PDB-7th3: Single-domain VHH intrabodies neutralize ricin toxin

ID or keywords:

Entry

Database: PDB / ID: 7th3

Title

Single-domain VHH intrabodies neutralize ricin toxin

Components

Ricin chain A
VHH antibody

Keywords

IMMUNE SYSTEM/TOXIN / Antibody-antigen complex / IMMUNE SYSTEM / IMMUNE SYSTEM-TOXIN complex

Function / homology

Function and homology information

rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function

Biological species

Ricinus communis (castor bean)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.292 Å

Authors

Rudolph, M.J.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins.
Authors: Czajka, T.F. / Vance, D.J. / Davis, S. / Rudolph, M.J. / Mantis, N.J.

History

Deposition	Jan 10, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7th3.cif.gz	170.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7th3.ent.gz	133.7 KB	Display	PDB format
PDBx/mmJSON format	7th3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7th3_validation.pdf.gz	428.8 KB	Display	wwPDB validaton report
Full document	7th3_full_validation.pdf.gz	435.2 KB	Display
Data in XML	7th3_validation.xml.gz	18.6 KB	Display
Data in CIF	7th3_validation.cif.gz	26.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/th/7th3 ftp://data.pdbj.org/pub/pdb/validation_reports/th/7th3	HTTPS FTP

-
Related structure data

Related structure data	7tgfC 7tgiC 7th2C 1rtcS 4lgrS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#161 - May 2013 Ricin similarity (15) #69 - Sep 2005 Cholera Toxin similarity (15) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Ricin chain A

B: VHH antibody

44 kDa, 2 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)	38.337, 67.113, 68.100
Angle α, β, γ (deg.)	90.000, 91.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ricin chain A Mass: 29936.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody	VHH antibody Mass: 14081.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG'
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.19 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 418 mM ammonium chloride, 22% PEG 3350

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.292→50 Å / Num. obs: 15311 / % possible obs: 98.6 % / Redundancy: 3.2 % / B_iso Wilson estimate: 33.23 Å² / R_merge(I) obs: 0.04 / R_pim(I) all: 0.026 / R_rim(I) all: 0.048 / Χ²: 0.527 / Net I/σ(I): 9.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.3-2.34	3.1	0.177	777	0.962	0.115	0.212	0.467	99.6
2.34-2.38	3.2	0.176	763	0.962	0.115	0.211	0.468	99.6
2.38-2.43	3.3	0.168	770	0.967	0.108	0.2	0.459	99.6
2.43-2.48	3.4	0.153	744	0.971	0.098	0.182	0.494	99.7
2.48-2.53	3.3	0.137	792	0.981	0.087	0.163	0.491	99.7
2.53-2.59	3.3	0.126	773	0.981	0.08	0.149	0.503	99.6
2.59-2.66	3.3	0.104	745	0.983	0.067	0.124	0.484	99.3
2.66-2.73	3.3	0.092	781	0.989	0.059	0.109	0.45	98.9
2.73-2.81	3.3	0.079	746	0.992	0.05	0.094	0.453	98
2.81-2.9	3.2	0.074	754	0.99	0.048	0.088	0.496	98
2.9-3	3.1	0.064	765	0.993	0.042	0.077	0.515	97.8
3-3.12	2.9	0.052	748	0.995	0.036	0.063	0.505	97.4
3.12-3.26	2.7	0.046	740	0.996	0.033	0.056	0.569	95.1
3.26-3.44	3.3	0.041	765	0.998	0.026	0.049	0.572	99.2
3.44-3.65	3.5	0.035	770	0.998	0.022	0.041	0.623	99.5
3.65-3.93	3.5	0.032	786	0.999	0.02	0.037	0.663	99.9
3.93-4.33	3.4	0.029	780	0.998	0.018	0.034	0.688	99.5
4.33-4.95	3.3	0.024	769	0.999	0.015	0.028	0.513	99.5
4.95-6.24	3	0.024	753	0.998	0.016	0.029	0.532	95.7
6.24-50	3.3	0.023	790	0.999	0.015	0.027	0.568	96.8

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.11.1_2575	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1RTC,4LGR

1rtc

4lgr

Resolution: 2.292→47.797 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 33.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2723	701	4.58 %
R_work	0.2477	14595	-
obs	0.2489	15296	97.84 %

Solvent computation

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

Displacement parameters

B_iso max: 110.49 Å² / B_iso mean: 48.5935 Å² / B_iso min: 16.45 Å²

Refinement step

Cycle: final / Resolution: 2.292→47.797 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2928	0	0	239	3167
B_iso mean	-	-	-	47.01	-
Num. residues	-	-	-	-	374

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2997
X-RAY DIFFRACTION	f_angle_d	0.629	4076
X-RAY DIFFRACTION	f_chiral_restr	0.043	453
X-RAY DIFFRACTION	f_plane_restr	0.005	534
X-RAY DIFFRACTION	f_dihedral_angle_d	15.153	1785

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.292-2.4685	0.3894	124	0.3309	2839	96
2.4685-2.7169	0.352	97	0.3147	3004	99
2.7169-3.11	0.3225	163	0.2996	2881	98
3.11-3.918	0.2737	138	0.2299	2939	98
3.918-47.797	0.2239	179	0.201	2932	98

