88510.02571.4569-88.7898-23.8872-78.7356
182.49980.49721.14565.28360.81616.01050.33270.2934-0.01040.62191.048-1.13891.6799-0.0328-0.38430.92130.07790.14322.113-0.21491.2808-93.2867-33.2441-62.4961
195.0459-0.69040.70882.9541-1.87542.69920.25431.4801-1.4123-0.33512.1862-1.29363.46620.12550.40042.14960.69630.64091.1526-0.33431.3278-92.938-43.0208-71.9975
202.5302-2.9977-1.82984.58340.62221.94870.34440.5045-2.6994-1.0272-0.17170.2680.2008-0.222-0.33141.5434-0.0314-0.14141.8303-0.38392.5404-131.9299-53.7667-138.9206
214.79690.37450.65082.7587-2.0071.07130.35720.915-1.4106-1.6139-3.6836-0.17582.6134-0.4019-0.36452.5052-0.30020.02441.817-1.33012.3965-123.0518-59.6382-147.2425
226.3666-1.79543.03240.6106-1.13627.7218-0.0447-0.21593.062-0.7591-0.2820.74150.26861.15040.04722.1081-0.00770.78462.6498-1.30432.9986-107.0087-54.3323-138.2643
235.3895-1.1242-2.77098.30670.42021.35570.1435-0.2086-0.1213-2.463-0.09131.499-0.2261-0.50630.06341.7322-0.2159-0.34260.98480.18951.3433-102.8189-91.5188-150.0916
245.0159-2.06722.93136.2297-1.54651.28040.63630.5202-1.1102-0.8175-1.25430.49410.16960.7529-0.44781.43110.2759-0.06211.5325-0.02381.7565-119.9987-48.248-140.6156
255.1114-2.1826-1.08646.0743-0.32364.06150.5649-0.90380.81450.9497-0.2286-0.5398-0.03360.5454-0.08061.2402-0.04120.07191.0551-0.19021.2691-81.8887-53.5412-128.58
262.4352-3.9089-3.51543.92374.35535.65360.5560.13060.6621-0.15170.4029-1.4341-0.3229-0.00770.2841.1781-0.24910.37751.4545-0.04791.4102-92.6875-57.7482-109.8755
27-0.03970.17570.03920.51010.32790.12051.73510.36570.7573-1.93730.471-0.21260.962-3.50730.29012.43910.68290.02943.3013-0.15671.9515-69.8115-111.334-159.6486
282.0634-2.3824-1.79386.42991.48662.118-0.6623-0.3609-1.10060.8763-0.25661.42550.14160.21271.19461.0839-0.27650.19941.9731-0.30721.5389-101.9007-78.4512-118.5277
292.9726-0.91082.4657-0.1015-1.18913.37751.0730.5806-1.52820.18390.15840.14881.00870.31320.00251.18950.0841-0.26531.14680.00721.2954-115.7147-77.0707-170.1752
303.06391.0859-0.91151.88421.29471.5738-1.9193-0.0363-0.2172.018-1.7865-0.3392-0.25761.8318-0.46032.67580.8582-0.51443.4860.32992.1306-54.2418-78.7691-115.8427
314.20830.92872.05780.2598-0.31482.0243-1.3147-0.4882.12980.12240.0871-0.135-1.6616-0.06960.43231.3462-0.114-0.24121.5153-0.09131.5146-96.1621-61.4091-158.7691
324.06560.3662.2740.96070.1142.0356-0.7709-0.42010.65840.16750.0961-0.18-0.9004-0.34030.74021.055-0.02980.11141.45-0.25621.0037-109.1192-70.1499-156.9016
332.8109-0.2463.04280.0357-0.07893.4791-1.1837-3.48491.9769-1.2504-3.21541.329-2.6829-0.31190.77522.7226-0.0558-0.31312.7861-0.70683.3481-176.2499-80.2189-202.1172
344.9703-0.38423.80752.14191.45013.2359-1.61752.629-0.03850.22280.7083-0.6468-0.94742.0760.88751.0239-0.20440.06541.97420.51940.978-118.516-66.5406-182.3212
350.7603-0.3770.02375.62852.77161.66630.16750.23670.0295-0.6417-0.14420.0757-0.3008-0.18810.30821.31670.0611-0.17821.26220.00390.7927-97.8843-62.7646-120.1335
363.9278-4.3112-2.29084.74942.4981.3296-2.8602-1.05582.00240.0559-1.16380.0646-1.67460.5275-0.19562.03640.38330.32732.35350.07813.6568-108.10465.9517-74.4916
