PDB-8tfl: Ricin in complex with Fab SylH3

ID or keywords:

Entry

Database: PDB / ID: 8tfl

Title

Ricin in complex with Fab SylH3

Components

Ricin A chain
Ricin B chain
SylH3 Fab heavy chain
SylH3 Fab light chain

Keywords

TOXIN / Ricin toxin / monoclonal antibody

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

Mus musculus (house mouse)

Ricinus communis (castor bean)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.89 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2023
Title: Structural Basis of Antibody-Mediated Inhibition of Ricin Toxin Attachment to Host Cells.
Authors: Vance, D.J. / Rudolph, M.J. / Davis, S.A. / Mantis, N.J.

History

Deposition	Jul 11, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tfl.cif.gz	394.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8tfl.ent.gz	321.8 KB	Display	PDB format
PDBx/mmJSON format	8tfl.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/tf/8tfl ftp://data.pdbj.org/pub/pdb/validation_reports/tf/8tfl	HTTPS FTP

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Related structure data

Related structure data	8tfhC 2aaiS 3fmgS 4m7kS 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

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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) #99 - Mar 2008 Cadherin similarity (1) #76 - Apr 2006 Hemagglutinin similarity (1) #83 - Nov 2006 Fibrin similarity (1)

Deposited unit

L: SylH3 Fab light chain

H: SylH3 Fab heavy chain

A: Ricin A chain

B: Ricin B chain

hetero molecules

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

1

A: Ricin A chain

B: Ricin B chain

hetero molecules

L: SylH3 Fab light chain

H: SylH3 Fab heavy chain

hetero molecules

defined by author&software
106 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.420, 126.927, 102.027
Angle α, β, γ (deg.)	90.00, 92.74, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 2 types, 2 molecules AB

#3: Protein	Ricin A chain / rRNA N-glycosidase Mass: 29087.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase
#4: Protein	Ricin B chain Mass: 28918.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P02879

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Antibody , 2 types, 2 molecules LH

#1: Antibody	SylH3 Fab light chain Mass: 23327.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	SylH3 Fab heavy chain Mass: 23288.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 2 types, 3 molecules

#5: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAca1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2NCC/3=O][a2122h-1b_1-5_2NCC/3=O]/1-2/a4-b1	WURCS	PDB2Glycan 1.1.0
[][<C8N1O3>]{[(1+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#7: Sugar

ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-glucopyranosamine	COMMON NAME	GMML 1.0
a-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 2 types, 45 molecules

#6: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.74 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.5 M ammonium fluoride and 20% PEG 3,350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å

Detector

Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 1, 2020

Radiation

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

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 2.89→50 Å / Num. obs: 27100 / % possible obs: 97 % / Redundancy: 8 % / CC_1/2: 0.44 / Net I/σ(I): 8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.89-2.95	3.9	3.967	1243	0.442	0.783	2.161	4.562	0.959	90
2.95-3	4.3	2.25	1278	0.448	0.787	1.165	2.555	0.987	92.7
3-3.06	4.9	1.882	1298	0.625	0.877	0.92	2.107	0.979	93
3.06-3.12	5.3	1.099	1316	0.677	0.899	0.511	1.218	0.976	93.4
3.12-3.19	5.8	0.802	1296	0.786	0.938	0.355	0.881	1	94.9
3.19-3.27	5.9	0.598	1321	0.823	0.95	0.26	0.655	0.977	96.1
3.27-3.35	6.3	0.486	1355	0.898	0.973	0.204	0.529	1.02	96.2
3.35-3.44	6.6	0.431	1346	0.906	0.975	0.177	0.468	1.047	97.4
3.44-3.54	7	0.317	1370	0.939	0.984	0.127	0.342	1.096	96.5
3.54-3.65	7.9	0.241	1352	0.967	0.991	0.091	0.258	1.279	98.6
3.65-3.78	8.7	0.206	1373	0.974	0.993	0.075	0.22	1.657	98.3
3.78-3.94	9.3	0.203	1381	0.989	0.997	0.07	0.215	1.176	99
3.94-4.11	9.6	0.161	1407	0.994	0.998	0.055	0.171	1.289	98.4
4.11-4.33	9.8	0.124	1351	0.996	0.999	0.042	0.131	1.459	99.5
4.33-4.6	9.9	0.102	1386	0.996	0.999	0.035	0.108	1.773	98.9
4.6-4.96	10	0.092	1403	0.998	0.999	0.031	0.097	1.375	99
4.96-5.46	10.3	0.086	1383	0.997	0.999	0.028	0.091	1.238	99.5
5.46-6.24	10.5	0.087	1405	0.997	0.999	0.028	0.091	1.296	99.4
6.24-7.86	11.3	0.07	1392	0.999	1	0.022	0.073	1.439	99.8
7.86-50	10.5	0.038	1444	0.999	1	0.012	0.04	1.73	99.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2AAI, 4M7K, 3FMG

2aai

4m7k

3fmg

Resolution: 2.89→43.62 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2873	1309	4.87 %
R_work	0.2334	-	-
obs	0.2361	26886	95.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.89→43.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7298	0	84	44	7426

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002
X-RAY DIFFRACTION	f_angle_d	0.506
X-RAY DIFFRACTION	f_dihedral_angle_d	13.557	2742
X-RAY DIFFRACTION	f_chiral_restr	0.042	1155
X-RAY DIFFRACTION	f_plane_restr	0.004	1326

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 (%)
2.89-3.01	0.4375	158	0.34	2512	X-RAY DIFFRACTION	87
3.01-3.15	0.4341	140	0.3545	2770	X-RAY DIFFRACTION	94
3.15-3.31	0.3412	133	0.3008	2848	X-RAY DIFFRACTION	95
3.31-3.52	0.3177	160	0.2811	2866	X-RAY DIFFRACTION	97
3.52-3.79	0.3292	138	0.2511	2909	X-RAY DIFFRACTION	98
3.79-4.17	0.3457	145	0.2504	2819	X-RAY DIFFRACTION	96
4.17-4.78	0.2275	151	0.1978	2866	X-RAY DIFFRACTION	97
4.78-6.02	0.2666	136	0.2045	2985	X-RAY DIFFRACTION	99
6.02-43.62	0.218	148	0.1869	3002	X-RAY DIFFRACTION	99

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	3.0688	-0.7751	-0.8287	5.4173	-3.4055	6.0264	0.3922	0.8124	0.6692	-1.5486	-0.6233	-0.5476	-0.1003	0.4006	0.2217	1.2185	0.1658	0.1533	0.6132	0.1599	0.5812	20.9782	11.7404	-48.1609
2	2.9374	-1.6067	-0.176	4.6715	-2.6667	4.3531	0.4583	0.6759	0.0873	-1.1729	-0.6639	-0.0092	0.4051	0.4959	0.2905	1.0346	-0.0019	0.0298	0.4722	0.0609	0.5541	17.3863	13.3959	-45.6933
3	1.2969	-0.023	0.9839	-0.0727	0.0822	0.93	0.459	-0.6711	0.0467	-2.4375	1.11	-0.3272	-0.0111	-1.2647	-1.3984	2.0093	0.3711	0.0463	1.1211	0.3666	0.8486	11.285	30.2719	-58.247
4	6.8717	-5.7644	-2.8545	5.9712	1.2442	3.2144	1.3003	0.4829	1.1834	-0.6745	-0.489	-0.7819	-1.0425	-0.6752	-0.737	1.6771	0.1614	0.2013	0.8052	0.2289	0.7839	-3.7484	42.7284	-48.7663
5	3.2199	-1.6349	-0.4678	-0.0825	0.0111	0.2649	1.0492	-0.3997	1.2036	-1.1857	-0.4871	-0.2316	-0.2534	-0.0553	-0.6246	2.3177	0.3093	0.2856	0.6971	0.4117	0.785	-0.3632	42.0806	-45.9975
6	4.1537	0.5827	-0.9777	0.2452	0.551	1.7806	0.1063	0.8764	2.1154	0.6182	-0.0822	-0.7203	-0.9682	-0.0912	0.2046	2.3047	0.4	0.4129	1.0698	0.4628	1.4865	-4.8792	51.7327	-51.9089
7	7.5967	-3.3447	-2.4598	2.5563	1.6364	2.3223	0.293	-0.4393	-0.2759	0.2324	-0.5048	0.593	0.2235	-1.1814	0.0526	0.658	-0.0123	-0.0516	0.4217	0.1892	0.6134	-1.0198	14.1257	-30.5201
8	5.2996	-3.1202	-0.4885	3.197	1.6927	8.1315	-0.1673	-0.0682	-0.2608	-0.5256	0.5002	0.7019	-0.1391	-0.3191	-0.3036	0.4996	-0.1383	-0.1204	0.4485	0.1411	0.4903	6.0927	7.3302	-33.1838
9	7.5238	2.7575	-1.9728	6.7987	-3.8871	8.9233	0.7397	-0.7487	0.0005	1.0617	-0.2553	0.4931	0.4651	0.3251	-0.225	0.6139	-0.0627	-0.1588	0.4501	-0.009	0.414	12.8957	5.0312	-28.3877
10	6.3636	-2.5432	-0.8	4.8834	4.5637	8.2023	0.0326	-0.6025	-0.2109	-0.1117	0.173	0.236	-0.0147	0.0041	-0.0698	0.4439	-0.0486	-0.0513	0.4039	0.1511	0.4798	7.4179	10.9978	-26.7898
11	3.0219	-3.5696	-0.6491	4.7832	0.7149	1.3829	0.5408	0.1894	-0.243	-0.4696	-0.4357	0.1322	0.029	-0.2585	-0.0452	0.5924	-0.0466	-0.1315	0.4222	0.0717	0.4424	5.7991	12.4735	-35.0525
12	0.7993	0.7367	0.1445	4.527	1.5937	0.539	-0.0686	0.1255	-0.7318	-0.5484	0.2591	0.5265	-1.0992	0.7725	0.1821	1.8759	0.2781	-0.0402	1.0133	0.5664	1.0012	-13.1931	39.5183	-52.5945
13	3.8028	-0.7237	0.5955	2.8025	-1.7659	6.9537	0.38	0.6031	-0.2713	-1.0266	-0.0807	0.574	0.2777	-0.082	-0.3909	1.2287	0.1681	-0.18	0.624	0.0965	0.6691	-7.5045	30.9548	-44.7825
14	4.294	-1.3173	2.7558	6.3076	-5.5393	4.6515	0.1829	0.4627	-0.3569	-0.0728	-0.1889	0.3307	0.308	-0.6556	0.1831	0.9461	-0.0954	-0.1601	1.0126	0.1074	0.7915	-17.2438	28.889	-45.4908
15	2.8645	-2.3937	2.6841	3.8218	-1.9369	3.0307	-0.379	-0.5463	0.2097	0.8123	0.0952	0.565	-1.3406	-0.6693	0.1198	0.5751	0.0857	0.0081	0.6635	-0.0422	0.5104	32.5594	-9.915	9.7021
16	3.9095	-1.7381	1.6694	7.6396	0.9924	5.7029	-0.4562	-0.4796	0.5639	0.5839	0.1876	-0.5808	-0.9557	0.381	0.3013	0.5756	-0.049	-0.1276	0.67	0.0064	0.5038	47.2728	-13.1183	18.2783
17	2.9401	-0.5729	3.3206	1.0639	-0.0129	6.2676	-0.0728	0.1286	0.0711	0.0356	-0.0745	-0.2802	-0.208	0.247	0.131	0.3333	-0.0228	0.0205	0.388	0.0651	0.4168	38.915	-19.9137	0.572
18	6.5958	2.0366	2.285	8.3162	-0.0951	7.1035	0.3024	0.7836	-0.1093	-0.5889	-0.2524	-0.2155	0.5978	0.4394	-0.289	0.5061	0.0876	0.045	0.4441	0.0746	0.4195	33.1449	-19.0633	-29.1649
19	7.7953	0.7568	5.2119	7.2683	-1.924	8.5891	0.0022	0.6688	0.2462	-0.8189	-0.5102	-0.6943	-0.069	1.8815	0.4264	0.5435	-0.0176	0.0916	0.7564	0.163	0.4215	35.5662	-12.8415	-30.4916
20	2.2097	-2.773	0.2057	3.1019	-1.4934	8.7496	0.2624	0.2891	0.0019	-1.6665	-0.4618	0.4213	0.1425	-0.3912	0.2027	0.6866	-0.0657	-0.0702	0.4786	0.0291	0.4445	25.1253	-8.7802	-36.949
21	3.4196	-4.2055	1.0921	5.718	-1.228	7.9534	0.0551	-0.0105	-0.179	-0.0008	-0.4947	0.1789	-0.59	0.354	0.4477	0.2932	-0.1172	-0.0545	0.4625	0.0955	0.4262	23.3095	-11.8206	-26.4428
22	0.5015	-1.2718	0.6559	3.5053	-2.5481	4.8605	-0.31	0.3976	0.0616	0.1393	0.365	-0.0399	-0.0626	-0.0398	-0.3126	0.3699	-0.1089	-0.1297	0.5125	0.0637	0.5482	23.9559	-19.326	-21.4048
23	6.0677	-6.0573	-5.3711	5.6497	5.3444	5.0038	-0.1411	-0.2635	0.3185	0.65	0.1294	-0.4428	1.33	1.2635	-0.6255	0.5216	-0.0671	-0.1222	0.5615	0.2604	0.5884	23.0925	-32.0112	-1.158
24	7.866	4.1164	-6.0165	3.2233	-3.4958	5.437	-0.3145	-0.228	-0.979	-0.0673	0.4757	1.3391	0.828	-0.1324	-0.223	0.6249	0.0088	-0.0096	0.4816	0.1149	0.7511	22.078	-34.92	-5.699
25	4.6184	0.46	1.6654	6.9341	1.9623	6.8989	-0.039	-0.4074	-0.4532	-0.0471	-0.1316	0.9108	0.4832	-0.8213	0.3058	0.404	-0.0329	-0.0324	0.6466	0.1306	0.7236	15.7974	-26.7427	-11.6991
26	4.4217	1.8267	-0.6471	4.6369	-1.3673	4.7815	-0.5063	-0.3924	0.1138	0.2865	0.9559	1.1481	-0.5071	-1.0839	-0.577	0.3706	0.0533	-0.0171	0.6283	0.2766	0.7259	12.573	-23.9116	-1.6256
27	9.1407	-7.9111	-1.8155	6.2701	1.4544	3.4644	-1.1325	-0.088	-1.7746	1.4567	-0.0888	1.3342	0.0764	0.0191	0.806	0.5147	-0.0633	0.0282	0.6676	0.2839	0.6481	21.8647	-22.3827	1.2297

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 75 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 76 through 101 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 102 through 112 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 113 through 149 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 150 through 186 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 187 through 210 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 1 through 17 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 18 through 43 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 44 through 60 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 61 through 99 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 100 through 127 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 128 through 142 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 143 through 192 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 193 through 216 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 5 through 50 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 51 through 160 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 161 through 264 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 2 through 42 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 43 through 66 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 67 through 83 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 84 through 118 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 119 through 139 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 140 through 155 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 156 through 180 )
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 181 through 221 )
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 222 through 248 )
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 249 through 262 )

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