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	2.7042	1.6519	-0.4419	3.0604	0.1595	4.9846	0.3213	0.2855	0.0519	0.0809	0.2603	-1.3141	-0.4288	0.958	-0.369	0.4814	-0.0016	0.0759	0.1796	0.0651	0.1938	57.5879	1.9849	21.6407
2	2.4092	1.6757	-0.4623	5.5661	0.4777	4.2266	-0.0988	0.2997	0.0444	-0.4208	0.6533	0.0263	-0.2413	-0.3508	-0.3849	0.2428	-0.0114	-0.004	0.2243	0.0273	0.2201	52.4288	1.7966	13.8042
3	0.5109	1.0405	-0.5483	3.2472	0.4259	2.6949	-0.3103	0.1177	-0.0619	-0.2714	0.5715	-0.503	0.7065	-0.5571	-0.2535	0.5736	-0.2916	-0.0669	0.4971	0.0943	0.5012	45.4058	-12.4795	6.2779
4	1.2361	-0.003	0.4383	2.8461	0.224	0.895	-0.2101	0.1453	-0.4078	0.9366	0.8351	-0.5819	1.4067	-0.6087	-0.2495	0.5413	-0.9972	0.5054	-1.1158	1.5315	-0.8799	47.325	-17.8992	17.4909
5	3.4358	-0.2637	-0.3519	5.2547	0.3753	3.6119	0.0794	0.4789	-0.1769	0.453	0.027	-0.9571	-0.0074	0.1673	-0.2935	0.3838	-0.1002	-0.1263	0.1615	0.1287	0.266	55.3486	-4.5824	25.1433
6	2.585	-1.6862	1.1464	2.8099	1.1945	5.3148	0.1246	-0.235	0.1065	0.2477	0.1624	0.0595	0.7254	-0.9827	-0.242	0.3334	-0.1665	-0.007	0.3443	0.1897	0.2333	50.1104	-5.8922	30.9805
7	2.7892	-0.901	0.4279	3.2079	0.6361	3.8866	0.6062	-0.8208	-0.5572	0.2478	0.2045	-0.1425	1.743	-1.1084	-0.2678	0.8825	-0.2118	-0.1881	0.3986	0.1568	0.2659	51.1211	-10.9312	35.4899
8	1.9723	-0.4944	-0.3921	0.139	0.0949	3.8071	0.2298	-0.341	0.2268	-0.1175	-0.4423	0.8237	-0.481	-1.1735	-0.0933	0.5256	0.0633	0.2406	1.0601	0.0054	0.5146	34.9064	3.6929	30.2287
9	1.7708	-0.1922	0.8486	2.5466	-1.338	4.2727	-0.3289	-0.3727	0.2064	0.0966	0.5918	0.5648	-1.0718	-2.3218	-0.1282	0.1545	0.2459	0.1141	0.8903	0.1777	0.3478	40.8235	2.4005	21.0733
10	1.5315	-0.8855	-0.9248	3.6632	-2.5833	3.644	-0.3749	-0.3015	0.3499	-0.3477	0.1995	0.719	-0.1144	-1.538	-0.3399	0.5303	0.1851	-0.0352	1.387	0.1026	0.7205	26.1764	3.2606	11.7835
11	0.4106	0.6026	0.2254	2.3772	2.2007	2.7566	-0.0307	0.9195	0.1553	-0.332	0.0085	0.7491	1.7098	-1.2345	-0.2814	0.2522	-0.2103	-0.2467	0.9929	0.2673	0.4511	37.0138	-10.8242	7.7962
12	1.8328	-0.5184	0.7522	3.1097	-0.2413	1.4177	0.0989	0.0806	-0.5527	0.024	-0.2066	-0.7199	0.4363	-0.2021	0.0607	0.4697	-0.1559	-0.0479	0.167	-0.0285	0.4233	59.6286	-8.7552	-15.3135
13	3.8809	0.2508	7.8908	4.2027	-4.1648	2.0021	0.6933	-0.223	0.4191	0.4845	0.2104	0.7359	-0.1658	-1.085	-0.3372	0.3397	-0.529	-0.1421	0.4054	0.0675	0.3657	45.3643	-16.5207	-3.3786
14	2.7248	-1.3686	0.7029	2.6864	0.8365	3.4543	0.0742	0.0263	0.43	0.0731	0.0507	-0.0215	0.1823	-0.3535	-0.1355	0.2194	-0.0633	0.0088	0.3204	0.083	0.2911	54.9365	-2.1305	-4.5447
15	4.5615	0.968	0.0981	6.1573	1.318	1.4481	0.1293	0.133	0.1923	-0.3198	-0.0958	0.5944	0.3329	-0.7862	-0.2849	0.4181	-0.1144	-0.1281	0.4309	0.0986	0.3557	51.1078	-3.7889	-13.6742
16	3.1491	1.1257	-1.1883	0.6193	-0.631	2.3147	0.0273	-0.0787	-0.1184	0.0252	0.0772	0.1186	0.4636	-0.1556	-0.1417	0.3561	-0.1262	-0.0514	0.2872	0.0376	0.2682	59.4271	-4.1248	-6.7848

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 17 )	A	5 - 17
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 32 )	A	18 - 32
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 33 through 42 )	A	33 - 42
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 43 through 52 )	A	43 - 52
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 53 through 65 )	A	53 - 65
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 67 through 98 )	A	67 - 98
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 99 through 122 )	A	99 - 122
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 123 through 140 )	A	123 - 140
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 141 through 230 )	A	141 - 230
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 231 through 241 )	A	231 - 241
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 242 through 263 )	A	242 - 263
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 2 through 24 )	B	2 - 24
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 25 through 31 )	B	25 - 31
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 32 through 60 )	B	32 - 60
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 61 through 83 )	B	61 - 83
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 84 through 120 )	B	84 - 120

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi