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- PDB-9t1m: Nuclear export protein/Non-structural protein 2 (NEP/NS2) in comp... -

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Basic information

Entry
Database: PDB / ID: 9t1m
TitleNuclear export protein/Non-structural protein 2 (NEP/NS2) in complex with artificial alpha Rep protein
Components
  • Alpha Rep E4
  • Nuclear export protein
KeywordsVIRAL PROTEIN / Nuclear export protein / non-structural protein 2 / influenza virus / synthetic protein
Function / homologyInfluenza nuclear export protein NS2 / Influenza non-structural protein (NS2) / Nuclear export protein
Function and homology information
Biological speciessynthetic construct (others)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsStelfox, A.J. / Ballandras-Colas, A. / Crepin, T.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-23-CE11-01 France
Citation
Journal: J.Mol.Biol. / Year: 2025
Title: Monomeric Structure of Influenza A Virus NEP/NS2 Obtained With an Artificial Protein Highlights Conformational Plasticity.
Authors: Stelfox, A.J. / Bessonne, M. / Bourhis, J.M. / Erba, E.B. / Albanese, P. / Compte, D.P. / Nevers, Q. / Urvoas, A. / Valerio-Lepiniec, M. / Minard, P. / Ruigrok, R.W.H. / Crepin, T. / Delmas, ...Authors: Stelfox, A.J. / Bessonne, M. / Bourhis, J.M. / Erba, E.B. / Albanese, P. / Compte, D.P. / Nevers, Q. / Urvoas, A. / Valerio-Lepiniec, M. / Minard, P. / Ruigrok, R.W.H. / Crepin, T. / Delmas, B. / Ballandras-Colas, A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha Rep E4
B: Nuclear export protein
C: Alpha Rep E4
E: Alpha Rep E4


Theoretical massNumber of molelcules
Total (without water)71,0544
Polymers71,0544
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Size exclusion chromatography with multi angle light scattering shows a 1:1 complex of alphaRep E4 (C) and NEP (B)., mass spectrometry, Native mass spectrometry shows a 1: ...Evidence: light scattering, Size exclusion chromatography with multi angle light scattering shows a 1:1 complex of alphaRep E4 (C) and NEP (B)., mass spectrometry, Native mass spectrometry shows a 1:1 complex of alphaRep E4 (C) and NEP (B)., cross-linking, UV cross linking followed by mass spectrometry shows a 1:1 complex of alphaRep E4 (C) and NEP (B). AlphaRep E4 binds the N-terminal alpha helices 1 and 2 of NEP, confirming that this assembly is the one that is relevant in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.809, 136.809, 71.362
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11C-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 15 through 16 or resid 18...
d_2ens_1(chain "C" and (resid 15 through 16 or resid 18...
d_3ens_1(chain "E" and (resid 15 through 16 or resid 18...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSVALVALAA15 - 1615 - 16
d_12METMETASPASPAA18 - 3218 - 32
d_13ALAALAASPASPAA34 - 4334 - 43
d_14ALAALAVALVALAA46 - 4746 - 47
d_15PROPROILEILEAA49 - 5149 - 51
d_16ALAALAGLYGLYAA53 - 5953 - 59
d_17VALVALARGARGAA61 - 6261 - 62
d_18THRTHRVALVALAA64 - 9264 - 92
d_19ALAALAASPASPAA94 - 10594 - 105
d_110ARGARGVALVALAA107 - 109107 - 109
d_111PROPROASPASPAA111 - 120111 - 120
d_112TYRTYRGLUGLUAA122 - 144122 - 144
d_113LEULEUGLYGLYAA146 - 152146 - 152
d_114ALAALAARGARGAA154 - 155154 - 155
d_115VALVALALAALAAA157 - 158157 - 158
d_116ASNASNTHRTHRAA160 - 164160 - 164
d_21LYSLYSVALVALCC15 - 1615 - 16
d_22METMETASPASPCC18 - 3218 - 32
d_23ALAALAASPASPCC34 - 4334 - 43
d_24ALAALAVALVALCC46 - 4746 - 47
d_25PROPROILEILECC49 - 5149 - 51
d_26ALAALAGLYGLYCC53 - 5953 - 59
d_27VALVALARGARGCC61 - 6261 - 62
d_28THRTHRVALVALCC64 - 9264 - 92
d_29ALAALAASPASPCC94 - 10594 - 105
d_210ARGARGVALVALCC107 - 109107 - 109
d_211PROPROASPASPCC111 - 120111 - 120
d_212TYRTYRGLUGLUCC122 - 144122 - 144
d_213LEULEUGLYGLYCC146 - 152146 - 152
d_214ALAALAARGARGCC154 - 155154 - 155
d_215VALVALALAALACC157 - 158157 - 158
d_216ASNASNTHRTHRCC160 - 164160 - 164
d_31LYSLYSVALVALED15 - 1615 - 16
d_32METMETASPASPED18 - 3218 - 32
d_33ALAALAASPASPED34 - 4334 - 43
d_34ALAALAVALVALED46 - 4746 - 47
d_35PROPROILEILEED49 - 5149 - 51
d_36ALAALAGLYGLYED53 - 5953 - 59
d_37VALVALARGARGED61 - 6261 - 62
d_38THRTHRVALVALED64 - 9264 - 92
d_39ALAALAASPASPED94 - 10594 - 105
d_310ARGARGVALVALED107 - 109107 - 109
d_311PROPROASPASPED111 - 120111 - 120
d_312TYRTYRGLUGLUED122 - 144122 - 144
d_313LEULEUGLYGLYED146 - 152146 - 152
d_314ALAALAARGARGED154 - 155154 - 155
d_315VALVALALAALAED157 - 158157 - 158
d_316ASNASNTHRTHRED160 - 164160 - 164

