PDB-7tgf: Single-domain VHH intrabodies neutralize ricin toxin.

ID or keywords:

Entry

Database: PDB / ID: 7tgf

Title

Single-domain VHH intrabodies neutralize ricin toxin.

Components

Ricin chain A
VHH camelid antibody

Keywords

IMMUNE SYSTEM/TOXIN / N-glycosidase / VHH antibody / 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: 1.347 Å

Authors

Rudolph, M.J. / Mantis, N.

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 7, 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
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7tgf.cif.gz	243.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7tgf.ent.gz	197.5 KB	Display	PDB format
PDBx/mmJSON format	7tgf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7tgf_validation.pdf.gz	453.6 KB	Display	wwPDB validaton report
Full document	7tgf_full_validation.pdf.gz	457.2 KB	Display
Data in XML	7tgf_validation.xml.gz	20.5 KB	Display
Data in CIF	7tgf_validation.cif.gz	30.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tg/7tgf ftp://data.pdbj.org/pub/pdb/validation_reports/tg/7tgf	HTTPS FTP

-
Related structure data

Related structure data	7tgiC 7th2C 7th3C 1rtcS 6cwgS 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 camelid antibody

hetero molecules

44.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	50.830, 50.830, 260.009
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-403- HOH

#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 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody	VHH camelid antibody Mass: 14342.784 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Antibody / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.9 Å³/Da / Density % sol: 35.14 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 100 mM sodium citrate pH 4.0, 30% PEG 6000, and 1 M lithium chloride

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-E / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.347→50 Å / Num. obs: 77109 / % possible obs: 100 % / Redundancy: 11.7 % / B_iso Wilson estimate: 17.43 Å² / R_merge(I) obs: 0.074 / R_pim(I) all: 0.022 / R_rim(I) all: 0.077 / Χ²: 0.682 / Net I/σ(I): 5.3

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
1.35-1.37	8.7	2.084	3793	0.523	0.735	2.213	0.434	100
1.37-1.4	11	1.844	3726	0.688	0.579	1.935	0.427	100
1.4-1.43	11.7	1.621	3790	0.778	0.494	1.696	0.431	100
1.43-1.45	11.7	1.327	3795	0.838	0.403	1.388	0.435	100
1.45-1.49	11.8	1.078	3752	0.879	0.327	1.127	0.447	100
1.49-1.52	11.5	0.813	3804	0.924	0.249	0.851	0.451	100
1.52-1.56	10.8	0.616	3789	0.937	0.196	0.647	0.463	100
1.56-1.6	12	0.5	3817	0.968	0.151	0.523	0.466	100
1.6-1.65	12.3	0.414	3812	0.975	0.122	0.432	0.482	100
1.65-1.7	12.2	0.321	3808	0.982	0.095	0.335	0.495	100
1.7-1.76	12.1	0.249	3816	0.988	0.075	0.26	0.528	100
1.76-1.83	11.3	0.183	3814	0.993	0.056	0.191	0.569	100
1.83-1.92	12	0.14	3819	0.995	0.042	0.147	0.623	99.9
1.92-2.02	12.7	0.106	3843	0.997	0.031	0.11	0.725	100
2.02-2.14	12.5	0.086	3879	0.997	0.025	0.09	0.825	100
2.14-2.31	12	0.071	3883	0.998	0.021	0.074	0.918	100
2.31-2.54	12.2	0.06	3899	0.998	0.018	0.063	0.983	100
2.54-2.91	12.8	0.053	3936	0.999	0.015	0.055	1.11	100
2.91-3.66	11.7	0.047	4027	0.999	0.014	0.049	1.283	100
3.66-50	11.8	0.044	4307	0.999	0.013	0.046	1.235	99.9

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1RTC, 6CWG

1rtc

6cwg

Resolution: 1.347→49.886 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1807	3707	4.82 %
R_work	0.1583	73242	-
obs	0.1594	76949	99.9 %

Solvent computation

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

Displacement parameters

B_iso max: 102.57 Å² / B_iso mean: 29.2293 Å² / B_iso min: 11.23 Å²

Refinement step

Cycle: final / Resolution: 1.347→49.886 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3018	0	28	364	3410
B_iso mean	-	-	35.61	40.11	-
Num. residues	-	-	-	-	388

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3187
X-RAY DIFFRACTION	f_angle_d	1.102	4352
X-RAY DIFFRACTION	f_chiral_restr	0.088	480
X-RAY DIFFRACTION	f_plane_restr	0.007	579
X-RAY DIFFRACTION	f_dihedral_angle_d	14.502	1183

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 (%)
1.3472-1.365	0.3543	112	0.2933	2730	98
1.365-1.3837	0.3374	125	0.2683	2797	100
1.3837-1.4034	0.2824	161	0.2433	2746	100
1.4034-1.4244	0.2462	120	0.2308	2752	100
1.4244-1.4466	0.261	140	0.2333	2784	100
1.4466-1.4704	0.2207	148	0.2188	2743	100
1.4704-1.4957	0.2317	154	0.205	2795	100
1.4957-1.5229	0.2193	140	0.1941	2735	100
1.5229-1.5522	0.2257	141	0.1984	2778	100
1.5522-1.5839	0.2017	148	0.1806	2779	100
1.5839-1.6183	0.2205	118	0.1799	2767	100
1.6183-1.656	0.2161	145	0.1798	2804	100
1.656-1.6974	0.2067	138	0.1747	2817	100
1.6974-1.7433	0.213	146	0.1703	2771	100
1.7433-1.7946	0.1953	151	0.1655	2784	100
1.7946-1.8525	0.1988	141	0.1673	2800	100
1.8525-1.9187	0.2	149	0.1583	2793	100
1.9187-1.9955	0.1617	143	0.149	2833	100
1.9955-2.0864	0.1563	145	0.1396	2797	100
2.0864-2.1964	0.1876	167	0.1387	2815	100
2.1964-2.334	0.16	166	0.137	2830	100
2.334-2.5142	0.1657	139	0.1431	2854	100
2.5142-2.7672	0.1579	147	0.1483	2883	100
2.7672-3.1675	0.1799	135	0.1448	2921	100
3.1675-3.9905	0.1529	132	0.1335	2963	100
3.9905-49.886	0.1698	156	0.1675	3171	100

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	3.0541	1.8103	-3.0099	1.729	-0.9273	4.3855	0.1242	-0.6893	-0.0438	0.0823	-0.1267	-0.1767	-0.0806	0.5033	0.1442	0.1515	-0.0103	0.008	0.1507	-0.0034	0.1724	13.5183	8.3176	30.6409
2	2.1112	0.3414	-0.9356	0.5778	-0.5685	2.015	0.1203	-0.054	0.1914	0.0099	-0.0788	-0.0646	-0.2654	0.1516	-0.0362	0.1651	-0.0164	0.0079	0.1203	-0.0128	0.1696	14.4783	17.1255	18.6737
3	1.3914	-0.2794	0.1742	1.7848	-0.3045	1.7229	0.0091	0.0092	-0.0986	-0.0768	-0.0769	-0.0458	0.1367	0.135	0.0822	0.1144	0.0116	0.0035	0.1088	0.0118	0.1189	15.913	-2.3534	21.3464
4	1.3966	-0.0045	-0.5884	0.8659	-0.0966	1.6382	0.0912	0.2226	0.0859	-0.0835	-0.026	0.0893	-0.127	-0.2757	-0.0878	0.1202	0.0227	-0.0047	0.1906	-0.0084	0.1295	2.7245	10.7724	11.3759
5	2.1111	-0.4399	0.6421	7.9174	-6.6346	9.2875	0.2096	0.0199	0.1168	0.1138	0.0361	0.5214	-0.3419	-0.3388	-0.2678	0.1923	0.075	0.0181	0.2262	-0.0401	0.2408	-19.6209	33.5228	19.0356
6	2.2001	-0.4984	-1.1833	4.5269	-2.1473	6.1104	0.1813	-0.1507	-0.0715	0.319	-0.0197	0.2891	0.12	0.1784	-0.2253	0.1436	0.0125	0.0003	0.1483	-0.0173	0.1698	-12.5873	22.7144	22.1294
7	7.9209	0.6097	5.329	1.3403	-0.4048	4.099	0.198	0.7864	-0.4096	-0.644	-0.0476	0.4478	0.2115	0.2301	-0.1512	0.2979	0.0869	-0.1052	0.3303	-0.0432	0.2632	-13.5689	24.4754	9.2255
8	2.671	-1.0927	-0.4793	7.7716	-3.7702	7.034	0.1499	0.4892	0.406	-0.1397	-0.3784	-0.6477	-0.1281	0.8377	0.3334	0.1319	0.0012	0.0258	0.3259	0.0399	0.2318	-3.1668	29.1036	15.1842
9	4.8137	0.0041	0.1791	4.0092	-0.1038	1.069	-0.0303	-0.5759	0.351	0.092	-0.0307	0.1116	-0.243	0.1103	-0.0413	0.1304	0.0188	0.0116	0.266	-0.0258	0.1958	-10.9434	32.1106	23.8099
10	2.5875	-0.9476	1.5409	7.7136	-4.078	4.2646	0.2966	0.1923	0.0412	-0.6486	-0.2186	0.2411	0.1539	0.2345	-0.0883	0.1678	0.0651	0.0126	0.2274	-0.0184	0.1675	-15.9408	30.1756	11.8521
11	1.4277	0.8524	1.4428	2.8618	0.6977	8.0064	-0.018	0.1454	-0.0771	0.1349	0.1103	0.2486	-0.0376	-0.3607	-0.0311	0.1822	0.0733	0.034	0.2978	0.0042	0.2147	-7.1626	16.7716	15.5131
12	1.9097	-1.7483	0.1057	6.177	-2.3969	2.6943	0.0707	-0.0308	-0.1411	0.0311	0.0435	0.5107	-0.0756	-0.2229	-0.1262	0.1596	0.0379	-0.0142	0.2818	-0.0169	0.2642	-19.6164	22.8604	16.7206
13	5.6623	-1.0554	-5.8352	0.2849	1.0854	6.0137	-0.4947	1.3407	-0.1617	-1.1768	0.042	0.3194	0.4505	-0.936	0.1451	0.5251	0.117	0.0241	0.4842	0.0643	0.3844	-29.2332	40.4823	6.5369

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 56 )	A	18 - 56
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 160 )	A	57 - 160
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 161 through 263 )	A	161 - 263
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 25 )	B	2 - 25
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 26 through 39 )	B	26 - 39
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 40 through 51 )	B	40 - 51
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 52 through 67 )	B	52 - 67
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 68 through 83 )	B	68 - 83
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 84 through 99 )	B	84 - 99
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 100 through 109 )	B	100 - 109
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 110 through 123 )	B	110 - 123
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 124 through 130 )	B	124 - 130

-
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://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