373.8017-0.6429-0.21743.45533.01313.6384-0.0596-0.71550.36590.8418-1.07050.0663-0.73380.31780.13773.8476-0.7967-2.61672.33061.87148.0441-116.17714.2732-73.0675
386.2223-1.9414-0.08033.9115-0.11280.57470.86870.37172.2258-0.63550.04220.5187-1.011-0.1716-0.0820.7171-0.21262.1373.95233.03816.5511-116.6642-5.1908-73.3309
392.9296-0.7564-0.26939.75973.96943.5292-0.09970.28571.35330.89-1.14790.1935-0.0153-1.04860.24641.52950.08760.36191.8713-0.12372.0875-114.1942-30.773-81.1462
403.2477-2.0538-3.32334.94511.06665.1174-0.8737-0.0898-0.31472.6368-0.61110.07142.1255-0.69890.4491.90630.11180.38421.4429-0.13891.1582-100.7412-67.6295-100.0697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 87 through 99 )
2X-RAY DIFFRACTION2chain 'F' and (resid 100 through 106 )
3X-RAY DIFFRACTION3chain 'F' and (resid 107 through 126 )
4X-RAY DIFFRACTION4chain 'F' and (resid 127 through 142 )
5X-RAY DIFFRACTION5chain 'F' and (resid 143 through 151 )
6X-RAY DIFFRACTION6chain 'F' and (resid 152 through 162 )
7X-RAY DIFFRACTION7chain 'F' and (resid 163 through 170 )
8X-RAY DIFFRACTION8chain 'F' and (resid 171 through 188 )
9X-RAY DIFFRACTION9chain 'F' and (resid 189 through 195 )
10X-RAY DIFFRACTION10chain 'F' and (resid 196 through 201 )
11X-RAY DIFFRACTION11chain 'C' and (resid 87 through 98 )
12X-RAY DIFFRACTION12chain 'C' and (resid 99 through 106 )
13X-RAY DIFFRACTION13chain 'C' and (resid 107 through 112 )
14X-RAY DIFFRACTION14chain 'C' and (resid 113 through 126 )
15X-RAY DIFFRACTION15chain 'C' and (resid 127 through 142 )
16X-RAY DIFFRACTION16chain 'C' and (resid 143 through 162 )
17X-RAY DIFFRACTION17chain 'C' and (resid 163 through 170 )
18X-RAY DIFFRACTION18chain 'C' and (resid 171 through 195 )
19X-RAY DIFFRACTION19chain 'C' and (resid 196 through 201 )
20X-RAY DIFFRACTION20chain 'D' and (resid 4 through 50 )
21X-RAY DIFFRACTION21chain 'D' and (resid 51 through 74 )
22X-RAY DIFFRACTION22chain 'D' and (resid 75 through 84 )
23X-RAY DIFFRACTION23chain 'D' and (resid 85 through 203 )
24X-RAY DIFFRACTION24chain 'E' and (resid 3 through 85 )
25X-RAY DIFFRACTION25chain 'E' and (resid 86 through 203 )
26X-RAY DIFFRACTION26chain 'I' and (resid 190 through 304 )
27X-RAY DIFFRACTION27chain 'I' and (resid 305 through 316 )
28X-RAY DIFFRACTION28chain 'I' and (resid 317 through 362 )
29X-RAY DIFFRACTION29chain 'A' and (resid 190 through 298 )
30X-RAY DIFFRACTION30chain 'A' and (resid 299 through 316 )
31X-RAY DIFFRACTION31chain 'A' and (resid 317 through 362 )
32X-RAY DIFFRACTION32chain 'V' and (resid 190 through 298 )
33X-RAY DIFFRACTION33chain 'V' and (resid 299 through 316 )
34X-RAY DIFFRACTION34chain 'V' and (resid 317 through 362 )
35X-RAY DIFFRACTION35chain 'N' and (resid 190 through 298 )
36X-RAY DIFFRACTION36chain 'N' and (resid 299 through 304 )
37X-RAY DIFFRACTION37chain 'N' and (resid 305 through 311 )
38X-RAY DIFFRACTION38chain 'N' and (resid 312 through 316 )
39X-RAY DIFFRACTION39chain 'N' and (resid 317 through 330 )
40X-RAY DIFFRACTION40chain 'N' and (resid 331 through 362 )

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