PDB-6u51: Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan ...

ID or keywords:

Entry

Database: PDB / ID: 6u51

Title

Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB) Complexed with Sudan ebolavirus Nucleoprotein C-terminal Domain 610-738

Components

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

Keywords

IMMUNE SYSTEM /

Antibody /

nanobody /

Ebola /

filovirus

Function / homology

Ebola 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 species

Lama glama (llama)

Sudan ebolavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.52 Å

Authors

Taylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A.

Funding support

United States, 3items

Organization	Grant number	Country
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

Citation

Journal: 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

Deposition	Aug 26, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 11, 2019	Group: Database references / Category: citation / Item: _citation.title
Revision 1.3	Jan 1, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6u51.cif.gz	206.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6u51.ent.gz	145.7 KB	Display	PDB format
PDBx/mmJSON format	6u51.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u5/6u51 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/6u51	HTTPS FTP

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Related structure data

Related structure data	6u50C 6u52C 6u53C 6u54C 6u55C 4w2pS 6apoS 6apqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6u52-d 6uio-1 3k2z-d 3nrf-1 3ctd-1 3sb3-1 3qqa-1 2fjr-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #136 - Apr 2011 Nanobodies similarity (1) #178 - Oct 2014 Ebola Virus Proteins similarity (3)

Deposited unit

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

B: Nucleoprotein

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

D: Nucleoprotein

58.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	117.881, 117.881, 144.959
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22
Space group name Hall	P6₁2(x,y,z+5/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: x-y,-y,-z #7: -x,-x+y,-z+2/3 #8: -x,-y,z+1/2 #9: y,x,-z+1/3 #10: -y,-x,-z+5/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/6

#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: 16055.630 Da / Num. of mol.: 2 / Fragment: C-terminal domain (residues 610-738) 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.: 23 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.74 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 30% polyethylene glycol 3000, 0.1 M N-Cyclohexyl-2-aminoethanesulfonic acid (CHES) pH 9.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.52→145 Å / Num. obs: 20678 / % possible obs: 99.5 % / Redundancy: 10.4 % / B_iso Wilson estimate: 49.28 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.057 / R_rim(I) all: 0.195 / Net I/σ(I): 12.1
Reflection shell	Resolution: 2.52→2.66 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2853 / CC_1/2: 0.379 / R_pim(I) all: 0.66 / R_rim(I) all: 2.23 / % possible all: 97

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
XDS		data reduction
XDS		data scaling
MR-Rosetta		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6APO, 6APQ, 4W2P

6apo

6apq

4w2p

Resolution: 2.52→58.94 Å / SU ML: 0.3855 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.707
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2504	1999	9.69 %
R_work	0.2082	18626	-
obs	0.2124	20625	99.54 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 57.6 Å²

Refinement step

Cycle: LAST / Resolution: 2.52→58.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3322	0	0	23	3345

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0043	3400
X-RAY DIFFRACTION	f_angle_d	0.8321	4606
X-RAY DIFFRACTION	f_chiral_restr	0.0676	480
X-RAY DIFFRACTION	f_plane_restr	0.0041	606
X-RAY DIFFRACTION	f_dihedral_angle_d	19.4774	1252

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.52-2.58	0.4178	132	0.3445	1227	X-RAY DIFFRACTION	94.05
2.58-2.65	0.3693	138	0.3344	1292	X-RAY DIFFRACTION	99.72
2.65-2.73	0.3682	141	0.3229	1309	X-RAY DIFFRACTION	100
2.73-2.82	0.3526	141	0.292	1307	X-RAY DIFFRACTION	100
2.82-2.92	0.3378	141	0.2855	1318	X-RAY DIFFRACTION	100
2.92-3.04	0.3132	140	0.2505	1305	X-RAY DIFFRACTION	100
3.04-3.17	0.3167	142	0.2595	1324	X-RAY DIFFRACTION	100
3.17-3.34	0.3137	141	0.2337	1318	X-RAY DIFFRACTION	99.93
3.34-3.55	0.2777	142	0.2215	1328	X-RAY DIFFRACTION	100
3.55-3.82	0.2475	143	0.1995	1332	X-RAY DIFFRACTION	99.93
3.82-4.21	0.2043	145	0.1631	1342	X-RAY DIFFRACTION	99.87
4.21-4.82	0.1458	145	0.1398	1352	X-RAY DIFFRACTION	100
4.82-6.07	0.1975	148	0.1684	1388	X-RAY DIFFRACTION	100
6.07-58.94	0.222	160	0.1889	1484	X-RAY DIFFRACTION	99.94