NCS oper:
IDCodeMatrixVector
1given(0.426385362184, 0.836150172426, -0.345033928864), (-0.589629987763, -0.0323406840998, -0.807025747844), (-0.685953351509, 0.54754631704, 0.479229621632)8.04976922887, 44.169274864, 56.494458828
2given(-0.408419445715, -0.845910532303, 0.34297073884), (-0.91242698534, 0.367681424914, -0.179686855938), (0.025895033994, -0.386323363404, -0.92199984062)64.4604163707, 61.8218243726, 17.3928671918

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Components

#1: Protein Alpha Rep E4


Mass: 18903.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein Nuclear export protein / NEP / Non-structural protein 2 / NS2


Mass: 14343.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/WSN/1933(H1N1)) / Gene: NEP, NS, NS2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0ABF7SXM9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 13 mg.mL-1 protein consisting of 1:1 molar ratio NEP and alpha-Rep E4 0.2 M sodium acetate pH 5.0, 12-16 % PEG 6K, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 30, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.33→68.42 Å / Num. obs: 25648 / % possible obs: 94.4 % / Redundancy: 10.7 % / Biso Wilson estimate: 50.66 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.06 / Net I/σ(I): 11.2
Reflection shellResolution: 2.62→2.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 924 / CC1/2: 0.96 / Rpim(I) all: 0.44 / % possible all: 61.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→68.4 Å / SU ML: 0.2998 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3801
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 1218 4.77 %
Rwork0.2172 24315 -
obs0.2188 25533 77.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.52 Å2
Refinement stepCycle: LAST / Resolution: 2.33→68.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 0 117 4669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00154609
X-RAY DIFFRACTIONf_angle_d0.40246189
X-RAY DIFFRACTIONf_chiral_restr0.0336682
X-RAY DIFFRACTIONf_plane_restr0.0043812
X-RAY DIFFRACTIONf_dihedral_angle_d11.34831785
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.739883365588
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.11391685526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.430.3269100.3368264X-RAY DIFFRACTION7.62
2.43-2.540.423450.32671004X-RAY DIFFRACTION28.9
2.54-2.670.36791230.31052199X-RAY DIFFRACTION63.95
2.67-2.840.32411640.27733357X-RAY DIFFRACTION97.1
2.84-3.060.28231490.26533498X-RAY DIFFRACTION99.95
3.06-3.370.3091730.27073479X-RAY DIFFRACTION100
3.37-3.850.3071670.22763408X-RAY DIFFRACTION97.28
3.85-4.850.1961910.17223502X-RAY DIFFRACTION99.97
4.86-68.40.18831960.17963604X-RAY DIFFRACTION99.71
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)
15.371153583412.40842890005-4.474581431232.74154521446-1.937681112723.706201953820.2637424153521.111809394870.946354916032-0.08628669019660.4224210025990.279959633523-2.09391518893-0.721408376664-0.6667269558530.9158210129480.1598860518810.09269881055920.7360548183850.1730805776320.74160071124324.39399223423.68021366319-15.001035617
26.09976082404-5.776893123572.486099390829.009310229880.3304743840893.55965332057-0.515640812143-0.525661521838-0.04933671624640.336931412850.650341636493-0.1649751579240.1169835297110.101066695666-0.02240426470311.012710693350.01226104264320.1298665866690.5241956266530.1774718936560.73201104472925.80956331-4.33049061732-19.5176946319
