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- PDB-6u52: Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan ... -

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Basic information

Entry
Database: PDB / ID: 6u52
TitleAnti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB) Complexed with Sudan ebolavirus Nucleoprotein C-terminal Domain 634-738
Components
  • Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)
  • 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)
B: Nucleoprotein
C: Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4669
Polymers53,2894
Non-polymers1775
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-67 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.977, 44.984, 66.438
Angle α, β, γ (deg.)90.000, 105.937, 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
Components on special symmetry positions
IDModelComponents
11B-932-

HOH

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Components

#1: Antibody Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)


Mass: 13056.438 Da / Num. of mol.: 2
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.: 2 / 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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 10% polyethylene glycol 6000, 1.0 M lithium chloride, 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→45.14 Å / Num. obs: 38124 / % possible obs: 96.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.25 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5705 / CC1/2: 0.471 / Rpim(I) all: 0.849 / Rrim(I) all: 1.573 / % possible all: 99.8

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Processing

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

6u51


Resolution: 1.9→23.31 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.012
RfactorNum. reflection% reflection
Rfree0.2434 1996 5.25 %
Rwork0.1981 --
obs0.2004 38041 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 5 266 3624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783498
X-RAY DIFFRACTIONf_angle_d0.9484752
X-RAY DIFFRACTIONf_chiral_restr0.0836493
X-RAY DIFFRACTIONf_plane_restr0.0059631
X-RAY DIFFRACTIONf_dihedral_angle_d18.84291299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.35211450.35032615X-RAY DIFFRACTION99.57
1.95-20.37351470.31982647X-RAY DIFFRACTION99.89
2-2.060.32681460.30832635X-RAY DIFFRACTION99.29
2.06-2.130.3352880.33431590X-RAY DIFFRACTION60.75
2.13-2.20.33141450.2722608X-RAY DIFFRACTION99.31
2.2-2.290.36911480.25142661X-RAY DIFFRACTION99.61
2.29-2.390.29831450.22532621X-RAY DIFFRACTION99.82
2.39-2.520.27261450.24062629X-RAY DIFFRACTION98.93
2.52-2.680.26871460.22662667X-RAY DIFFRACTION99.43
2.68-2.880.27531460.22262635X-RAY DIFFRACTION99.86
2.88-3.170.27451460.22472658X-RAY DIFFRACTION99.4
3.17-3.630.23391480.18082657X-RAY DIFFRACTION99.43
3.63-4.570.18451490.14542680X-RAY DIFFRACTION99.09
4.57-23.310.18521520.15152742X-RAY DIFFRACTION98.74
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)
12.98912834191-0.990581565652-2.846121069461.845919690451.033172534063.925790105830.4751362927830.169607241557-0.0636248589184-0.276089407037-0.3099646254930.125915218886-0.685214548024-0.210175183813-0.1456363227130.4177271850090.0220824213560.006479141029270.6485866949070.0265924691810.34248028055414.02197766180.1781103974527.97594637774
25.68144120111-1.79869602581-2.20530212863.749313060661.546986912493.914553201480.2105852920920.209998208079-0.233186564729-0.321544419879-0.257278766778-0.0376375468699-0.2631918759890.200179252270.0891198675660.318021126558-0.007291201761980.01891817607150.4826159645770.01035338494580.30631321573127.5030693914-6.253702224083.93204438879
32.59601425539-1.90086136995-0.8699225202652.858567615860.2717165241792.322106028220.007910652651660.3173044209950.01914570834160.061518315024-0.0392000663176-0.0346107539355-0.171335369014-0.1132433928540.003988809468840.274244940422-0.017664655709-0.001915222766570.404389028594-0.007017909360180.25537954391316.0439054972-2.311326071116.9047749939
42.99193892515-2.335041383530.5267474089172.254346871040.4493302621713.739049497790.02039006746250.319242908854-1.13929974359-0.3909645037180.2648028956460.1501678485710.993756762727-0.00230476929537-0.426013939870.869529911838-0.2752592845010.2299911367420.553901921574-0.2819478189010.80895132334315.8401672815-20.33149722628.95481407328