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.07703606145	-2.15125464704	0.794374544976	2.36417464406	-0.905137812047	1.90934185359	-0.0631065965648	0.00807351664897	0.480246384688	0.22037766696	-0.112190394775	-0.186978435973	0.0920764623151	0.126321474827	0.127564486391	0.361324064464	0.0205729399119	0.0443586733046	0.419595830451	-0.0126366466515	0.385343522605	39.8410087076	40.454572349	48.8124954874
2	3.72567629109	1.28162724058	0.89546849361	4.34068125364	0.107287862187	3.43180928301	-0.358572170019	-0.287420490692	-0.673337060395	0.556043857546	0.142701020162	0.232842003316	0.294471869012	0.0289443187603	0.16751850574	0.42701999819	0.0658839091339	0.0840874742562	0.46528611772	0.0513793978876	0.398301050993	32.5522368646	35.0899263894	55.5638423301
3	3.51058214555	-0.398883421302	1.28455936821	7.15149521419	-2.32412559325	4.29630174507	-0.0809765052636	-0.107047251615	0.226681397743	1.15408128163	0.331445884768	0.131187149227	-0.514083860813	0.456103054594	-0.254793231184	0.412492066941	0.0124011306887	0.0342624995728	0.390805141547	-0.0220874052891	0.385528616849	40.0806981933	44.0330015956	55.537109899
4	1.90241463942	-2.03232083917	-0.21597683452	3.08155438928	0.142537838572	0.807047195607	0.0616696109393	0.0780545389039	-0.302459957212	-0.0807696837748	-0.0407108456176	0.0952872023684	0.305782785751	0.0931313607963	0.0144024658127	0.412785192567	0.0351030456309	0.0550793646031	0.274873345642	-0.0178472426019	0.377771487517	35.9295622323	35.5090553356	47.7758344705
5	2.57301796136	0.429373602521	-0.524262873976	1.32292280831	0.800735026397	2.70483737249	-0.142885544701	0.788242044313	-0.116186571209	-0.328417129316	0.107890266121	0.0573236390289	0.174378600006	-0.49266416799	0.0825664281959	0.355260384786	0.0409898010846	-0.0277688297265	0.671204439874	0.00681093336063	0.408870574428	8.92370519333	52.0511549325	42.6710512502
6	2.55045212829	0.972723833548	-0.158345510547	3.4665638782	-0.120644595229	5.36624829395	0.15761574891	0.346527322884	0.0856147223999	-0.234835860118	-0.131640795636	-0.0128313447818	-0.0896763950279	0.530183710339	0.0474290068346	0.384021890146	0.0937629840711	0.00526352461726	0.48740500926	0.0115674027662	0.393300496148	25.6872392484	54.1717062427	37.6153669831
7	5.42517687429	3.37652718977	-0.62378229426	3.00602913981	2.01137838617	6.64744584213	-0.922377872865	0.0988812264504	0.420927441408	-0.651986853946	0.520122950239	0.188291768934	-2.12606866459	1.37528487599	0.474451032392	1.15369070252	-0.432259751848	-0.079879061802	1.43920337236	-0.11542797937	0.864465043144	37.3764690456	65.8433973394	29.9463185452
8	0.822128960902	-0.676354578145	-1.01011211221	0.599754694019	0.622350276963	2.1840222319	0.128821939357	0.213082919162	0.250541453422	-1.97272384802	-0.246807984854	-0.486496882105	-0.380672147865	-0.522340408729	-0.014932248199	1.61991924554	0.0468623538272	-0.0192480949315	0.870512562075	0.0656903551431	1.01159295866	23.3896740404	67.4915559366	25.1743405943
9	3.69542624225	1.78118745305	0.75872307686	3.10178081911	0.158289731054	3.09691305176	-0.326164350944	0.083672306955	0.448362225263	-0.621741814158	0.0457543164457	-0.0703672865714	-0.502928211714	0.435987472029	0.225358169205	0.636441838895	-0.0257938400476	-0.0115056067776	0.468154339403	0.0239720817393	0.390638229756	21.6551987086	61.8245976801	33.424500692
10	1.30217948621	-1.11944940066	0.585223951792	2.72194293647	-0.822772883207	1.54726663038	-0.191293547044	-0.254099087981	0.189658635983	0.37313428355	0.238434058694	0.0350493648628	-0.0951974929882	-0.179386015068	-0.0567192596157	0.306813288196	-0.0129293129003	0.052638230057	0.420700909325	0.0156318449146	0.362181924959	-1.82172471064	54.3277504984	59.7930845514
11	7.85882995867	-0.927680524066	3.84602046986	1.32255541131	-0.574090108803	4.59671528456	0.814492455625	1.26584534703	-1.13773411367	-0.359474790675	-0.110307728849	-0.0619304003146	0.599906399843	0.532169778346	-0.551302413799	0.396712967521	0.0201520119175	-0.0583745735794	0.492881999207	-0.114373720425	0.411004118642	2.57668331238	54.3504281808	50.377098409
12	0.808458386121	-0.606381762378	-0.771123405647	2.0782412172	-0.90272559788	1.91785504026	0.0236933922895	0.0831546382111	0.0761763050994	0.0640230226715	-0.0613396716863	0.215031782786	-0.120309482876	0.0469680442653	0.0396467347371	0.299752028415	0.000462921035086	0.00491436012067	0.338601851418	0.00336274230282	0.375650180181	0.875117295362	59.0207094328	56.1234773701
13	5.97194959525	-4.01137786119	1.11085128493	4.13066734268	-0.868951190862	2.30798919192	-0.0534068863698	0.0843941983682	-0.592331038639	0.0497517649748	0.175137999397	0.519268500654	0.220640748259	-0.17236651119	-0.0863383699012	0.300147590398	-0.00851416354833	-0.0447679775052	0.36677807115	0.0245431869288	0.427824016208	-1.94972897581	48.2473841334	54.477558875
14	3.39165123767	1.27579368558	-1.98483183518	3.78490650839	-1.07873799931	2.67720329553	-0.699895031283	0.0817805011797	-0.198891911397	-1.08341816371	0.153037124721	-0.564394442516	1.43116355445	0.0939907292482	0.353180691715	0.535439397558	0.0742356783109	0.144530078128	0.30395212352	-0.077917194054	0.529699353227	22.96214103	29.5857402365	51.516645934
15	2.75783962421	-1.10024589264	-0.359988147927	2.24148944473	-0.588355834057	3.25211913113	-0.066135258731	-0.301595591095	-0.173016966776	-0.205961324407	0.00542595107736	-0.100955341355	0.51237927501	0.135864519291	0.0512949418772	0.419765690239	0.0164801453879	0.0430750966025	0.296376329653	0.0146416952377	0.442846996467	16.2776076728	35.5175997097	61.1712549285
16	4.49825890294	2.02992266532	-0.0513135519274	2.84887192718	-0.92970135164	3.02081812744	0.41104755987	-1.05484612317	0.465556982394	0.790308451878	-0.396940483475	0.611654698242	-0.252627685721	-0.02942451657	-0.0370767552672	0.732947766712	0.0441463276182	-0.0234022334545	0.69934435029	-0.0481283731452	0.617009605198	7.03054977164	37.8639689238	76.2153550886
17	1.39309130585	-0.351907084034	-0.640396338177	0.188532714421	-0.143925332215	1.19108535442	0.236515041607	-1.6955275787	-0.710835210067	0.618723372314	-0.32825374414	-0.246386278707	0.76552429987	0.157443667511	-0.01861885912	1.06942390258	0.0343563029549	0.0106432369252	1.00855975794	0.175698248156	0.795619669875	10.0082096496	31.4243561279	84.3577309595
18	3.89063438687	-0.486937247047	0.352511711084	1.4618547913	-0.0682113388578	2.67783992454	0.162223375979	-0.240612604461	-0.34725611284	-0.0562303189005	-0.18772820881	-0.294878117372	0.212903207284	-0.0979938931368	-0.00589383099771	0.521386823975	0.0456831637807	-0.0587633849948	0.402682411446	0.075275107544	0.424198961328	15.4454123919	30.5607217962	71.6700820657

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 3 through 39 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 40 through 63 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 64 through 82 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 83 through 120 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 645 through 672 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 673 through 702 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 703 through 712 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 713 through 720 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 721 through 738 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 3 through 39 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 40 through 56 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 57 through 100 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 101 through 120 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 645 through 658 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 659 through 692 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 693 through 705 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 706 through 721 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 722 through 738 )

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Movie

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Structure viewers

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Viewer log

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This page

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Open data

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Basic information

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi