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- PDB-6e5u: Crystal structure of the mRNA export receptor NXF1/NXT1 in comple... -

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Basic information

Entry
Database: PDB / ID: 6e5u
TitleCrystal structure of the mRNA export receptor NXF1/NXT1 in complex with influenza virus NS1 protein
Components
  • (Non-structural protein 1) x 2
  • NTF2-related export protein 1
  • Nuclear RNA export factor 1
KeywordsRNA BINDING PROTEIN / mRNA nuclear export
Function / homology
Function and homology information


nuclear RNA export factor complex / symbiont-mediated suppression of host mRNA processing / nuclear pore central transport channel / symbiont-mediated suppression of host PKR/eIFalpha signaling / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus ...nuclear RNA export factor complex / symbiont-mediated suppression of host mRNA processing / nuclear pore central transport channel / symbiont-mediated suppression of host PKR/eIFalpha signaling / nuclear inclusion body / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / poly(A)+ mRNA export from nucleus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / mRNA export from nucleus / nuclear pore / protein export from nucleus / small GTPase binding / cytoplasmic stress granule / protein transport / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / nuclear speck / mRNA binding / host cell nucleus / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / Nuclear transport factor 2/Mtr2 / Influenza virus non-structural protein, effector domain / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Influenza A virus NS1 protein ...Nuclear RNA export factor Tap, RNA-binding domain / Tap, RNA-binding / Nuclear transport factor 2/Mtr2 / Influenza virus non-structural protein, effector domain / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / S15/NS1, RNA-binding / Nuclear Transport Factor 2; Chain: A, - #50 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Nuclear Transport Factor 2; Chain: A, / Leucine-rich repeat / Leucine-rich repeat domain superfamily / RNA-binding domain superfamily / Helix Hairpins / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / Nucleotide-binding alpha-beta plait domain superfamily / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1 / Nuclear RNA export factor 1 / NTF2-related export protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsXie, Y. / Ren, Y.
CitationJournal: Nat Microbiol / Year: 2019
Title: Structural basis for influenza virus NS1 protein block of mRNA nuclear export.
Authors: Zhang, K. / Xie, Y. / Munoz-Moreno, R. / Wang, J. / Zhang, L. / Esparza, M. / Garcia-Sastre, A. / Fontoura, B.M.A. / Ren, Y.
History
DepositionJul 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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
A: Nuclear RNA export factor 1
B: NTF2-related export protein 1
C: Nuclear RNA export factor 1
D: NTF2-related export protein 1
E: Nuclear RNA export factor 1
F: NTF2-related export protein 1
G: Nuclear RNA export factor 1
H: NTF2-related export protein 1
K: Non-structural protein 1
L: Non-structural protein 1
M: Non-structural protein 1
U: Non-structural protein 1
V: Non-structural protein 1
X: Non-structural protein 1
Y: Non-structural protein 1
J: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)395,81016
Polymers395,81016
Non-polymers00
Water00
1
A: Nuclear RNA export factor 1
B: NTF2-related export protein 1
C: Nuclear RNA export factor 1
D: NTF2-related export protein 1
L: Non-structural protein 1
M: Non-structural protein 1
U: Non-structural protein 1
Y: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)197,9058
Polymers197,9058
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Nuclear RNA export factor 1
F: NTF2-related export protein 1
G: Nuclear RNA export factor 1
H: NTF2-related export protein 1
K: Non-structural protein 1
V: Non-structural protein 1
X: Non-structural protein 1
J: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)197,9058
Polymers197,9058
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.905, 101.905, 949.476
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Nuclear RNA export factor 1 / Tip-associated protein / Tip-associating protein / mRNA export factor TAP


Mass: 57482.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NXF1, TAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBU9
#2: Protein
NTF2-related export protein 1 / Protein p15


Mass: 15859.757 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NXT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKK6
#3: Protein
Non-structural protein 1 / NS1


Mass: 8449.549 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NS1, NS / Production host: Escherichia coli (E. coli) / References: UniProt: I7CAR2
#4: Protein
Non-structural protein 1 / NS1


Mass: 17160.717 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NS1, NS / Production host: Escherichia coli (E. coli) / References: UniProt: I7CAR2

