PDB-5fpq: Structure of Homo sapiens acetylcholinesterase phosphonylated by ...

ID or keywords:

Entry

Database: PDB / ID: 5fpq

Title

Structure of Homo sapiens acetylcholinesterase phosphonylated by sarin.

Components

ACETYLCHOLINESTERASE

Keywords

HYDROLASE / SIGNALING PROTEIN / ACETYLCHOLINESTERASE / SARIN / HI-6 / QM / DENSITY FUNCTIONAL THEORY CALCULATIONS / MICHAELIS COMPLEX.

Function / homology

Function and homology information

negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Allgardsson, A. / Berg, L. / Akfur, C. / Hornberg, A. / Worek, F. / Linusson, A. / Ekstrom, F.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of a Prereaction Complex between the Nerve Agent Sarin, its Biological Target Acetylcholinesterase, and the Antidote Hi-6.
Authors: Allgardsson, A. / Berg, L. / Akfur, C. / Hornberg, A. / Worek, F. / Linusson, A. / Ekstrom, F.J.

History

Deposition	Dec 2, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 11, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 1, 2016	Group: Database references
Revision 2.0	Jan 17, 2018	Group: Atomic model / Data collection / Category: atom_site / diffrn_source Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _diffrn_source.pdbx_synchrotron_site
Revision 2.1	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5fpq.cif.gz	421.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5fpq.ent.gz	349.6 KB	Display	PDB format
PDBx/mmJSON format	5fpq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5fpq_validation.pdf.gz	447.3 KB	Display	wwPDB validaton report
Full document	5fpq_full_validation.pdf.gz	454.9 KB	Display
Data in XML	5fpq_validation.xml.gz	37.8 KB	Display
Data in CIF	5fpq_validation.cif.gz	52.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fp/5fpq ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fpq	HTTPS FTP

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Related structure data

Related structure data	5fppC 4ey4S 5foq C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2gyu-d 5foq-d 2h9y-d 5hf9-d 6fse-d 6wv1-1 4b82-d 6fsd-d 4ey6-d 5fum-d 4bc0-1 6tt0-1 6ntg-1 2jf0-d 2ha3-d 1q83-d 2jgf-d 1h22-1 2whr-d 2jgj-d 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5fppC

4ey4S

5foq

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#54 - Jun 2004 Acetylcholinesterase similarity (15) #194 - Feb 2016 Designer Insulins similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1) #14 - Feb 2001 Insulin similarity (1) #184 - Apr 2015 Glucagon similarity (1) #149 - May 2012 Leptin similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#54 - Jun 2004
Acetylcholinesterase
similarity (15)
#194 - Feb 2016
Designer Insulins
similarity (1)
#52 - Apr 2004
Growth Hormone
similarity (1)
#141 - Sep 2011
O-GlcNAc Transferase
similarity (1)
#14 - Feb 2001
Insulin
similarity (1)
#184 - Apr 2015
Glucagon
similarity (1)
#149 - May 2012
Leptin
similarity (1)
#202 - Oct 2016
Dipeptidyl Peptidase 4
similarity (1)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)

Deposited unit

A: ACETYLCHOLINESTERASE

B: ACETYLCHOLINESTERASE

hetero molecules

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

1

A: ACETYLCHOLINESTERASE

hetero molecules

B: ACETYLCHOLINESTERASE

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

2

B: ACETYLCHOLINESTERASE

A: ACETYLCHOLINESTERASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	104.869, 104.869, 323.250
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	ACETYLCHOLINESTERASE / ACHE Mass: 59567.191 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 33-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P22303, acetylcholinesterase
#2: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	OTHER_DETAILS: SARIN PHOSPHONYLATION PRODUCT COVALENTLY ATTACHED TO SER203D

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.31 Å³/Da / Density % sol: 71.44 % / Description: NONE
Crystal grow	pH: 7 / Details: PH 7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.919
Detector	Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.919 Å / Relative weight: 1
Reflection	Resolution: 2.4→47.2 Å / Num. obs: 81717 / % possible obs: 99.6 % / Observed criterion σ(I): 3.9 / Redundancy: 5 % / B_iso Wilson estimate: 32.71 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shell	Highest resolution: 2.4 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 3.9 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EY4

4ey4

Resolution: 2.4→45.41 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 19.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2103	4144	5.1 %
R_work	0.1767	-	-
obs	0.1784	81198	99.36 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→45.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8282	0	16	113	8411

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8687
X-RAY DIFFRACTION	f_angle_d	1.081	11874
X-RAY DIFFRACTION	f_dihedral_angle_d	14.655	3143
X-RAY DIFFRACTION	f_chiral_restr	0.079	1256
X-RAY DIFFRACTION	f_plane_restr	0.005	1578

