PDB-4cmz: An intertwined homodimer of the PDZ homology domain of periaxin

ID or keywords:

Entry

Database: PDB / ID: 4cmz

Title

An intertwined homodimer of the PDZ homology domain of periaxin

Components

PERIAXIN

Keywords

CELL CYCLE / DOMAIN SWAPPING / INTERTWINING

Function / homology

Function and homology information

axon ensheathment / EGR2 and SOX10-mediated initiation of Schwann cell myelination /

peripheral nervous system myelin maintenance /

regulation of RNA splicing /

T-tubule /

cell junction /

nucleus /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 2.7 Å

Authors

Han, H. / Kursula, P.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Periaxin and Ahnak Nucleoprotein 2 Form Intertwined Homodimers Through Domain Swapping
Authors: Han, H. / Kursula, P.

History

Deposition	Jan 20, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 2, 2014	Provider: repository / Type: Initial release
Revision 1.1	Apr 9, 2014	Group: Database references
Revision 1.2	Aug 27, 2014	Group: Database references
Revision 1.3	Dec 17, 2014	Group: Data collection
Revision 1.4	Mar 7, 2018	Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status 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	4cmz.cif.gz	119.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4cmz.ent.gz	98 KB	Display	PDB format
PDBx/mmJSON format	4cmz.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/cm/4cmz ftp://data.pdbj.org/pub/pdb/validation_reports/cm/4cmz	HTTPS FTP

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Related structure data

Related structure data	4cn0C C: citing same article (ref.)
Similar structure data	1mqe-d 1mqw-d 6p7o-d 5n0g-d 2bbu-d 5dip-d 2cqo-d 5uqi-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1)

Deposited unit

A: PERIAXIN

B: PERIAXIN

C: PERIAXIN

30.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PERIAXIN

B: PERIAXIN

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

2

C: PERIAXIN

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

Unit cell

Length a, b, c (Å)	79.840, 79.840, 81.070
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	B-2001- HOH

#1: Protein	PERIAXIN Mass: 10045.292 Da / Num. of mol.: 3 / Fragment: PDZ DOMAIN, RESIDUES 14-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q9BXM0
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.48 Å³/Da / Density % sol: 50.31 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 30% PEG 2000 MME, 0.15 M KBR, pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.915
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.915 Å / Relative weight: 1
Reflection	Resolution: 2.7→40 Å / Num. obs: 15882 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / B_iso Wilson estimate: 79.68 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 21
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software

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

Refinement

Method to determine structure:

MIRAS
Starting model: NONE

Resolution: 2.7→39.92 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 29.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.241	744	4.7 %
R_work	0.2031	-	-
obs	0.2049	15882	99.87 %

Solvent computation

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

Displacement parameters

B_iso mean: 91.6 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→39.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2062	0	0	13	2075

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2124
X-RAY DIFFRACTION	f_angle_d	0.994	2869
X-RAY DIFFRACTION	f_dihedral_angle_d	12.844	810
X-RAY DIFFRACTION	f_chiral_restr	0.074	326
X-RAY DIFFRACTION	f_plane_restr	0.006	381

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 (%)
2.7003-2.9087	0.3966	160	0.3338	3040	X-RAY DIFFRACTION	100
2.9087-3.2013	0.3214	168	0.253	3007	X-RAY DIFFRACTION	100
3.2013-3.6643	0.2598	148	0.2176	3017	X-RAY DIFFRACTION	100
3.6643-4.6155	0.207	128	0.1833	3040	X-RAY DIFFRACTION	100
4.6155-39.9243	0.2131	140	0.185	3034	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	6.2521	-4.0653	-0.7005	8.1786	-1.6263	8.2038	-0.5372	-1.3843	-0.2886	1.0433	-0.0854	-1.1207	-0.8021	0.4286	0.7325	0.9484	-0.2441	-0.3095	0.803	-0.0523	0.5916	47.3067	16.123	33.0166
2	2.7987	-0.469	3.244	1.3843	0.6574	5.1202	0.7793	-0.6097	-1.0725	0.6145	0.2402	-1.6913	0.3259	0.9829	-0.7474	0.8435	0.1039	-0.2096	0.5507	-0.1823	0.7642	42.1568	6.6323	15.6972
3	4.7007	-0.1531	4.5089	0.1192	-0.2779	4.4767	0.2644	-1.4708	-1.245	3.0508	-0.3979	0.7524	2.027	-0.5449	-0.1476	1.5859	-0.2368	0.27	0.8006	0.0706	0.743	31.2686	7.7741	31.7164
4	4.3924	2.2692	3.5213	4.5394	0.1325	3.6713	0.8673	-0.9227	-1.9877	2.3915	-0.1836	0.4327	1.876	0.3846	-0.3397	1.0462	0.0764	-0.0563	0.4292	-0.0364	0.9788	36.5137	4.1818	30.4418
5	7.7343	6.3532	-6.8745	5.6006	-5.1709	6.7081	-0.8311	-0.0589	-1.9878	1.2501	-0.7006	-3.5214	1.0394	0.069	1.3566	0.8304	0.1543	-0.309	0.6759	-0.1762	1.2527	43.6355	-2.4868	20.3256
6	2.0011	-2.2844	3.2113	8.8639	-1.9456	4.536	-0.5512	-1.2326	-1.5034	1.5449	-0.2411	-0.4442	1.2812	0.0329	-0.0425	1.1541	0.177	-0.2288	0.5195	-0.0952	0.7077	45.446	5.4805	26.7922
7	3.9209	-0.9097	0.1798	6.0974	0.0818	5.5971	0.167	0.5688	-0.9963	0.0634	-0.1986	1.033	1.0189	-0.3006	-0.1437	0.6768	-0.1363	-0.04	0.3908	-0.1871	0.6251	30.7873	12.032	15.0985
8	8.9633	2.2762	-5.8307	7.3199	-2.4034	5.5648	-0.5845	1.0351	-1.0373	0.2766	-0.4475	0.959	-0.086	-1.6365	1.0825	0.8638	-0.063	0.347	0.5741	-0.2907	0.9115	23.9611	18.2943	22.638
9	6.8376	-1.3866	4.5514	1.8892	1.7521	7.4712	0.1675	1.2145	0.6869	0.3779	-0.9735	-0.14	-0.703	0.7318	0.071	0.7854	0.1645	-0.0112	0.4839	0.0421	0.5142	33.1057	29.2874	5.9956
10	2.9912	2.7379	1.2917	2.7319	1.2052	0.5594	-0.2699	1.2717	0.1496	-1.27	-0.6247	-0.474	0.0342	-0.5569	0.1859	0.9691	0.1106	0.1325	0.7466	0.0596	0.4533	37.0132	30.0908	4.2729
11	6.1352	3.4509	4.8749	6.0194	3.2897	3.9464	-0.161	-0.1761	1.2512	1.9311	0.5139	2.415	-0.16	-0.8821	-0.2572	0.487	0.014	0.2275	0.4595	0.0058	0.7178	25.8265	25.9917	21.6011
12	3.841	1.0152	2.6755	3.0303	-2.2947	5.3372	-0.0796	0.0931	-0.318	-1.5642	-0.4681	1.0614	0.1898	-1.0968	0.5926	0.6751	0.0018	-0.1568	0.6065	-0.2045	0.7336	26.3147	17.0615	5.278
13	0.8262	-1.5844	-1.3402	6.2222	4.5829	3.5894	1.4625	-1.7906	0.6148	2.3979	-2.1654	-0.5676	0.0477	-3.095	1.0446	1.2967	0.2683	-0.3367	1.7955	-0.3723	1.4292	15.8441	25.519	9.2758
14	0.3705	-1.5778	1.6789	6.7275	-7.152	7.6034	1.6001	-1.9952	3.0106	2.6968	1.2244	2.2503	-1.2985	-2.3374	-2.4811	1.2618	0.4742	0.2467	1.4951	-0.3041	1.1683	22.6252	30.1176	13.9439
15	5.3816	-0.204	0.9001	6.7767	-0.9251	5.8578	0.0362	-0.4045	-0.7394	0.4658	-0.1952	0.2488	0.7559	0.0254	0.1062	0.5789	-0.049	0.1049	0.2505	-0.0155	0.3929	34.3087	12.9114	21.6824
16	6.9788	1.4887	6.7293	8.7687	-0.4517	7.4872	0.1514	-2.5514	-0.3738	0.9459	-0.2422	0.806	2.0736	-0.5279	-0.0964	1.2243	-0.2146	-0.0132	1.0814	0.5621	0.8368	-8.9769	2.4563	16.5174
17	2.0381	-2.5176	1.0947	9.5526	-5.5662	3.3438	0.4991	0.7205	-0.5882	-1.3335	-1.1941	0.3992	1.6745	0.756	0.1308	0.6191	-0.1413	-0.1342	0.7927	0.1914	0.7145	-6.9069	6.579	1.1187
18	1.7023	1.9413	-0.7381	8.458	3.4738	5.8968	1.2585	-0.9883	1.2407	-0.9881	-0.2176	-0.4466	0.3779	0.0369	-1.1132	0.5355	-0.0896	-0.0476	0.6457	0.169	1.0239	-4.3733	17.1152	-2.0916
19	0.2468	0.1598	-0.0472	0.2697	-0.0877	0.0289	0.2921	-1.2955	1.0336	1.7761	-0.4645	-0.6977	-1.5156	1.8698	0.9467	0.9007	-0.2037	-0.2207	1.194	0.0643	1.1242	-1.1181	20.5565	9.4795
20	3.7372	-4.5653	3.1497	6.751	-4.7609	3.3654	-0.7662	-2.5282	0.5559	3.4849	-0.1792	-1.236	-0.4291	0.5964	0.9795	1.0796	0.223	-0.1965	1.3871	-0.0156	0.9398	5.9493	12.9057	17.7645
21	2.0009	-8.9555	7.9212	2.0006	-6.4113	5.6423	-0.4755	-1.1048	0.4613	3.405	2.1614	-0.2022	-1.3348	0.4454	0.6629	1.3708	0.2227	-0.0363	1.2932	0.314	0.972	-4.4743	18.7659	12.5253
22	3.9148	-4.0245	3.2937	4.3296	-4.547	9.9071	-0.3225	0.3384	0.9063	0.9483	0.388	-0.1482	-1.7432	0.9787	-0.2898	0.8723	-0.0964	-0.1731	1.2651	0.0641	0.9173	-9.0348	24.1845	2.2053
23	2.2449	-2.6292	0.1414	6.0589	-0.5336	0.0546	-0.6095	-0.5088	-0.3802	0.8788	0.5397	0.4389	-0.2164	0.4094	-0.5328	0.8036	0.0881	-0.6462	0.5585	0.2218	0.3724	-2.9061	10.4691	5.6909
24	3.8004	-2.6641	3.6477	3.3307	-4.0444	5.5993	0.2855	0.9204	0.7228	-0.7907	-0.9378	-0.392	-0.341	0.58	-1.2763	1.1115	0.0011	-0.6657	0.74	0.4283	1.0245	4.6851	13.7624	-11.8055
25	6.4906	-1.7995	-7.5768	0.4995	2.1006	8.8486	1.1134	0.4586	2.427	-0.5089	0.7455	-0.637	-2.5603	-0.1691	-0.5277	0.8401	-0.1292	-0.0941	0.6755	0.4441	1.6686	13.0933	16.4192	-5.4889
26	5.1615	1.0303	-3.6201	3.6119	-1.8416	2.9013	-1.2662	0.4169	0.4796	-1.3634	-0.3625	0.6675	-0.2911	0.7283	-0.2305	0.7767	-0.1814	-0.4759	0.6989	0.1742	0.8289	11.2768	1.9263	-4.7039

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 14 THROUGH 23 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 24 THROUGH 31 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 32 THROUGH 40 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 41 THROUGH 47 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 48 THROUGH 56 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 57 THROUGH 61 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 62 THROUGH 87 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 88 THROUGH 92 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 93 THROUGH 103 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 14 THROUGH 23 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 24 THROUGH 28 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 29 THROUGH 44 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 45 THROUGH 51 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 52 THROUGH 60 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 61 THROUGH 104 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 16 THROUGH 20 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 21 THROUGH 25 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 26 THROUGH 30 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 31 THROUGH 35 )
20	X-RAY DIFFRACTION	20	CHAIN 'C' AND (RESID 36 THROUGH 42 )
21	X-RAY DIFFRACTION	21	CHAIN 'C' AND (RESID 43 THROUGH 47 )
22	X-RAY DIFFRACTION	22	CHAIN 'C' AND (RESID 48 THROUGH 56 )
23	X-RAY DIFFRACTION	23	CHAIN 'C' AND (RESID 57 THROUGH 71 )
24	X-RAY DIFFRACTION	24	CHAIN 'C' AND (RESID 72 THROUGH 76 )
25	X-RAY DIFFRACTION	25	CHAIN 'C' AND (RESID 77 THROUGH 86 )
26	X-RAY DIFFRACTION	26	CHAIN 'C' AND (RESID 87 THROUGH 101 )

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