33.988238152972.077750041825.033952747929.10553264979-0.8285767079358.05866806846-0.4242770947922.295369384680.03818150873470.05268539421260.0164570604814-1.28960016712-0.8136875536551.688605411770.6350265065560.678623192184-0.2170572589740.04706864442180.9143839756280.08850503616660.43894475167555.1540229454-13.2473808445-6.47358561821
46.09220336748-1.96373123739-0.5278800757192.514176782750.670707997426.297371636720.002522525054870.3927212626260.3383771888180.111969995201-0.107976112386-0.436412573402-0.6290811218140.4001930099780.09079409437850.550106918177-0.1767111923760.01099278915980.4641779325810.1046936072070.31669302413251.8269900328-14.61380193733.18268477946
56.446269534440.511609321928-2.66925558565.15580007369-1.300365616644.31364814699-0.274104451137-0.5445065078240.5361198965350.04465518804280.388211994706-0.495258477693-0.8580456539070.721336993166-0.01744527693020.589411992468-0.207384023889-0.001043321316810.600022986634-0.04793565810450.34737211623348.8738349536-13.012466566214.6520086845
62.283583672980.1534012668180.2690845087715.48410598-2.028458958565.26980092877-0.241486605374-0.604382470093-0.03690222607170.4011138086180.093482110835-0.355091703585-0.5034137736630.5363906087350.154573489050.548768902481-0.0889750835706-0.0006080111901450.867161430087-0.01840772398340.25810705985148.2716620855-20.375334537828.5522073706
75.369462911830.4981043522020.9288518712886.193596896371.377976152174.786779403460.0514731490575-0.269732211716-0.1600716066580.6396080633880.06855959912920.3999517607210.00962793781171-0.806044639553-0.1599472763850.4071838189-0.02001384706820.06602856988610.7308531617240.1056526075080.3208065770173.3849147754-11.343395101825.5064701735
84.299956254110.318052317065-0.04691192125914.267208876671.008902279474.1552284571-0.106035527577-0.423077732054-0.514328879523-0.02976668631960.02864169857530.163858253550.35850321436-0.4275055610010.07716700991460.339363992855-0.0850598971987-0.00762407327280.7169395934090.04225610353750.27075427784874.9531527085-13.313051016810.9198790923
95.12131892469-0.706357364832-1.12716340085.1095008581-1.938944770475.28949591345-0.03450409948840.675275081092-0.628634808701-0.663720644565-0.2847451078960.1413604198120.254093985727-0.7154393428370.2340896324710.497476336543-0.1998907828620.009545820552050.695124875273-0.1190462373460.2779330811979.6720134809-19.102848674-0.456473243369
108.20948008814-6.11273348014-1.226128166478.019988346830.2985269803818.75129680736-0.79381896664-0.736410583553-1.848354590230.8844810296210.7457810018740.5300487338072.34809307717-0.3445752425090.03789739853781.1764857069-0.3033916576990.09307835329680.73702352257-0.117296276040.38801911328188.5552519311-25.2465605459-4.11074682749
114.39246329053-0.1345852975250.1294353187597.29067025411-3.421458271187.51893773552-0.288465721970.4537341486180.400517094271-0.2514950092540.1153388886230.229426518451-0.896840190081-0.2419109934160.09028302235550.3103887850850.0556283835297-0.02465244907250.336339360948-0.05700271778460.31623349347331.0376179592-22.6610909007-5.89988768304
121.690952971032.629761250732.60181716934.354359946813.967669245254.031617121810.786263801056-3.54124368366-2.214691114061.723741001910.4315441601911.029044757890.351327840839-2.45439157484-1.306947003551.53289851715-0.09751759248170.05899744110781.701348144860.529743318361.0235659930433.0032130782-36.392336211818.7234316241
