PDB-6kkg: Crystal structure of MAGI2-Dendrin complex

ID or keywords:

Entry

Database: PDB / ID: 6kkg

Title

Crystal structure of MAGI2-Dendrin complex

Components

Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
Peptide from Dendrin

Keywords

CELL ADHESION / MAGI2 /

Dendrin / Complex structure /

Slit diaphragm

Function / homology

Function and homology information

structural constituent of postsynaptic specialization /

extrinsic component of postsynaptic membrane / type II activin receptor binding / neuroligin clustering involved in postsynaptic membrane assembly / podocyte development /

slit diaphragm / positive regulation of synaptic vesicle clustering /

beta-1 adrenergic receptor binding / structural constituent of postsynaptic density / nerve growth factor signaling pathway ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Zhu, J.W. / Zhang, H.J. / Lin, L. / Zhang, R.G.

Citation

Journal: To Be Published
Title: Phase separation of MAGI2-mediated complex underlies formation of slit diaphragm complex in glomerular filtration barrier
Authors: Zhang, H.J. / Lin, L. / Lin, Z.J. / Liu, J.P. / Pan, L.F. / Zhang, M.J. / Zhu, J.W. / Zhang, R.G.

History

Deposition	Jul 25, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 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	6kkg.cif.gz	109.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6kkg.ent.gz	83.9 KB	Display	PDB format
PDBx/mmJSON format	6kkg.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/kk/6kkg ftp://data.pdbj.org/pub/pdb/validation_reports/kk/6kkg	HTTPS FTP

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Related structure data

Related structure data	2ysdS 2yseS S: Starting model for refinement
Similar structure data	3sd4-d 4uz3-1 5xx2-d 3g1g-d 4ii1-1 5zrz-d 1wk2-2 5y4b-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	#245 - May 2020 Spliceosomes similarity (6)

Deposited unit

A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2

B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2

C: Peptide from Dendrin

D: Peptide from Dendrin

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

1

A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2

C: Peptide from Dendrin

defined by author&software
Evidence: gel filtration
14.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2

D: Peptide from Dendrin

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

Unit cell

Length a, b, c (Å)	55.715, 55.715, 74.696
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 / / Activin receptor-interacting protein 1 / Acvrip1 / Atrophin-1-interacting protein 1 / AIP-1 / ...Activin receptor-interacting protein 1 / Acvrip1 / Atrophin-1-interacting protein 1 / AIP-1 / Membrane-associated guanylate kinase inverted 2 / MAGI-2 Mass: 11812.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Magi2, Acvrinp1, Aip1, Arip1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WVQ1
#2: Protein/peptide	Peptide from Dendrin / Mass: 2507.735 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ddn, Gm748, Kiaa0749 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80TS7
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.34 Å³/Da / Density % sol: 47.47 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 2.2M Ammonium Sulfate, 150mM Malate at pH 5.1, 4.0% v/v 1,2-Propanedio

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.91877 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 24, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.91877 Å / Relative weight: 1

Reflection

Resolution: 2.15→50 Å / Num. obs: 13900 / % possible obs: 98.6 % / Redundancy: 4.2 % / R_merge(I) obs: 0.082 / R_pim(I) all: 0.047 / R_rim(I) all: 0.095 / Χ²: 0.91 / Net I/σ(I): 7.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.15-2.19	4	0.455	684	0.856	0.265	0.528	0.887	100
2.19-2.23	4.4	0.429	720	0.88	0.232	0.488	0.859	100
2.23-2.27	4.4	0.34	713	0.93	0.184	0.388	0.897	100
2.27-2.32	4.4	0.32	701	0.949	0.174	0.365	0.847	100
2.32-2.37	4.4	0.298	682	0.926	0.162	0.34	0.935	100
2.37-2.42	4.3	0.268	731	0.937	0.147	0.307	0.887	99.9
2.42-2.48	4.2	0.224	705	0.966	0.124	0.257	0.951	100
2.48-2.55	4.2	0.206	706	0.962	0.115	0.237	0.944	100
2.55-2.62	3.9	0.181	681	0.969	0.105	0.209	1.046	100
2.62-2.71	4.1	0.151	710	0.978	0.085	0.173	0.939	100
2.71-2.81	4.5	0.146	716	0.98	0.078	0.166	0.993	100
2.81-2.92	4.4	0.114	708	0.982	0.062	0.13	0.928	100
2.92-3.05	4.4	0.101	707	0.985	0.054	0.115	0.962	99.6
3.05-3.21	4.2	0.083	689	0.988	0.046	0.095	0.923	99.6
3.21-3.41	3.9	0.07	676	0.987	0.042	0.082	0.92	97.8
3.41-3.68	4	0.07	704	0.987	0.041	0.081	0.913	96.8
3.68-4.05	4	0.063	667	0.988	0.037	0.074	0.84	93.8
4.05-4.63	3.9	0.062	639	0.988	0.037	0.072	0.781	90.9
4.63-5.83	3.8	0.065	656	0.989	0.039	0.077	0.824	94
5.83-50	4.2	0.071	705	0.988	0.039	0.082	0.885	99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.25	data extraction
DENZO		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2YSD, 2YSE

2ysd

2yse

Resolution: 2.15→24.125 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 28.86

	R_factor	Num. reflection	% reflection
R_free	0.2635	668	5.05 %
R_work	0.2017	-	-
obs	0.2049	13218	93.51 %

Solvent computation

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

Displacement parameters

B_iso max: 75.73 Å² / B_iso mean: 31.5 Å² / B_iso min: 12.84 Å²

Refinement step

Cycle: final / Resolution: 2.15→24.125 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1730	0	0	190	1920
B_iso mean	-	-	-	34.15	-
Num. residues	-	-	-	-	214

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1792
X-RAY DIFFRACTION	f_angle_d	1.18	2457
X-RAY DIFFRACTION	f_chiral_restr	0.041	246
X-RAY DIFFRACTION	f_plane_restr	0.006	329
X-RAY DIFFRACTION	f_dihedral_angle_d	13.362	667

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.15-2.3141	0.2768	123	0.2218	2111	79
2.3141-2.5467	0.2929	130	0.2234	2589	97
2.5467-2.9147	0.318	146	0.2298	2697	100
2.9147-3.6701	0.2726	130	0.193	2625	98
3.6701-24.125	0.2197	139	0.1824	2528	94

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	1.9824	0.7309	0.6361	1.7733	-0.3224	4.4925	-0.2626	-0.2898	0.7513	-0.1946	0.2635	1.6323	-0.7159	-0.0945	-0.1776	0.4281	0.0122	-0.1265	0.5683	-0.2268	1.1755	-26.1895	33.8443	6.8271
2	1.3543	-0.9941	1.5802	0.8698	-1.5337	2.8613	-0.2202	-0.2523	0.5689	0.7456	-0.3451	0.3449	-0.1455	-0.4484	-0.1605	0.3377	-0.0713	0.119	0.1616	-0.39	0.6317	-19.7423	30.052	12.1879
3	6.9589	3.0894	1.1459	3.1558	0.4975	2.6069	-0.1839	-0.1104	0.0214	0.4816	-0.3546	0.176	0.456	-0.5178	0.2464	0.3489	-0.092	0.2202	0.2522	-0.1336	0.3176	-17.1255	25.8069	11.2158
4	0.2723	-0.6562	0.9854	2.0363	-2.7597	3.9176	-0.3335	0.0143	-0.1538	0.4575	-0.2039	0.1002	-0.1844	-0.199	0.0446	0.1455	-0.0563	0.0654	0.2539	-0.0671	0.2897	-15.6724	25.9093	5.5209
5	2.2533	0.0113	-4.0909	-0.0113	-0.0203	7.3329	0.1079	0.8031	0.5505	-0.1172	-0.1344	0.1535	-0.8026	-0.4022	-0.0162	0.1853	0.0235	0.0123	0.3943	0.0397	0.4254	-16.2557	32.7666	-5.0601
6	4.0599	0.8018	2.4102	5.5404	0.0867	6.1245	-0.1117	-0.4668	0.8716	-0.2337	0.0217	-0.1564	-1.2287	-0.0784	0.2432	0.2742	-0.051	-0.0173	0.2951	-0.0096	0.3275	-6.5147	31.3099	-11.5377
7	4.9224	-0.9073	2.3129	3.6749	-0.5902	5.2647	-0.4074	-0.5867	0.6922	0.6829	0.0695	-0.7618	-0.5188	0.537	0.1145	0.3406	-0.1005	-0.0665	0.311	-0.0144	0.3651	-0.4915	27.1985	-0.2611
8	5.5363	3.0021	2.4773	3.5947	3.0039	5.8054	0.0384	-0.7961	-1.1444	0.5115	-0.2478	-1.0119	0.7702	0.3531	-0.4204	0.2728	-0.0831	-0.1589	0.3495	0.0685	0.3518	2.2276	23.2974	0.5958
9	4.504	-0.9527	-3.4746	1.1789	0.3581	3.1948	-0.5503	0.5893	-0.8439	0.0488	-0.3878	0.1833	0.3882	-0.4925	0.3799	0.2016	-0.0747	0.0578	0.2807	-0.069	0.1575	-5.1887	20.6679	-3.917
10	9.7359	-1.5713	-1.369	8.4004	-0.7855	8.4899	0.0656	1.3547	0.1407	-0.3877	-0.2589	-0.1722	0.5466	-0.0431	0.2794	0.1503	-0.0159	-0.0489	0.3168	-0.0229	0.2829	-1.0634	23.3917	-16.7794
11	7.8341	0.5858	-2.485	4.3627	0.5581	3.4709	0.2755	0.1567	1.4404	1.0988	-0.2157	-0.0963	-0.8201	-0.3103	0.0025	0.6029	0.0903	-0.1636	0.2738	0.0376	0.7517	-16.3112	39.6975	-24.2699
12	4.8999	1.619	0.4207	3.031	0.3615	4.5498	-0.2347	0.8303	0.0552	-0.3942	-0.4695	-0.6847	-0.1171	0.2859	-1.2839	0.1816	0.0292	-0.15	0.4444	0.2077	0.3726	-17.6567	27.2041	-31.6137
13	3.6212	2.6621	1.8232	3.2621	1.7572	4.9334	-0.2407	0.1174	0.6774	-0.0743	-0.7049	-0.09	-0.7636	0.3133	-0.7974	0.1521	-0.0899	0.0044	0.288	0.3452	0.248	-12.3181	29.2702	-24.9395
14	4.2257	2.6199	-5.9707	5.1345	-3.513	8.4049	0.4864	0.5053	0.1286	0.8403	0.2519	0.9259	-1.2156	-1.4859	-0.6077	0.3295	-0.0301	0.1035	0.2868	-0.0295	0.5012	-20.2569	30.5926	-12.4682
15	4.4434	-1.5834	0.007	4.0834	3.6291	6.9436	-0.1525	-0.0084	0.1077	-0.4692	-0.2211	0.8313	-0.2019	-0.3362	0.4317	0.2526	-0.0256	-0.052	0.2364	-0.0126	0.2761	-23.6312	18.5808	-10.2142
16	4.0505	-0.8731	-1.8427	4.1554	-2.8988	3.4993	-0	0.3415	-0.1413	-0.2767	-0.2656	0.2201	0.3272	0.4984	0.2302	0.1826	-0.0715	-0.0334	0.3051	-0.0155	0.1538	-17.9611	12.6175	-15.648
17	2.4103	0.8984	-1.3085	3.2893	2.7016	9.2983	0.0503	-0.4243	0.1057	1.0939	-0.6909	0.0032	0.6611	0.5053	-0.4385	0.3661	-0.1521	-0.0439	0.2077	-0.1347	0.2238	-19.7378	12.5695	-0.2056
18	8.3286	-1.9922	-5.0381	7.4371	1.4569	3.0617	-0.0198	0.2143	-0.2416	-0.5519	-0.1416	-1.3886	1.0227	0.6703	0.1855	0.3284	0.0133	0.1001	0.3633	0.0259	0.4264	2.3266	15.6058	0.9143
19	6.6235	-3.0896	-3.5022	8.672	2.1512	6.8601	-0.4023	0.4092	-0.2302	0.568	0.149	-0.0357	0.1154	-0.272	0.2528	0.1713	-0.0363	0.0462	0.136	-0.0135	0.2026	-9.8208	20.4333	7.6187
20	4.0873	1.6586	2.9459	4.3612	0.9973	2.1307	0.1574	-1.0901	-0.4479	1.7821	-0.7173	0.6544	0.561	-0.6019	-0.0512	0.5794	-0.1492	0.2645	0.3289	-0.0383	0.5943	-20.1068	17.9679	14.5294
21	5.4309	3.623	2.0785	2.5872	2.1076	3.8903	0.1825	-0.5441	0.5471	0.0285	-0.7391	0.6537	-0.2382	-1.1418	-0.0649	0.5038	-0.1432	0.3225	0.4148	-0.402	0.4136	-18.1999	28.8079	18.67
22	2.2711	-0.9676	0.34	4.1575	-3.9801	4.073	-0.1431	-0.1069	-0.7545	0.5204	0.3227	0.8091	0.8093	-0.4497	-0.1224	0.3902	0.0329	0.1077	0.3532	0.1043	0.3711	-14.6344	5.8028	-18.3126
23	1.7865	-1.0938	2.1726	3.7655	-1.79	2.7081	0.0572	0.1152	-0.0176	0.1127	-0.2709	-0.2841	0.1542	0.1202	0.0501	0.1328	0.053	0.0168	0.2643	0.0554	0.1737	-12.7894	18.7612	-25.118
24	7.3847	4.0996	-1.8283	5.9447	-4.2992	3.3958	-0.2069	1.6525	0.2016	-1.1111	-0.2845	-0.32	0.1863	0.5985	-0.3777	0.2864	0.0329	-0.0158	0.7376	0.2898	0.4401	-5.5282	26.3654	-32.1004
25	5.3451	3.5712	5.916	2.4	3.97	6.5684	-0.4775	0.0393	0.6998	0.1725	-0.5531	0.1353	-0.5898	0.4143	0.5486	0.3701	-0.0203	-0.0035	0.4444	0.1701	0.4267	-15.8086	30.1813	-36.195

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 301 through 306 )	A	301 - 306
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 307 through 311 )	A	307 - 311
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 312 through 325 )	A	312 - 325
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 326 through 331 )	A	326 - 331
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 332 through 340 )	A	332 - 340
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 341 through 352 )	A	341 - 352
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 353 through 358 )	A	353 - 358
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 359 through 367 )	A	359 - 367
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 368 through 377 )	A	368 - 377
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 378 through 387 )	A	378 - 387
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 301 through 306 )	B	301 - 306
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 307 through 316 )	B	307 - 316
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 317 through 331 )	B	317 - 331
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 332 through 340 )	B	332 - 340
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 341 through 358 )	B	341 - 358
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 359 through 377 )	B	359 - 377
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 378 through 387 )	B	378 - 387
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 222 through 226 )	C	222 - 226
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 227 through 231 )	C	227 - 231
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 232 through 236 )	C	232 - 236
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 237 through 241 )	C	237 - 241
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 222 through 226 )	D	222 - 226
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 227 through 231 )	D	227 - 231
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 232 through 236 )	D	232 - 236
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 237 through 241 )	D	237 - 241

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-Basic information

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-Download

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi