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- PDB-6u55: Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire ... -

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Basic information

Entry
Database: PDB / ID: 6u55
TitleAnti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire E (ZE) Complexed with Sudan ebolavirus Nucleoprotein C-terminal Domain 634-738
Components
  • Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire E (ZE)
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / Antibody / nanobody / Ebola / filovirus
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / Nucleoprotein
Function and homology information
Biological speciesLama glama (llama)
Sudan ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsTaylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI112851 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI105568 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)C06 RR012087 United States
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins.
Authors: Sherwood, L.J. / Taylor, A.B. / Hart, P.J. / Hayhurst, A.
History
DepositionAug 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 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: Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire E (ZE)
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,2802
Polymers26,2802
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-10 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.398, 28.298, 86.541
Angle α, β, γ (deg.)90.000, 114.453, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire E (ZE)


Mass: 12692.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Semi-synthetic single pot library Nomad 1 based upon Lama glama
Source: (gene. exp.) Lama glama (llama) / Plasmid: pecan219 / Production host: Escherichia coli (E. coli)
#2: Protein Nucleoprotein / / Nucleocapsid protein / Protein N


Mass: 13588.128 Da / Num. of mol.: 1 / Fragment: C-terminal domain (residues 634-738)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus (strain Boniface-76) / Strain: Boniface-76 / Gene: NP / Plasmid: pecan236/237 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QP77
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.8 M ammonium sulfate, 0.1 M citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.93→78.79 Å / Num. obs: 11116 / % possible obs: 65.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 44.05 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Net I/σ(I): 10.5
Reflection shellResolution: 1.93→2.04 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 556 / CC1/2: 0.56 / Rpim(I) all: 0.685 / Rrim(I) all: 1.69 / % possible all: 20.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U51