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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: 3.6 Å3/Da / Density % sol: 65.79 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 50 mM Sodium Citrate (pH 5.6), 6.5% PEG3350, 0.1 M NaCl, 0.1 M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 54178 / % possible obs: 98.3 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 20.1
Reflection shellResolution: 3.8→3.87 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.423 / Mean I/σ(I) obs: 1 / Num. unique obs: 2660 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WYK,3RW6,4WYK,4OPA

4wyk

3rw6

4wyk

4opa


Resolution: 3.8→44.126 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.59
RfactorNum. reflection% reflection
Rfree0.2825 2135 3.98 %
Rwork0.2356 --
obs0.2375 53634 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→44.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20434 0 0 0 20434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00520790
X-RAY DIFFRACTIONf_angle_d0.8828110
X-RAY DIFFRACTIONf_dihedral_angle_d5.52212700
X-RAY DIFFRACTIONf_chiral_restr0.0513204
X-RAY DIFFRACTIONf_plane_restr0.0053648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.88840.39131370.32743394X-RAY DIFFRACTION98
3.8884-3.98550.26821380.28463435X-RAY DIFFRACTION99
3.9855-4.09320.29231450.25933520X-RAY DIFFRACTION99
4.0932-4.21360.30851440.26123455X-RAY DIFFRACTION99
4.2136-4.34950.23711400.22983415X-RAY DIFFRACTION99
4.3495-4.50480.23321450.20433453X-RAY DIFFRACTION99
4.5048-4.68490.21871410.19183451X-RAY DIFFRACTION99
4.6849-4.89790.2281440.18893510X-RAY DIFFRACTION99
4.8979-5.15580.29661480.22413402X-RAY DIFFRACTION99
5.1558-5.47820.29481500.23033435X-RAY DIFFRACTION99
5.4782-5.90030.29241420.24453457X-RAY DIFFRACTION99
5.9003-6.49240.31691410.25173432X-RAY DIFFRACTION99
6.4924-7.4280.32591450.26083423X-RAY DIFFRACTION98
7.428-9.34390.29761370.23313423X-RAY DIFFRACTION98
9.3439-44.12910.28061380.23393294X-RAY DIFFRACTION94
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)
15.28314.6963-2.13464.88840.55048.95841.33170.30811.7070.6073-0.57372.3902-0.5693-0.7932-0.74083.20890.49570.21521.2050.11542.1265-81.914515.0195-21.4173
24.1838-2.0581-1.12175.32590.76253.4798-0.14980.129-0.43680.75450.02751.3284-0.6116-0.69960.18151.61780.85590.37290.4249-0.25121.3671-92.807787.8309-40.2852
32.8679-0.1699-0.90787.60720.23693.0959-0.3943-0.8969-0.91771.15690.253-0.2459-0.1450.1275-0.33062.09090.81030.55320.61250.14491.8813-78.350675.7032-47.062
45.83270.18992.69693.9409-3.61884.7301-0.85572.90322.9984-0.64470.41870.9636-1.06731.54410.52411.8384-0.3544-0.28912.21860.64582.5548-68.054198.7013-83.7819
53.8439-1.4484-0.18357.7405-1.58193.3365-0.41980.2061-0.13860.06020.1259-0.3650.2921-0.06810.05341.25910.47380.16180.4199-0.12781.6935-46.730931.8432-53.2193
64.4863-2.1334-0.22557.40290.6432.2483-0.0807-0.08980.05020.65640.18120.3744-0.2765-0.3761-0.00461.70310.95650.55720.4533-0.07651.2306-60.958644.2181-46.1966
76.80893.71782.59535.615-1.32233.08150.15510.9367-1.5310.5649-0.0486-0.05830.3826-0.8913-0.04351.78140.9302-0.19362.0067-0.4622.1487-129.926597.9277-136.3013