134.902847778281.127366424461.572725008955.72978087018-1.345910821647.656721574790.205677514091-0.6233038185320.1758427703170.1812351465860.02597004316990.4703397345080.102595620415-0.291408125582-0.1945572675490.1925208144680.02444261294110.02475909233160.3394635497110.01306111031730.29230988213424.7640374113-33.3612304799-5.91009397408
142.90306720652-0.72950028853.145154877824.10985470571-1.253723737213.09003090493-0.0743210056010.07343098146360.03776536881690.236622412168-0.167717682634-0.2383824971180.08890891231140.818169755110.1413043915140.3045070392390.09366632378580.001804520982660.336043367046-0.02695430725590.21845582666834.31342601-32.4574361927-5.94307099188
154.12910584835-0.3823469608592.8828657769.06624642425-1.216623828427.054170691280.567308009175-1.70211803504-0.04605722193530.728525130188-0.3794944929361.38799683586-0.190110371339-2.0114026173-0.06169926273110.7541031548390.1091753149280.2438196791041.067895964940.02588685195820.56732487049217.7470572046-23.873623952317.4383101317
167.30131389811-2.452562820644.159613751986.45278347388-3.161666752884.79746896620.8757086287580.5000817415040.680941280751-0.517770711958-0.4885448123010.6715572019310.481484385114-0.857552120347-0.4508617285060.4813322012990.007713778807890.01952047415360.6178200226780.02308733118550.25956421813322.2097303185-23.667448864110.0297101446
177.39063663763-0.4711759751751.613764388319.52862151466-0.772998557346.23916077678-0.0847508857682-1.569238050751.499190773070.936204351512-0.4084505020851.02791186677-0.95357760504-1.682021059510.254556986210.8679705200730.3857856068910.111189155160.982050966514-0.1964471237670.70558515250917.7725300737-13.246556856512.5676467381
182.687140330990.2298673443570.3076326948225.42175012446-1.770759598933.53589535134-0.330242128187-0.1268074514510.7271019045420.3548797370750.1755598917530.658046448328-1.52692352509-0.739339829090.1406913193360.7844437412150.233027465278-0.02921350498490.524637389898-0.04716568425280.39496531153425.1421718333-8.500183831732.7786295793
197.11175170246-5.41703182494.093776088889.23750094897-2.18050305084.64238846268-0.4564545066950.807924936052-0.5471307368210.001624233968890.4739223749570.0242087661599-1.918054789570.3665211691090.06769110688260.9241113562460.0774924888676-0.03543654588150.3419381238730.116375523610.28215285523829.3303381739-8.20097346473-7.8860741645
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 135 through 149 )CC135 - 149124 - 138
22chain 'C' and (resid 150 through 166 )CC150 - 166139 - 155
33chain 'E' and (resid 13 through 27 )ED13 - 271 - 15
44chain 'E' and (resid 28 through 72 )ED28 - 7216 - 60
55chain 'E' and (resid 73 through 103 )ED73 - 10361 - 91
66chain 'E' and (resid 104 through 167 )ED104 - 16792 - 155
77chain 'A' and (resid 12 through 72 )AA12 - 721 - 61
88chain 'A' and (resid 73 through 103 )AA73 - 10362 - 92
99chain 'A' and (resid 104 through 149 )AA104 - 14993 - 138
1010chain 'A' and (resid 150 through 166 )AA150 - 166139 - 155
1111chain 'B' and (resid 6 through 51 )BB6 - 511 - 46
1212chain 'B' and (resid 52 through 63 )BB52 - 6347 - 55
1313chain 'B' and (resid 64 through 92 )BB64 - 9256 - 84
1414chain 'B' and (resid 93 through 121 )BB93 - 12185 - 113
1515chain 'C' and (resid 12 through 27 )CC12 - 271 - 16
1616chain 'C' and (resid 28 through 41 )CC28 - 4117 - 30
1717chain 'C' and (resid 42 through 55 )CC42 - 5531 - 44
1818chain 'C' and (resid 56 through 117 )CC56 - 11745 - 106
1919chain 'C' and (resid 118 through 134 )CC118 - 134107 - 123

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