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 (%)
2.4-2.4273	0.2771	132	0.2179	2555	X-RAY DIFFRACTION	99
2.4273-2.4558	0.2579	132	0.2081	2548	X-RAY DIFFRACTION	99
2.4558-2.4858	0.2526	136	0.2077	2504	X-RAY DIFFRACTION	99
2.4858-2.5173	0.2465	127	0.1909	2533	X-RAY DIFFRACTION	99
2.5173-2.5504	0.2592	161	0.2001	2504	X-RAY DIFFRACTION	99
2.5504-2.5853	0.2626	120	0.1908	2523	X-RAY DIFFRACTION	99
2.5853-2.6222	0.2047	138	0.1916	2579	X-RAY DIFFRACTION	99
2.6222-2.6614	0.237	133	0.1861	2490	X-RAY DIFFRACTION	99
2.6614-2.703	0.2159	140	0.1862	2562	X-RAY DIFFRACTION	99
2.703-2.7473	0.2445	137	0.1909	2560	X-RAY DIFFRACTION	99
2.7473-2.7946	0.2216	146	0.1947	2485	X-RAY DIFFRACTION	99
2.7946-2.8454	0.2423	135	0.2008	2546	X-RAY DIFFRACTION	99
2.8454-2.9002	0.2403	148	0.2106	2529	X-RAY DIFFRACTION	99
2.9002-2.9594	0.273	135	0.2058	2544	X-RAY DIFFRACTION	100
2.9594-3.0237	0.2412	144	0.1987	2565	X-RAY DIFFRACTION	99
3.0237-3.094	0.2666	119	0.2084	2567	X-RAY DIFFRACTION	100
3.094-3.1714	0.2543	133	0.2071	2556	X-RAY DIFFRACTION	99
3.1714-3.2571	0.2334	129	0.2072	2561	X-RAY DIFFRACTION	100
3.2571-3.3529	0.2289	143	0.1992	2549	X-RAY DIFFRACTION	99
3.3529-3.4611	0.2162	143	0.1982	2562	X-RAY DIFFRACTION	99
3.4611-3.5847	0.2379	146	0.1935	2560	X-RAY DIFFRACTION	99
3.5847-3.7282	0.2095	132	0.1735	2585	X-RAY DIFFRACTION	99
3.7282-3.8978	0.1795	145	0.1573	2580	X-RAY DIFFRACTION	100
3.8978-4.1032	0.1816	150	0.1444	2556	X-RAY DIFFRACTION	100
4.1032-4.3601	0.1462	130	0.1363	2637	X-RAY DIFFRACTION	100
4.3601-4.6964	0.1452	135	0.1273	2594	X-RAY DIFFRACTION	100
4.6964-5.1684	0.1657	147	0.1344	2617	X-RAY DIFFRACTION	99
5.1684-5.9149	0.2036	131	0.1557	2641	X-RAY DIFFRACTION	99
5.9149-7.4468	0.2029	143	0.1737	2676	X-RAY DIFFRACTION	100
7.4468-45.4177	0.1843	154	0.1788	2786	X-RAY DIFFRACTION	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	1.4276	0.0907	0.515	0.7869	-0.0428	2.3159	-0.0246	-0.1097	-0.0389	0.0675	0.0131	-0.0556	-0.1586	0.1993	-0.0038	0.1594	-0.0087	-0.0496	0.2468	0.0397	0.1903	62.9177	32.1947	39.1464
2	2.4735	1.1463	0.5004	2.4525	0.1491	1.4212	-0.0573	-0.1476	0.0178	0.0901	0.0295	0.1616	-0.3305	-0.2472	0.0032	0.1948	0.0369	-0.0182	0.2712	0.012	0.1733	51.0673	35.8377	37.0123
3	1.3232	0.3381	0.1483	0.7857	-0.5353	1.5654	-0.0932	0.1613	0.0258	0.0655	0.1439	0.0739	-0.2348	-0.2431	-0.0259	0.1833	0.0515	-0.0312	0.2665	0.0063	0.1925	47.9071	33.6105	27.1921
4	1.229	0.7828	-0.3695	0.5492	-0.6775	1.6769	-0.0867	-0.0182	0.0129	-0.0871	0.0808	0.0295	0.0175	-0.4922	0.0859	0.1916	0.0279	-0.0331	0.3805	0.0288	0.2404	42.7174	27.0438	28.6871
5	0.4963	0.2025	0.673	0.0726	0.2528	1.496	0.0888	-0.0221	-0.1497	-0.0741	-0.0458	-0.0589	0.1033	0.1642	-0.0201	0.2132	0.0227	-0.0208	0.2961	0.0106	0.2481	56.6208	22.5201	11.1382
6	1.5383	-0.4632	1.0612	0.7785	-0.2941	0.9383	-0.1697	0.4215	0.2059	-0.1949	-0.0051	-0.0913	-0.3745	0.3598	0.0348	0.3072	-0.1894	-0.0467	0.3572	0.0928	0.2557	67.7767	42.2931	13.6956
7	0.6742	0.4072	0.9004	0.7774	0.2791	1.3115	0.1811	-0.0186	-0.1643	-0.0421	-0.1855	-0.0527	-0.1788	0.1649	0.0684	0.2714	-0.0299	-0.0398	0.3233	0.0137	0.2027	51.4319	32.4997	5.0517
8	0.8447	-0.2202	-0.3156	4.6571	-0.1174	0.2132	-0.0642	-0.3892	-0.0599	0.4001	-0.0539	0.0728	0.1244	-0.1321	0.1286	0.3751	-0.0913	0.0321	0.2602	0.0005	0.1958	102.2755	35.3433	57.6287
9	0.7453	-0.1043	-0.8429	0.0446	0.1559	0.9885	-0.2026	-0.2898	-0.3495	0.2537	-0.0052	0.0888	0.3401	0.305	0.125	0.293	-0.028	-0.0126	0.2358	0.0401	0.2031	112.0381	20.8749	44.079
10	1.02	0.1299	-0.3508	0.9259	-0.4434	0.6468	0.0408	-0.2012	0.0694	0.1691	-0.1372	-0.0647	-0.1905	0.3095	0.0541	0.2745	-0.1208	-0.0466	0.3186	0.0375	0.2521	119.1159	40.9072	40.9541
11	1.4669	-0.5767	-0.3649	1.4824	0.4698	1.2341	-0.0277	-0.1518	-0.0885	0.2868	-0.0716	0.0599	-0.0148	0.058	0.0982	0.1833	-0.0794	0.0161	0.1976	0.0074	0.186	107.7817	34.8396	40.8791
12	0.7522	-0.3082	-0.1669	1.0383	-0.1438	1.2084	0.1375	0.1698	-0.009	-0.0164	-0.1572	0.0318	0.0383	0.0968	0.016	0.135	-0.066	-0.0073	0.2246	0.0068	0.2373	111.7373	29.6781	29.1656
13	0.7787	-0.551	-0.105	0.6041	-0.2303	0.9233	0.147	0.1682	-0.0537	0.0499	-0.1292	0.1194	0.067	0.0282	-0.0295	0.1816	-0.0455	-0.0049	0.2987	-0.0448	0.2374	103.0289	37.0343	22.161
14	0.8298	0.0134	0.6803	0.5894	-0.3674	1.4332	0.031	-0.079	-0.0262	-0.0133	-0.1704	-0.2292	-0.1521	0.3548	0.1097	0.2448	-0.0579	-0.023	0.2933	0.0675	0.2326	117.3368	53.067	11.7117
15	0.9111	-0.2574	-0.325	0.4327	0.0366	0.8573	0.0811	0.0314	0.2179	0.1587	-0.1105	0.0368	-0.1381	0.0002	0.0147	0.2306	-0.0529	-0.0214	0.1917	-0.0045	0.218	104.4376	50.9172	30.8354
16	1.2272	0.1994	0.3867	0.8746	0.0539	2.2707	0.0168	-0.016	0.1811	0.0475	-0.0234	0.1732	-0.2453	-0.3891	0.0088	0.1801	0.037	0.0181	0.2287	-0.034	0.2828	91.7471	52.0273	32.7954
17	0.793	0.3654	-0.2341	0.2752	-0.3901	1.8051	-0.2108	0.0836	-0.0662	-0.1316	0.0135	0.3926	-0.2084	0.0801	0.0423	0.1849	0.0545	-0.0181	0.1689	0.0559	0.1728	100.9717	49.3503	14.2716

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 142 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 143 THROUGH 190 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 191 THROUGH 255 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 256 THROUGH 331 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 332 THROUGH 466 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 467 THROUGH 513 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 514 THROUGH 542 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 4 THROUGH 32 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 33 THROUGH 58 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 59 THROUGH 86 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 87 THROUGH 170 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 171 THROUGH 300 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 301 THROUGH 341 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 342 THROUGH 406 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 407 THROUGH 466 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 467 THROUGH 513 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 514 THROUGH 542 )

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Yorodumi