6u51


Resolution: 1.93→46.26 Å / SU ML: 0.3239 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.9869
RfactorNum. reflection% reflection
Rfree0.2631 1046 10 %
Rwork0.1925 --
obs0.1995 10462 65.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.25 Å2
Refinement stepCycle: LAST / Resolution: 1.93→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 0 25 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791758
X-RAY DIFFRACTIONf_angle_d1.04232385
X-RAY DIFFRACTIONf_chiral_restr0.0878256
X-RAY DIFFRACTIONf_plane_restr0.0054308
X-RAY DIFFRACTIONf_dihedral_angle_d19.5921639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.030.429460.3822416X-RAY DIFFRACTION20.25
2.03-2.160.3586740.3212658X-RAY DIFFRACTION32.81
2.16-2.320.35131060.3215966X-RAY DIFFRACTION47.33
2.32-2.560.39511460.3061305X-RAY DIFFRACTION64.01
2.56-2.920.33792080.26281871X-RAY DIFFRACTION91.38
2.92-3.680.2632280.19872062X-RAY DIFFRACTION99.48
3.68-46.260.22072380.14682138X-RAY DIFFRACTION99.04
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)
12.290013652661.077727996630.2626228321172.884821150752.050601903712.32107232988-0.18941295094-0.95283150256-0.6334532971780.222547245086-0.2420815786740.172278424912-0.263190853551-0.01740282144420.4697079655540.441530172910.04444809108820.0516370355640.9272371035490.1120384035090.194601044755-17.76112702472.0827399579335.5143925634
22.833626268681.789257983790.1910310834341.138260496790.2100379337581.37555060711-1.3001116159-2.223593869010.01657385622060.1253461680030.538823144881-0.104930920604-0.5055009087710.9509251028620.6831017488270.432849561968-0.0972963128667-0.0463896646620.7815943914060.03523058283890.311557663579-11.80229400176.0870592625134.5072249035
38.01785434132-3.280939354180.8463921873898.51735494076.318949369426.302566976260.1573016445550.08088554139970.747002742764-0.971133183724-0.537425887629-0.868889436035-1.027960720082.20476907558-0.6584745055390.47149684428-0.2606262175710.02313809904031.215413813990.07183168383970.3935025137910.9096675491777.1773815611828.7873125484
41.259619944350.0656656497427-2.780471567950.297137664135-0.8208688018777.883606464830.565802376625-1.036628311220.299529123291-0.11061716206-0.5145581619060.6990854282760.8567074796380.728067437275-0.2676376124880.420582855236-0.156666726075-0.05284351410110.247592808238-0.11203656690.397151874366-13.91695471290.31829964289224.9281131833
52.73915927905-0.0595488105913-1.81921609864.43996924848-2.085460116263.32163622903-0.2518844389670.11256927856-0.645521762995-0.0988741453316-0.2739840920040.1367363606030.971694080926-0.01304841802720.48346211820.589900545714-0.09134796390450.07257768969520.318320728088-0.06503146152070.402628206149-17.2891475664-2.8492053896222.0145497833
62.018948730391.43694220449-6.032690367181.49132079774-0.5350722716186.21636533388-0.577463581081.44049969168-0.303515073731-0.7890309646620.262259518387-0.633072580433-1.52670374541-0.9687904650070.3398953150790.552961913317-0.0781635127068-0.02396822806890.159514655490.1056278374140.381694689625-17.11427103659.3896468097319.2638107602
74.027446544520.2673928259361.153737713421.79725007787-0.2058852109892.7290055423-0.0438195919866-1.245752208560.92849851460.280300901307-0.1611254738870.0232671397482-0.7564140918450.2427771973840.2229321429850.653655119649-0.112336726968-0.06585220909940.641786286448-0.05817765413070.476219707706-11.592989268811.523559608930.4449446861
83.248535966940.663376740868-0.9918597161122.93519733441.096959973965.32738339079-0.2917037047620.183640557505-0.2925310874370.0858085038331-0.104587724041-0.191706573187-0.09731240625350.4483171528440.3307604976910.351061360228-0.05910569958050.008331793328110.362129634220.06143363071730.267330918548-11.23381823930.30005598459526.5025918183
95.789795577770.6933071531150.4299555109144.47210062367-0.6513922783713.65853838984-1.05867647233-1.018083020230.0259150721062-0.3525234354650.5536839725840.2451093231870.560961157437-0.5751146071560.1598208359850.452210894354-0.09657708783920.07019136904560.80074622271-0.009519333221420.387640427217-25.9071093132-2.0491833002434.2411911293
108.27894408599-3.249750678394.879824714492.72417040092-0.9033848325413.6101910222-0.913485994371-1.556144020460.510575846072-0.0698315561819-1.03486404012-1.131313428370.1883226604970.7321665543581.01074912350.40869795728-0.02123892753830.08056683988620.6285524924820.2290835262630.5001233551662.65192102807-0.2136548960278.8814779267
113.73372685223-0.7957352924950.660376728071.921528264150.7768178521143.68987900601-0.3656606604970.235385972179-0.3398028202030.178697690893-0.0780670953456-0.5242378538440.7202900480650.2660158273610.4207324720590.52925642908-0.0432582019803-0.02939830627820.3492343021160.1384775635730.493594458612-8.96825812577-6.2559500960514.308421809
127.102140144782.949964385170.2508121080063.651396550570.3335855505783.259487734560.269701885057-1.22165477066-0.5515064521510.201947310691-0.5220839337910.04731122033470.0254531958792-0.1324487824660.08554269570940.429226284173-0.0468349838263-0.03426583613480.3227607713040.02709455042620.334127621815-8.934769944762.7678058715812.5825380044
136.11062865618-1.48617946722-1.048002831593.25630300826-2.16184403837.25311558010.2039376712630.292647925166-0.651405942036-0.0807515510705-0.174593167441-0.1785493655440.71383583620.177610186252-0.0273238623390.3538627548080.007349787699110.01730869966080.330288973490.00180583379470.387231922456-6.440668245443.309286074741.25091996913
144.63804219828-0.383408404147-1.449281238884.498869210752.563044725359.985393869020.648335517290.1968673321921.33088961092-0.920241280521-0.364130011199-1.41531949199-1.120341979250.684855645858-0.5889680410190.4230611146050.3000801567940.1974838336030.6984646825010.1104091820510.536988133882-11.344427293111.6857412952-6.24867521544
151.617054891621.66881867056-0.6016406781355.415591921981.628097381726.35808043927-0.3088129534632.102780692590.816094188793-0.797812043564-0.531654952613-1.412543430810.9319841429870.09363002924410.8893975673590.7430616751690.1450985620770.2344641940721.32229735750.1461722840780.96037218319-10.684007482114.96646483-15.3539850439
166.441526351751.1867803716-1.094508620839.40124265978-1.977594588215.84268420416-0.8376507965730.237106762574-0.0366719851923-0.5109698182681.00165038152-1.59070578325-0.763686504175-0.530209247205-0.2209696483540.5030905517130.1794854859260.04834164386660.875089731312-0.01506212586740.424676707669-20.054411231514.6440429508-9.24581042112
172.74787773706-1.889460565951.88450466763.74110784103-1.811882184741.255554322670.08814923815670.248910853423-0.331284825939-0.08860446621350.1582492106250.298669573393-0.148520075935-0.492779443116-0.1318853755110.3539453715830.03491828145760.006535840767410.342315909137-0.0504473362520.358963296707-19.67916438347.98076663914-0.767019302127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 32 )
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 39 )
5X-RAY DIFFRACTION5chain 'A' and (resid 40 through 51 )
6X-RAY DIFFRACTION6chain 'A' and (resid 52 through 66 )
7X-RAY DIFFRACTION7chain 'A' and (resid 67 through 82 )
8X-RAY DIFFRACTION8chain 'A' and (resid 83 through 110 )
9X-RAY DIFFRACTION9chain 'A' and (resid 111 through 117 )
10X-RAY DIFFRACTION10chain 'B' and (resid 637 through 645 )
11X-RAY DIFFRACTION11chain 'B' and (resid 646 through 659 )
12X-RAY DIFFRACTION12chain 'B' and (resid 660 through 672 )
13X-RAY DIFFRACTION13chain 'B' and (resid 673 through 692 )
14X-RAY DIFFRACTION14chain 'B' and (resid 693 through 701 )
15X-RAY DIFFRACTION15chain 'B' and (resid 702 through 707 )
16X-RAY DIFFRACTION16chain 'B' and (resid 708 through 715 )
17X-RAY DIFFRACTION17chain 'B' and (resid 716 through 737 )

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