PDB-8z22: Crystal structure of the liprin-alpha2/RIM1 complex

ID or keywords:

Entry

Database: PDB / ID: 8z22

Title

Crystal structure of the liprin-alpha2/RIM1 complex

Components

Liprin-alpha-2
Regulating synaptic membrane exocytosis 1

Keywords

PROTEIN BINDING / Coiled coil / Complex

Function / homology

Function and homology information

structural constituent of presynapse / Receptor-type tyrosine-protein phosphatases / dense core granule cytoskeletal transport / Acetylcholine Neurotransmitter Release Cycle / structural constituent of postsynaptic density / regulation of dendritic spine development / Serotonin Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Jin, G. / Wei, Z.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the liprin-alpha2/RIM1 complex
Authors: Jin, G. / Wei, Z.

History

Deposition	Apr 12, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 2, 2025	Provider: repository / Type: Initial release
Revision 1.1	Apr 9, 2025	Group: Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8z22.cif.gz	208.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8z22.ent.gz	166.1 KB	Display	PDB format
PDBx/mmJSON format	8z22.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/z2/8z22 ftp://data.pdbj.org/pub/pdb/validation_reports/z2/8z22	HTTPS FTP

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Related structure data

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	#167 - Nov 2013 SNARE Proteins similarity (5) #196 - Apr 2016 Lead Poisoning similarity (5) #148 - Apr 2012 Ras Protein similarity (5) #239 - Nov 2019 Phospholipase A2 similarity (5)

Deposited unit

A: Regulating synaptic membrane exocytosis 1

B: Regulating synaptic membrane exocytosis 1

C: Liprin-alpha-2

D: Liprin-alpha-2

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

1

A: Regulating synaptic membrane exocytosis 1

B: Regulating synaptic membrane exocytosis 1

C: Liprin-alpha-2

D: Liprin-alpha-2

defined by author
Evidence: gel filtration
65 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.663, 92.697, 66.583
Angle α, β, γ (deg.)	90.00, 102.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Regulating synaptic membrane exocytosis 1 Mass: 19229.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Author's sequence reference is Genbank: XM_017596673.1 Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rims1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8I6GEN0
#2: Protein	Liprin-alpha-2 / Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 / PTPRF- ...Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 / PTPRF-interacting protein alpha-2 Mass: 13251.786 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPFIA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75334
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.71 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 28% V/V 2-Propanol; 0.1M BIS-TRIS pH 6.5; 3% V/V Polyethylene glycol 200

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.98 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.75→50 Å / Num. obs: 18054 / % possible obs: 98.9 % / Redundancy: 6.3 % / CC_1/2: 0.995 / CC star: 0.999 / R_merge(I) obs: 0.149 / R_pim(I) all: 0.065 / R_rim(I) all: 0.163 / Χ²: 0.937 / Net I/σ(I): 4.3 / Num. measured all: 112901

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
2.75-2.8	5.9	1.151	914	0.714	0.913	0.513	1.264	0.761	98
2.8-2.85	5.9	1.001	864	0.693	0.905	0.45	1.101	0.727	98.6
2.85-2.9	6.6	0.842	923	0.864	0.963	0.35	0.913	0.733	99.5
2.9-2.96	6.6	0.709	899	0.894	0.972	0.295	0.769	0.794	99.3
2.96-3.03	6.4	0.574	887	0.922	0.979	0.241	0.623	0.757	99.7
3.03-3.1	6.4	0.503	927	0.906	0.975	0.214	0.548	0.796	99.9
3.1-3.17	6.5	0.397	887	0.957	0.989	0.167	0.432	0.792	99.1
3.17-3.26	6.3	0.336	907	0.961	0.99	0.143	0.366	0.759	99.5
3.26-3.36	6.2	0.257	884	0.973	0.993	0.111	0.281	0.79	99.2
3.36-3.46	5.6	0.286	902	0.926	0.981	0.132	0.316	1.114	97.4
3.46-3.59	6.4	0.226	889	0.977	0.994	0.096	0.247	0.869	99.4
3.59-3.73	6.2	0.324	915	0.952	0.988	0.147	0.356	1.803	99.7
3.73-3.9	6.4	0.188	910	0.988	0.997	0.081	0.205	1.208	99.2
3.9-4.11	6.4	0.145	888	0.992	0.998	0.062	0.159	1.18	99.3
4.11-4.36	6.3	0.087	904	0.996	0.999	0.037	0.095	0.92	98.8
4.36-4.7	6	0.076	887	0.996	0.999	0.033	0.083	0.934	97.5
4.7-5.17	6.6	0.073	921	0.997	0.999	0.031	0.079	0.987	99.6
5.17-5.92	6.5	0.085	906	0.995	0.999	0.036	0.092	0.902	99.2
5.92-7.46	6	0.073	908	0.996	0.999	0.032	0.08	0.915	97.8
7.46-50	6	0.05	932	0.998	1	0.022	0.054	1	98.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
SCALEPACK		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→38.8 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.234	894	5 %
R_work	0.205	-	-
obs	0.2065	17881	98.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.75→38.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3832	0	0	20	3852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3882
X-RAY DIFFRACTION	f_angle_d	0.5	5212
X-RAY DIFFRACTION	f_dihedral_angle_d	21.236	1550
X-RAY DIFFRACTION	f_chiral_restr	0.04	581
X-RAY DIFFRACTION	f_plane_restr	0.004	677

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 (%)
2.75-2.92	0.3225	148	0.2899	2802	X-RAY DIFFRACTION	99
2.92-3.15	0.2579	149	0.2449	2847	X-RAY DIFFRACTION	100
3.15-3.46	0.2743	150	0.235	2845	X-RAY DIFFRACTION	99
3.46-3.96	0.2865	147	0.2484	2791	X-RAY DIFFRACTION	98
3.97-4.99	0.1746	149	0.1619	2834	X-RAY DIFFRACTION	99
4.99-38.8	0.2096	151	0.1743	2868	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	7.2752	-2.8123	0.8699	1.5929	-0.4238	0.0962	-0.2166	0.4962	0.3043	0.3439	-0.085	-0.0768	-0.0743	0.0901	0.322	0.5587	0.0136	-0.0106	0.6516	-0.0227	0.4711	6.454	0.7136	4.5677
2	5.1919	-1.2007	1.5689	3.9535	-0.5466	8.3959	0.2613	-0.1605	0.5534	0.4725	-0.1022	-0.3126	-0.5752	1.3352	0.0469	0.6192	-0.0813	-0.0495	0.5652	-0.0407	0.5088	28.8661	-0.8461	29.4673
3	4.2499	-0.6453	0.1753	2.9011	-0.7915	1.339	-0.5219	0.2341	0.2857	-0.0789	0.2673	-0.0411	-0.3022	-0.4386	0.1902	0.3496	0.0274	0.0046	0.6301	-0.0118	0.4016	17.3839	-7.3312	16.8788
4	1.2692	0.1205	-0.6255	2.2275	0.9661	2.9858	-0.4724	-0.3404	-0.6054	0.4976	0.209	-0.1803	0.718	0.1885	0.3337	0.5127	0.044	-0.0614	0.3455	-0.0109	0.5252	28.1468	-17.6684	26.0871
5	2.34	0.7856	0.7854	1.2205	0.7829	2.3545	-0.1134	0.1836	-0.1915	0.1084	-0.0211	0.205	0.154	-0.4311	0.1193	0.591	-0.0519	0.0547	0.4454	-0.0273	0.4117	17.5779	-14.2659	21.3829
6	0.7184	-0.6055	0.1982	3.0706	1.0992	1.1476	0.0464	0.7032	-0.175	0.8243	-0.3284	-0.4445	0.4841	0.1475	0.2954	0.5827	-0.0554	0.0099	0.3629	-0.0001	0.4475	25.6377	-19.2122	28.458
7	1.6285	-0.3155	0.1841	0.7035	0.3194	3.7307	0.0476	0.3008	0.2896	0.15	0.2489	0.0675	-0.2333	0.3622	-0.1483	0.4934	-0.019	0.032	0.4719	0.032	0.4133	21.4774	-1.5555	26.5746
8	4.4373	0.4436	3.3129	1.2105	-0.1522	2.6407	0.3288	-0.6375	-0.6739	0.0802	0.1008	-0.3988	1.2216	0.107	-0.1886	0.7216	-0.0278	-0.056	0.5372	0.0856	0.5464	16.7076	-15.4157	46.3802
9	5.8001	0.1238	0.8775	2.7508	-1.0834	4.3268	0.1645	-0.2569	0.2724	-0.1633	0.1409	0.1617	-0.1395	-0.8684	-0.2782	0.3765	0.0342	0.0303	0.4915	0.0292	0.4649	12.516	-0.0165	55.3315
10	5.6201	-0.3168	1.9699	3.3014	1.4586	3.6268	-0.3962	0.0367	0.2215	0.2362	0.2573	-0.895	0.1617	0.7445	0.2479	0.3515	0.1061	0.0666	0.6453	-0.0448	0.4848	28.84	-5.2543	52.463
11	2.571	-0.9903	1.1756	1.5177	-0.6913	3.1764	-0.1821	-0.4706	0.3924	-0.2058	-0.0205	-0.3074	0.0699	-0.2336	0.2213	0.3617	-0.0012	0.0157	0.465	-0.0555	0.4565	23.5337	0.6097	54.4104
12	4.62	0.2521	4.1951	2.4318	1.6855	8.3291	-0.126	0.2536	0.9537	-0.7459	-0.3016	0.2845	-0.8782	-0.7689	0.1037	0.5502	0.1111	-0.0999	0.4963	0.0821	0.5384	11.5641	6.0355	47.6901
13	5.1536	0.3137	1.5926	2.9586	0.2987	4.9937	-0.2953	0.8975	0.2575	-0.1847	0.1227	-0.686	-0.4664	1.7893	0.1009	0.4891	-0.0424	0.1014	0.6789	0.0408	0.4952	30.3747	-3.3076	49.6661
14	4.5647	-0.6798	-0.4181	2.3684	-0.7409	3.0958	-0.3618	-0.0162	-0.2841	-0.1928	0.3294	0.3574	0.2062	-0.2627	-0.0154	0.3796	0.0289	-0.0212	0.4265	-0.0021	0.3833	9.4714	-5.4883	50.0375
15	4.6578	-2.0899	1.7653	1.3281	0.3342	4.1367	0.4134	0.2428	-1.004	-0.6369	-0.3624	0.0167	0.8014	0.1448	-0.0505	0.5844	-0.0568	0.0379	0.659	0.0029	0.4107	18.0227	-13.673	41.6145
16	4.2101	-0.7402	0.8164	0.4725	0.0296	0.6312	-0.0898	-0.4904	0.0385	0.0457	0.1272	0.0721	-0.0168	0.0143	-0.0659	0.3952	-0.0127	0.0183	0.465	0.1563	0.4629	-7.7236	0.4774	69.824

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 310 through 400 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1163 through 1182 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1183 through 1203 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1204 through 1225 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1226 through 1258 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1259 through 1279 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1280 through 1313 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1164 through 1182 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1183 through 1203 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1204 through 1225 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1226 through 1247 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1248 through 1259 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1260 through 1279 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 1280 through 1299 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 1300 through 1313 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 309 through 401 )

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