PDB-5a5c: Structure of an engineered neuronal LRRTM2 adhesion molecule

ID or keywords:

Entry

Database: PDB / ID: 5a5c

Title

Structure of an engineered neuronal LRRTM2 adhesion molecule

Components

LRRTM

Keywords

SIGNALING PROTEIN / LRRTM /

SYNAPSE /

ADHESION /

LEUCINE RICH REPEAT /

NEUREXIN

Function / homology

Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) /

Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta

Function and homology information

Biological species

SYNTHETIC CONSTRUCT (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.097 Å

Authors

Paatero, A. / Rosti, K. / Shkumatov, A.V. / Brunello, C. / Kysenius, K. / Huttunen, H. / Kajander, T.

Citation

Journal: Biochemistry / Year: 2016
Title: Crystal Structure of an Engineered LRRTM2 Synaptic Adhesion Molecule and a Model for Neurexin Binding.
Authors: Anja Paatero / Katja Rosti / Alexander V Shkumatov / Celeste Sele / Cecilia Brunello / Kai Kysenius / Prosanta Singha / Ville Jokinen / Henri Huttunen / Tommi Kajander /

Abstract: Synaptic adhesion molecules are key components in development of the brain, and in the formation of neuronal circuits, as they are central in the assembly and maturation of chemical synapses. Several ...

History

Deposition	Jun 17, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 17, 2016	Group: Source and taxonomy
Revision 1.2	Mar 2, 2016	Group: Database references
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5a5c.cif.gz	738.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5a5c.ent.gz	629.8 KB	Display	PDB format
PDBx/mmJSON format	5a5c.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/a5/5a5c ftp://data.pdbj.org/pub/pdb/validation_reports/a5/5a5c	HTTPS FTP

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Related structure data

Related structure data	SASDBG3C SASDBH3C 3m18S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3zyn-1 4h7a-d 5mx1-2 5mfl-3 3zyn-2 5ve3-2 6k1c-d 4v2e-2 5z8x-2 5cmp-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

SASDBG3C

SASDBH3C

3m18S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LRRTM

B: LRRTM

C: LRRTM

D: LRRTM

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

1

A: LRRTM

defined by software
40 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: LRRTM

defined by software
40 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: LRRTM

defined by software
40 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: LRRTM

defined by software
40 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	235.994, 57.324, 144.451
Angle α, β, γ (deg.)	90.00, 115.49, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	LRRTM Mass: 40046.391 Da / Num. of mol.: 4 / Fragment: LEUCINE RICH REPEAT DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Cell line (production host): 9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.75 Å³/Da / Density % sol: 54 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2013 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 102458 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.35 % / R_merge(I) obs: 0.08 / Net I/σ(I): 12.11
Reflection shell	Resolution: 2.1→2.22 Å / Redundancy: 4.32 % / R_merge(I) obs: 1.02 / Mean I/σ(I) obs: 1.22 / % possible all: 97.9

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M18

3m18

Resolution: 2.097→44.737 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 29.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2356	5077	5 %
R_work	0.1954	-	-
obs	0.1973	102336	99.49 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.816 Å² / k_sol: 0.347 e/Å³

Displacement parameters

B_iso mean: 53.7 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-11.223 Å²	0 Å²	-5.6679 Å²
2-	-	24.9514 Å²	0 Å²
3-	-	-	-13.7284 Å²

Refinement step

Cycle: LAST / Resolution: 2.097→44.737 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10257	0	0	421	10678

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	10491
X-RAY DIFFRACTION	f_angle_d	1.684	14279
X-RAY DIFFRACTION	f_dihedral_angle_d	14.613	3771
X-RAY DIFFRACTION	f_chiral_restr	0.086	1681
X-RAY DIFFRACTION	f_plane_restr	0.012	1859

