PDB-6d9g: X-ray Structure of the FAB Fragment of 15B8, a Murine Monoclonal ...

ID or keywords:

Entry

Database: PDB / ID: 6d9g

Title

X-ray Structure of the FAB Fragment of 15B8, a Murine Monoclonal Antibody Specific for the Human Serotonin Transporter

Components

Antibody heavy chain Fab
Antibody light chain Fab

Keywords

IMMUNE SYSTEM / Antibody

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Coleman, J.A. / Yang, D. / Gouaux, E.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2019
Title: Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport.
Authors: Jonathan A Coleman / Dongxue Yang / Zhiyu Zhao / Po-Chao Wen / Craig Yoshioka / Emad Tajkhorshid / Eric Gouaux /

Abstract: The serotonin transporter (SERT) regulates neurotransmitter homeostasis through the sodium- and chloride-dependent recycling of serotonin into presynaptic neurons. Major depression and anxiety ...The serotonin transporter (SERT) regulates neurotransmitter homeostasis through the sodium- and chloride-dependent recycling of serotonin into presynaptic neurons. Major depression and anxiety disorders are treated using selective serotonin reuptake inhibitors-small molecules that competitively block substrate binding and thereby prolong neurotransmitter action. The dopamine and noradrenaline transporters, together with SERT, are members of the neurotransmitter sodium symporter (NSS) family. The transport activities of NSSs can be inhibited or modulated by cocaine and amphetamines, and genetic variants of NSSs are associated with several neuropsychiatric disorders including attention deficit hyperactivity disorder, autism and bipolar disorder. Studies of bacterial NSS homologues-including LeuT-have shown how their transmembrane helices (TMs) undergo conformational changes during the transport cycle, exposing a central binding site to either side of the membrane. However, the conformational changes associated with transport in NSSs remain unknown. To elucidate structure-based mechanisms for transport in SERT we investigated its complexes with ibogaine, a hallucinogenic natural product with psychoactive and anti-addictive properties. Notably, ibogaine is a non-competitive inhibitor of transport but displays competitive binding towards selective serotonin reuptake inhibitors. Here we report cryo-electron microscopy structures of SERT-ibogaine complexes captured in outward-open, occluded and inward-open conformations. Ibogaine binds to the central binding site, and closure of the extracellular gate largely involves movements of TMs 1b and 6a. Opening of the intracellular gate involves a hinge-like movement of TM1a and the partial unwinding of TM5, which together create a permeation pathway that enables substrate and ion diffusion to the cytoplasm. These structures define the structural rearrangements that occur from the outward-open to inward-open conformations, and provide insight into the mechanism of neurotransmitter transport and ibogaine inhibition.

History

Deposition	Apr 29, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 5, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 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	6d9g.cif.gz	490.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6d9g.ent.gz	411.2 KB	Display	PDB format
PDBx/mmJSON format	6d9g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6d9g_validation.pdf.gz	441.3 KB	Display	wwPDB validaton report
Full document	6d9g_full_validation.pdf.gz	445.2 KB	Display
Data in XML	6d9g_validation.xml.gz	34 KB	Display
Data in CIF	6d9g_validation.cif.gz	48.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d9/6d9g ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d9g	HTTPS FTP

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Related structure data

Related structure data	0437C 8940C 8941C 8942C 8943C 6dzvC 6dzwC 6dzyC 6dzzC 5i66S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2uyl-4 6u3z-2 5mub-2 4jzn-2 2pcp-2 5dq9-1 4yhn-1 1ce1-d 6tcn-1 3oz9-d 5weq-d 5dsc-2 6be3-d 4jha-d 3i75-d 6tcp-3 6z3k-3 6tcp-2 5dq9-3 4s1d-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Antibody heavy chain Fab

B: Antibody light chain Fab

C: Antibody heavy chain Fab

D: Antibody light chain Fab

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

1

A: Antibody heavy chain Fab

B: Antibody light chain Fab

defined by author&software
48.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Antibody heavy chain Fab

D: Antibody light chain Fab

defined by author&software
48.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.870, 85.490, 141.700
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Antibody	Antibody heavy chain Fab Mass: 24516.510 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody	Antibody light chain Fab Mass: 23558.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.61 Å³/Da / Density % sol: 52.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.2 M ammonium sulfate, 0.08 M sodium citrate pH 5.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.3→19.93 Å / Num. obs: 45074 / % possible obs: 99.12 % / Redundancy: 10.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.092 / Net I/σ(I): 17.88
Reflection shell	Resolution: 2.3→2.382 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.413 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 4199 / CC_1/2: 0.668 / % possible all: 94.2

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Processing

Software

Name	Version	Classification
PHENIX	dev_2597	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5i66

5i66

Resolution: 2.3→19.93 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 22.93

	R_factor	Num. reflection	% reflection
R_free	0.2282	4236	4.99 %
R_work	0.1948	-	-
obs	0.1965	84866	98.37 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.3→19.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6628	0	0	364	6992

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6798
X-RAY DIFFRACTION	f_angle_d	0.595	9249
X-RAY DIFFRACTION	f_dihedral_angle_d	11.201	4029
X-RAY DIFFRACTION	f_chiral_restr	0.045	1026
X-RAY DIFFRACTION	f_plane_restr	0.003	1179

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 (%)
2.3-2.3261	0.3582	118	0.3024	2294	X-RAY DIFFRACTION	84
2.3261-2.3534	0.3264	126	0.3131	2391	X-RAY DIFFRACTION	89
2.3534-2.3821	0.3809	134	0.2853	2532	X-RAY DIFFRACTION	91
2.3821-2.4122	0.3436	140	0.2816	2561	X-RAY DIFFRACTION	95
2.4122-2.4439	0.2903	138	0.2716	2662	X-RAY DIFFRACTION	97
2.4439-2.4773	0.3182	143	0.2642	2676	X-RAY DIFFRACTION	98
2.4773-2.5126	0.2697	142	0.2505	2714	X-RAY DIFFRACTION	99
2.5126-2.5501	0.312	142	0.2558	2688	X-RAY DIFFRACTION	100
2.5501-2.5898	0.3115	144	0.2495	2786	X-RAY DIFFRACTION	100
2.5898-2.6322	0.2443	142	0.2281	2681	X-RAY DIFFRACTION	100
2.6322-2.6775	0.2774	150	0.22	2738	X-RAY DIFFRACTION	100
2.6775-2.7261	0.2708	144	0.2155	2717	X-RAY DIFFRACTION	100
2.7261-2.7783	0.2806	143	0.216	2739	X-RAY DIFFRACTION	100
2.7783-2.8349	0.2441	142	0.214	2747	X-RAY DIFFRACTION	100
2.8349-2.8964	0.2468	141	0.2092	2737	X-RAY DIFFRACTION	100
2.8964-2.9635	0.2443	138	0.2025	2736	X-RAY DIFFRACTION	100
2.9635-3.0374	0.2636	143	0.2073	2698	X-RAY DIFFRACTION	100
3.0374-3.1192	0.2611	148	0.2013	2735	X-RAY DIFFRACTION	100
3.1192-3.2106	0.2455	143	0.2008	2760	X-RAY DIFFRACTION	100
3.2106-3.3138	0.2555	144	0.2004	2724	X-RAY DIFFRACTION	100
3.3138-3.4317	0.1977	147	0.1963	2744	X-RAY DIFFRACTION	100
3.4317-3.5683	0.2023	142	0.1736	2701	X-RAY DIFFRACTION	100
3.5683-3.7297	0.2027	143	0.1688	2746	X-RAY DIFFRACTION	100
3.7297-3.925	0.2048	134	0.1679	2733	X-RAY DIFFRACTION	100
3.925-4.1688	0.1921	144	0.1634	2735	X-RAY DIFFRACTION	100
4.1688-4.4873	0.1591	146	0.1369	2711	X-RAY DIFFRACTION	100
4.4873-4.9327	0.1869	144	0.1357	2744	X-RAY DIFFRACTION	100
4.9327-5.6324	0.1797	146	0.1658	2743	X-RAY DIFFRACTION	100
5.6324-7.0439	0.1803	147	0.2095	2723	X-RAY DIFFRACTION	100
7.0439-19.9521	0.2228	138	0.2043	2734	X-RAY DIFFRACTION	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	8.0845	5.8076	2.0005	8.5783	1.2767	0.8472	-0.221	1.5672	1.0019	-1.6101	0.9545	1.1129	-0.3825	0.5564	-0.845	0.9622	0.0502	0.1431	0.705	0.1357	0.5389	-31.6005	-25.8653	-2.5405
2	4.1344	2.443	-1.4793	5.1963	-3.9394	6.3926	0.1133	-0.4981	-0.3018	-0.1583	-0.3249	-0.454	0.4323	0.6487	0.1552	0.5112	0.1125	0.025	0.5124	0.0215	0.4049	-29.9185	-29.6603	8.7309
3	5.0434	4.3863	-2.1082	7.0641	-1.1069	5.0599	-0.145	0.3539	-0.3826	-0.5277	-0.0223	-0.6653	0.3246	0.3124	0.1233	0.4765	0.103	0.0208	0.5226	0.0785	0.3713	-29.8462	-29.696	5.3409
4	2.046	0.9415	-1.8112	2.5192	-1.3194	3.5898	0.0667	0.0571	-0.0986	0.1196	0.0781	0.025	-0.1532	-0.2785	-0.1566	0.2924	0.0235	-0.0138	0.3332	-0.007	0.3315	-35.5075	-8.5971	36.6346
5	3.8012	1.7894	4.0462	3.1222	3.4009	8.3774	0.073	-0.0963	-0.089	-0.0889	-0.0352	0.0458	0.202	-0.5027	0.0128	0.4149	-0.0158	0.0138	0.4232	0.0516	0.3518	-39.805	-18.6528	2.0842