52.709914023650.140511876883-1.054274971352.1664979112-0.9076352228762.44439951328-0.0443275656938-0.0692366004247-0.02535542265530.1882322849330.0362748473318-0.160537997579-0.01410547911350.1147025658610.02456982226640.252005410419-0.00306052101645-0.01624186157510.352017108803-0.03929849461590.273683569825.0771774322-4.3288292783117.6596660319
60.7480221150640.0678910854767-0.01735349614131.337202523110.9823467149012.63694275717-0.122177859590.1862597229910.0527286053780.02648977456290.08054834216420.06813074659790.0670718615302-0.1311072795740.08053600784940.289183876279-0.014187969354-0.001291522307770.320604984049-0.007266745392810.27426335301314.8049088243-7.7264274882614.6333401136
73.708822503090.5914697931161.940375087086.05976874165-0.687242926465.862150533580.3049170923590.164350226488-0.434134808968-0.853477349469-0.228671994497-0.3791574946410.343608116135-0.253903324476-0.02287682780780.4206559352230.07692984481420.005657350198920.477271581468-0.1154293370830.38053049628224.6715640181-13.04407850380.255963847863
85.05512562924-2.152865149440.6706693353693.42334088492-0.9910851958913.00736707928-0.0786325520076-0.561958589639-0.205018929446-0.0360184095860.3322604433410.1604205349180.184408188581-0.201688730416-0.2471803019810.2454169885010.0137048510216-0.01624303134690.41238945707-0.004894634814450.285407592895-4.11258263654-0.99170647587637.1806491642
92.31551753868-0.07264692167121.04005594721.57645093972-1.216983991842.04449396158-0.266571046531-0.2366302355170.3027147582410.3511691558820.194805099318-0.00722302762843-0.2416200673080.2012084081040.05982720559820.2694624799450.0326669817583-0.01512754838530.354779629821-0.04456781707790.3351685493391.616174738865.9266133396335.2345625425
104.634110668430.08829818634031.115263924693.147432658771.155877467683.50043364885-0.06448901323830.06547572035560.26388863957-0.333292060559-0.03648027375110.1177654418590.214974046449-0.05651425862390.1067039107130.3626230195030.01934781836320.002712467678850.2749379452960.03195576775280.306349244412.31897583644.0796672387624.5310555836
113.96758300179-0.242567885079-0.2274445096994.60700625490.2127984586944.35865603247-0.1111933984450.0802432324137-0.1180442438090.1869364147740.284773157144-0.388263614694-0.02360538606140.500454640341-0.1650508597110.3278312697670.02652334234283.42265171762E-50.28102234615-0.03086272959850.3663315503255.393596587858.4288089653823.244246115
128.55665775206-2.037096592525.131941362975.44062920992-0.8058240484936.826901269360.7528728681780.525082914250.2794990498620.00867835153947-0.945718455788-1.071105546590.8199878451570.3187664324520.1069088754540.452529111867-0.03036903461420.05469414719590.5839510262910.06687177469630.9380163759548.562664118516.983311623720.1294889622
132.186653257781.944372990251.939523574.96806226835-1.627483321585.598760440690.3331779782220.618550290190.22835247674-2.32016110117-0.018955518981-1.062273903620.6199216385510.414935051499-0.1862653014390.7333388054160.01237644310460.1537577399850.4112890649740.1626788431630.5867733010864.4577143262715.265919627813.4911776799
147.795017569790.03314959629311.186325167956.949861866110.504816445345.481833806720.4256410545470.561407232844-0.08244916443710.3551499498340.519506635091-0.113408065389-1.37876638984-0.352373724276-0.9162078343081.17331531181-0.1493672338330.2580525677410.891380040220.1540474296270.9998614711877.0568497248621.45468354959.54421368092
154.902095647180.436418684037-0.07417251415884.045936252410.4363399178783.412574713231.251878709420.2458334187150.520435562096-1.618853335020.144562870680.5718028713671.056625980590.283785689441-1.282909189820.8644158699160.122135464833-0.1197113879040.6765689637740.1116179482771.193909255442.0751101480225.495688732417.7394791492
161.169503734831.26545335289-0.9799715767161.989681443880.1375708305293.107874342240.1074227587640.3124876880180.823007158348-0.2138911826050.452494565650.678815323923-0.506394832871-0.062589118371-0.2068053206610.4501727112440.0215059396281-0.02632772756120.4497709221710.01128845034820.7337585456032.5634890526224.205969675624.5876174261
175.50431277505-0.427313722624-1.709717699384.47565519952-1.568466159678.97206382075-0.2291590858420.3394127644210.897784850739-0.1872180573890.254802778439-0.0528934604531-0.12749375311-0.885485537425-0.003735097966520.313487242972-0.00736802769037-0.0264885435250.3385455332650.04367306624120.465806992082-2.840263915114.363802702724.7680076677
182.57813801272-1.24673212597-1.281072032581.27909069285-0.1324265923382.95571183259-0.208272561867-0.3778043463580.1027791335320.104439153540.183146821304-0.0113263034061-0.01380283862560.2670147593420.01075940925290.2977190520050.0518622391107-0.04240793488590.475517363888-0.03223344333530.2793740474476.34499755767-1.7808988285954.4190749137
194.727957866460.008619608392370.479505881054.48597907036-1.275878642792.8142585119-0.05376332736110.3687183698460.365103971749-0.1862125056860.1526841476160.319829829816-0.30974754608-0.527355031035-0.02492700575340.3465462597830.0269305034631-0.04208046952520.447756607265-0.02058935880.3065812980961.388743016724.0606801817245.6086352975
205.00030628459-0.245159856376-0.4713221806643.9798325521-0.04016547963475.139066978020.0601624861539-0.4141976964670.5668218490580.278408048375-0.0339806455159-0.418324266243-0.7150679434560.733764424336-0.01689432176230.4506709336040.0233662237521-0.04525806997050.538195437785-0.05101194025060.338682008679.864139470175.2809684356653.6274579231
213.31160357752-0.309363255869-0.2598138910351.297770769360.7530048705133.082699353520.08474354519870.0588407601182-0.1679816214610.0391933675767-0.1695325574170.0106703509763-0.0972231560591-0.4763481246920.05353139004050.3192275712760.0530329236332-0.0144191416910.3664734049010.00538235877230.3028398755862.5720234653-3.9446577881748.1886907456
225.652106224232.55099866776-0.8647497094542.91648331556-1.779367728734.88765306309-0.287985161325-0.8058209615410.7847956642140.7562626955860.3354975014420.642795959243-0.555317058307-1.32268656431-0.00622498088490.4485320446580.1620672874620.0338097854810.882731525441-0.09085975203280.376837262019-6.354965495992.3746698862562.5060918993
232.38152179092-0.4340218750510.688347322431.5801648341-0.6710214965313.89452682147-0.03916130530650.0860109906479-0.220960823066-0.01008736070670.1232608378470.1888342897240.017393912767-0.0405130441572-0.0870113440540.3205500366170.0160748984729-0.002954891235080.356598666121-0.004307866201090.32355218420915.392027709-15.681825668329.8086350523
242.95560150099-2.054872537461.837567574133.53046155715-0.3204148300681.48473219282-0.112334725124-0.498689374465-0.0587288075590.2644351339340.159634709868-0.09099376375210.0477707322766-0.182936122001-0.05968955444620.3021065383920.04770950119280.02885113543840.499248046040.05050116335730.35938320134126.2898748984-20.909329399646.6345533552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 23 )
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 39 )
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 45 )
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 113 )
7X-RAY DIFFRACTION7chain 'A' and (resid 114 through 120 )
8X-RAY DIFFRACTION8chain 'B' and (resid 645 through 658 )
9X-RAY DIFFRACTION9chain 'B' and (resid 659 through 672 )
10X-RAY DIFFRACTION10chain 'B' and (resid 673 through 684 )
11X-RAY DIFFRACTION11chain 'B' and (resid 685 through 692 )
12X-RAY DIFFRACTION12chain 'B' and (resid 693 through 697 )
13X-RAY DIFFRACTION13chain 'B' and (resid 698 through 702 )
14X-RAY DIFFRACTION14chain 'B' and (resid 703 through 709 )
15X-RAY DIFFRACTION15chain 'B' and (resid 710 through 714 )
16X-RAY DIFFRACTION16chain 'B' and (resid 719 through 726 )
17X-RAY DIFFRACTION17chain 'B' and (resid 727 through 738 )
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 39 )
19X-RAY DIFFRACTION19chain 'C' and (resid 40 through 63 )
20X-RAY DIFFRACTION20chain 'C' and (resid 64 through 82 )
21X-RAY DIFFRACTION21chain 'C' and (resid 83 through 113 )
22X-RAY DIFFRACTION22chain 'C' and (resid 114 through 120 )
23X-RAY DIFFRACTION23chain 'D' and (resid 643 through 684 )
24X-RAY DIFFRACTION24chain 'D' and (resid 685 through 738 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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