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 (%)
2.097-2.1208	0.5013	149	0.4803	2913	X-RAY DIFFRACTION	90
2.1208-2.1458	0.4345	188	0.3983	3141	X-RAY DIFFRACTION	100
2.1458-2.1719	0.4333	178	0.3826	3200	X-RAY DIFFRACTION	100
2.1719-2.1994	0.4459	176	0.3761	3265	X-RAY DIFFRACTION	100
2.1994-2.2284	0.3879	153	0.3363	3182	X-RAY DIFFRACTION	100
2.2284-2.2589	0.3888	162	0.3223	3254	X-RAY DIFFRACTION	100
2.2589-2.2911	0.3425	176	0.302	3271	X-RAY DIFFRACTION	100
2.2911-2.3253	0.3337	157	0.2705	3190	X-RAY DIFFRACTION	100
2.3253-2.3617	0.309	162	0.2431	3250	X-RAY DIFFRACTION	100
2.3617-2.4004	0.299	158	0.2571	3226	X-RAY DIFFRACTION	100
2.4004-2.4418	0.3474	158	0.2487	3227	X-RAY DIFFRACTION	100
2.4418-2.4862	0.2926	171	0.2339	3279	X-RAY DIFFRACTION	100
2.4862-2.534	0.2956	162	0.2192	3230	X-RAY DIFFRACTION	100
2.534-2.5857	0.2882	176	0.2238	3262	X-RAY DIFFRACTION	100
2.5857-2.6419	0.2796	166	0.2253	3219	X-RAY DIFFRACTION	100
2.6419-2.7034	0.2634	177	0.2143	3245	X-RAY DIFFRACTION	100
2.7034-2.771	0.2552	162	0.2042	3239	X-RAY DIFFRACTION	100
2.771-2.8459	0.2557	172	0.2125	3235	X-RAY DIFFRACTION	100
2.8459-2.9296	0.2466	170	0.2079	3230	X-RAY DIFFRACTION	100
2.9296-3.0242	0.2711	173	0.2073	3298	X-RAY DIFFRACTION	100
3.0242-3.1322	0.2616	169	0.227	3208	X-RAY DIFFRACTION	100
3.1322-3.2576	0.2635	174	0.2069	3274	X-RAY DIFFRACTION	100
3.2576-3.4058	0.2119	172	0.1969	3265	X-RAY DIFFRACTION	100
3.4058-3.5853	0.2386	170	0.1925	3287	X-RAY DIFFRACTION	100
3.5853-3.8098	0.2057	171	0.1743	3275	X-RAY DIFFRACTION	100
3.8098-4.1038	0.1758	170	0.1472	3276	X-RAY DIFFRACTION	100
4.1038-4.5164	0.182	173	0.1375	3263	X-RAY DIFFRACTION	100
4.5164-5.1691	0.1608	176	0.1328	3323	X-RAY DIFFRACTION	100
5.1691-6.5093	0.1905	175	0.1598	3299	X-RAY DIFFRACTION	100
6.5093-44.747	0.1994	181	0.1706	3433	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	0.6182	-0.3137	0.2286	0.1764	-0.1268	0.0611	0.1593	0.5139	-0.129	0.0606	-0.2749	0.055	0.0805	-0.3687	-0.008	0.3273	-0.0614	-0.0075	0.8727	-0.1989	0.3258	-60.376	-22.7914	-47.5889
2	1.1759	-1.5713	0.1635	3.1604	-1.0382	0.7779	0.1858	0.0393	0.219	-0.7755	-0.127	-0.5176	0.341	-0.1083	-0.0152	0.4615	0.046	-0.0132	0.8108	-0.1113	0.3877	-48.1951	-21.3095	-53.8983
3	1.3508	-0.0123	0.8456	-0.013	0.0268	1.07	0.014	0.2216	0.1921	0.0052	-0.042	-0.0943	0.0797	-0.2456	0.0036	0.3094	0.0029	0.0239	0.2826	-0.026	0.3621	-35.2603	-12.7577	-37.584
4	0.7873	-0.0532	0.0131	0.6589	-0.2704	0.6247	-0.0174	-0.73	0.0203	0.1966	-0.0194	-0.0651	0.0242	0.0861	-0.0288	0.4003	0.0197	-0.015	0.3868	-0.0868	0.3339	-22.7022	-15.2062	-9.7189
5	0.5439	-0.1526	-0.1548	0.6775	0.2813	0.1174	0.1426	0.5842	-0.0143	-0.1234	-0.1989	0.0295	-0.0681	-0.2589	-0.0013	0.3605	0.1394	0.016	0.711	0.0925	0.297	8.4859	-8.2877	-69.0931
6	0.5258	-0.0316	-0.7162	0.3859	-0.3064	1.2785	0.0151	0.5225	-0.0463	-0.026	-0.1659	0.0831	-0.0533	-0.2713	0.0002	0.2875	0.038	0.0099	0.4544	-0.0458	0.3412	-4.6465	-17.4924	-53.4517
7	0.6731	0.0202	-0.2793	0.6758	0.456	0.8341	-0.0479	-0.0756	0.1085	0.0777	-0.0172	-0.0652	-0.0197	0.2646	-0.0023	0.3046	0.0762	0.0203	0.1364	0.0329	0.2683	-1.1437	-19.1864	-25.6251
8	0.2652	-0.3445	-0.2127	0.3785	0.2294	0.2377	-0.1206	-0.1502	0.0731	0.1149	-0.241	-0.1437	-0.2717	0.2601	-0.0025	0.4552	-0.0071	-0.0292	0.5183	-0.0562	0.3168	4.9517	-8.0384	-8.3872
9	0.3375	-0.0165	-0.2098	0.0079	-0.0931	0.8695	0.0127	0.121	0.2387	0.072	-0.0815	0.058	-0.5021	-0.4013	-0.0015	0.5729	0.1392	-0.007	0.3482	-0.0009	0.4664	-4.1533	6.1597	-37.5639
10	0.9656	-0.5083	-1.1314	1.0758	0.6198	1.3214	0.0312	-0.0208	-0.0066	0.0013	-0.0836	-0.1297	-0.1205	0.4668	0.0001	0.2775	-0.0297	-0.0242	0.2735	0.0869	0.3135	16.0276	-3.4047	-44.063
11	2.2417	-0.4748	-0.9672	1.2151	0.0149	0.8909	-0.2168	0.1691	-0.3563	0.0749	-0.0277	0.1233	-0.0948	0.0586	-0.0469	0.2157	0.0328	0.0525	0.3319	0.0579	0.4366	22.1079	-30.0484	-55.984
12	0.0785	-0.0738	-0.0036	0.1649	0.1509	0.2295	-0.2932	0.4572	0.0706	-0.2258	0.1182	0.2063	-0.3803	-0.0743	0.009	0.3252	-0.0622	0.0249	0.6725	-0.1981	0.7629	17.933	-44.7145	-69.9228
13	1.1451	0.2746	0.4888	0.3127	-0.3743	1.0636	0.1828	0.3247	-0.3082	0.1907	-0.1108	-0.1026	0.4969	0.2228	0.0241	0.6108	0.0181	-0.0395	0.3058	-0.1157	0.5006	-33.0415	-37.3202	-30.4461
14	1.2071	-0.9845	0.6707	1.1275	-0.5771	0.9225	0.0466	-0.3365	-0.0142	0.3251	-0.0793	0.0165	0.1557	-0.7325	-0.0017	0.4617	-0.1331	0.0435	0.4946	-0.0681	0.3026	-52.0975	-26.0051	-22.2081
15	1.8214	-0.0773	-0.1173	1.6945	-0.5999	0.49	-0.3097	0.0984	0.5555	0.4212	0.1062	-0.1508	-0.1245	-0.5425	-0.0562	0.3747	0.1377	-0.0454	0.6625	-0.1125	0.4331	-63.0235	-1.0309	-29.5991
16	2.164	-0.8029	-0.2541	3.0032	-1.5043	2.2181	0.1365	0.9241	0.2079	-0.3776	0.1703	-0.2327	-0.1227	0.0167	-0.8398	0.556	0.0899	-0.0026	1.152	0.3351	0.5374	-70.4408	11.4197	-44.8104

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:64)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 65:76)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 77:235)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 236:330)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID -1:69)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 70:181)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 182:302)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 303:330)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 1:60)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 61:190)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 191:315)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 316:329)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 1:72)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 73:196)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 197:311)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 312:329)

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