6	7.0388	-3.381	1.2595	1.9012	0.5749	5.2556	-2.3095	3.2151	5.094	-3.2482	1.2322	-1.0265	-6.9878	5.6024	0.8618	1.9857	-0.5535	-0.347	1.2104	0.1832	1.7241	-38.1549	-3.3089	3.2862
7	5.1965	4.775	4.6702	4.4103	4.3695	4.4374	0.6885	-0.4456	0.9678	-0.292	-1.4763	1.8994	-0.794	0.1274	0.6851	0.9352	-0.0621	0.0968	1.1419	-0.3883	0.8912	-38.8084	-14.3411	-8.1514
8	2.8502	-0.8042	1.2368	2.9632	0.1737	5.4122	0.2846	0.2656	-0.0694	-0.5122	-0.1701	-0.0737	0.1814	0.2298	-0.1236	0.362	0.0677	0.0247	0.2822	0.0255	0.3168	5.5612	-28.6251	14.9407
9	0.4528	-0.1114	0.1681	1.0545	-1.0505	3.8732	0.1186	0.0831	-0.0666	-0.1496	-0.0081	-0.0532	0.1094	0.1397	-0.1296	0.3221	-0.0032	0.0186	0.2204	0.0168	0.3639	4.1054	-26.2031	25.6034
10	3.8975	-3.3678	1.2661	2.8687	-1.0837	0.4015	0.4436	-1.1938	1.0722	0.2724	0.5835	0.9805	-0.9662	-0.2859	-1.0053	0.8845	0.3184	0.0657	1.4264	-0.4498	1.1868	-15.8491	-19.8725	61.3512
11	5.6381	-1.5924	-1.0883	3.1048	0.4949	3.1735	0.0758	-0.1113	0.0726	0.0929	-0.005	0.1556	0.0806	-0.1144	-0.0798	0.2275	-0.0074	-0.0371	0.1672	0.0122	0.2551	-6.1362	-28.4917	45.9687
12	2.2228	-0.1752	-1.1079	2.2155	0.6361	3.1389	0.0665	0.0907	0.1586	-0.3605	-0.0732	-0.1404	-0.1368	-0.0458	0.0008	0.3625	0.0363	0.0036	0.2621	0.0398	0.3011	-4.2984	-7.6613	17.5317
13	3.0739	-1.8699	2.5517	2.2366	-2.3998	5.9513	0.0832	-0.0635	-0.0132	-0.0445	-0.0128	-0.1483	0.153	0.3804	-0.0337	0.2647	0.0017	0.0214	0.2423	-0.0412	0.2952	-2.1491	-14.986	50.795
14	7.5832	-2.4707	-4.7422	7.1306	6.2727	8.9019	0.3187	-0.031	-0.2182	0.5059	-0.213	-0.4701	0.7364	0.7344	-0.1315	0.5224	0.0971	-0.0325	0.5552	-0.0278	0.3174	8.0821	-25.6974	64.7383
15	5.4856	-6.3913	4.4156	8.0788	-6.0398	5.2269	-0.2841	-0.3228	0.2459	0.395	0.2273	-0.3594	-0.3118	-0.2035	0.0862	0.4173	-0.0253	-0.0419	0.3299	-0.0125	0.3377	-3.2097	-11.0997	60.7899
16	1.7858	1.1957	0.5743	4.2261	1.3983	3.2891	0.0269	-0.1559	-0.1051	0.1486	-0.0124	0.0519	0.2988	-0.2634	-0.024	0.2953	-0.0565	0.008	0.3762	0.0369	0.3303	-42.1267	-29.7102	39.4573

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain C and resid 144:161)
2	X-RAY DIFFRACTION	2	(chain C and resid 162:188)
3	X-RAY DIFFRACTION	3	(chain C and resid 189:240)
4	X-RAY DIFFRACTION	4	(chain D and resid 21:133)
5	X-RAY DIFFRACTION	5	(chain D and resid 134:218)
6	X-RAY DIFFRACTION	6	(chain D and resid 219:226)
7	X-RAY DIFFRACTION	7	(chain D and resid 227:236)
8	X-RAY DIFFRACTION	8	(chain A and resid 20:100)
9	X-RAY DIFFRACTION	9	(chain A and resid 101:153)
10	X-RAY DIFFRACTION	10	(chain A and resid 154:161)
11	X-RAY DIFFRACTION	11	(chain A and resid 162:241)
12	X-RAY DIFFRACTION	12	(chain B and resid 21:131)
13	X-RAY DIFFRACTION	13	(chain B and resid 132:204)
14	X-RAY DIFFRACTION	14	(chain B and resid 205:212)
15	X-RAY DIFFRACTION	15	(chain B and resid 213:236)
16	X-RAY DIFFRACTION	16	(chain C and resid 20:143)

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