82.0212-0.983-0.25513.72520.58892.26150.22070.3501-0.4818-0.1105-0.46910.7120.77430.22130.08991.52631.1145-0.19680.804-0.44821.9859-72.274752.1874-117.603
98.4315-4.5716-0.3368.66270.68834.754-0.42510.30630.7186-0.54110.17180.599-0.5486-0.1728-0.00561.28790.7466-0.2160.827-0.34321.7611-75.534470.7745-110.8706
107.4528-2.55914.38726.9257-3.44278.58030.1363-1.3032-0.10072.5509-1.0288-0.6617-1.41441.58990.59591.7596-0.3942-0.18452.03850.26581.0954-50.43968.2227-74.1845
115.4796-2.01051.35857.5113-0.58353.04970.0837-0.36980.7501-0.1761-0.4816-0.3397-0.4364-0.41930.0811.06380.65560.02790.708-0.15871.4904-97.6424120.0932-104.6652
124.8668-2.2671-0.02368.1573-0.47352.50750.5360.5149-0.8311-0.185-0.19590.41751.02870.2358-0.02521.49551.1204-0.34320.6349-0.45671.5499-94.0684101.6162-111.628
135.97361.8354-0.58629.6338-1.46472.53871.1675-1.59130.46220.1560.5577-2.9012-2.0703-0.912-1.79272.23820.701-0.06682.7905-0.20492.1923-123.9319122.9691-170.5265
147.7746-6.32465.94865.2314-4.86474.5576-1.7398-5.9530.0359-0.53070.1135-1.56242.1740.17611.53492.30920.12280.78883.6840.53382.9598-46.062614.42628.8436
156.92481.1850.24373.0343-2.72432.7095-1.12292.4195-0.6731-1.46742.6666-0.50122.54092.2455-1.25244.4785-0.1811-0.34072.4654-1.24083.9803-57.63568.027612.7101
164.5541.47165.30988.7538-0.84876.98-0.966-0.71360.24-1.47860.073-0.2881-0.87650.33361.02482.5309-0.42810.75182.0053-0.5681.5467-79.108421.107618.2132
173.16632.77453.07487.1838-2.31238.22560.30862.2981.7749-1.75230.9955-1.84710.41591.4677-1.23572.25141.08780.8542.78020.31033.0914-85.6375125.3495-139.4785
188.50580.0337-1.70017.6185-4.08413.3604-0.3294-1.12870.8548-1.3495-0.49670.5481-0.6523-0.760.91291.96560.2-0.02062.4196-0.63761.5501-123.094897.3841-176.0284
192.77683.2263-1.62273.8697-2.66066.6212-0.224-1.31010.26643.5601-0.3003-1.9596-3.2184-0.62390.32043.36830.4796-0.75741.5434-0.42992.1555-37.028240.0916-18.5853
205.0795.03865.30126.63416.02265.8847-3.98073.0587-3.1215-8.62942.113-1.0572-0.53680.09151.59436.1899-0.36110.83772.6104-0.68953.7071-112.2417129.7078-166.5899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 205:354 )A205 - 354
2X-RAY DIFFRACTION2( CHAIN A AND RESID 376:549 )A376 - 549
3X-RAY DIFFRACTION3( CHAIN B AND RESID 3:140 )B3 - 140
4X-RAY DIFFRACTION4( CHAIN C AND RESID 205:354 )C205 - 354
5X-RAY DIFFRACTION5( CHAIN C AND RESID 376:549 )C376 - 549
6X-RAY DIFFRACTION6( CHAIN D AND RESID 3:140 )D3 - 140
7X-RAY DIFFRACTION7( CHAIN E AND RESID 205:354 )E205 - 354
8X-RAY DIFFRACTION8( CHAIN E AND RESID 376:549 )E376 - 549
9X-RAY DIFFRACTION9( CHAIN F AND RESID 3:140 )F3 - 140
10X-RAY DIFFRACTION10( CHAIN G AND RESID 205:354 )G205 - 354
11X-RAY DIFFRACTION11( CHAIN G AND RESID 376:549 )G376 - 549
12X-RAY DIFFRACTION12( CHAIN H AND RESID 3:140 )H3 - 140
13X-RAY DIFFRACTION13( CHAIN K AND RESID 2:72 )K2 - 72
14X-RAY DIFFRACTION14( CHAIN L AND RESID 8:45 )L8 - 45
15X-RAY DIFFRACTION15( CHAIN M AND RESID 2:72 )M2 - 72
16X-RAY DIFFRACTION16( CHAIN U AND RESID 88:202 )U88 - 202
17X-RAY DIFFRACTION17( CHAIN V AND RESID 88:202 )V88 - 202
18X-RAY DIFFRACTION18( CHAIN X AND RESID 88:202 )X88 - 202
19X-RAY DIFFRACTION19( CHAIN Y AND RESID 88:202 )Y88 - 202
20X-RAY DIFFRACTION20( CHAIN J AND RESID 8:45 )J8 - 45

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