PDB-5f67: An exquisitely specific PDZ/target recognition revealed by the st...

ID or keywords:

Entry

Database: PDB / ID: 5f67

Title

An exquisitely specific PDZ/target recognition revealed by the structure of INAD PDZ3 in complex with TRP channel tail

Components

Inactivation-no-after-potential D protein
TRP C terminal Tail

Keywords

PROTEIN BINDING / INAD / TRP / PDZ / atypical

Function / homology

Function and homology information

rhabdomere microvillus membrane / : / Ion homeostasis / TRP channels / myosin III binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / detection of light stimulus involved in sensory perception / inaD signaling complex / light-activated monoatomic ion channel activity / cellular response to anoxia ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Ye, F. / Shang, Y. / Liu, W. / Zhang, M.

Citation

Journal: Structure / Year: 2016
Title: An Exquisitely Specific PDZ/Target Recognition Revealed by the Structure of INAD PDZ3 in Complex with TRP Channel Tail
Authors: Ye, F. / Liu, W. / Shang, Y. / Zhang, M.

History

Deposition	Dec 5, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 24, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5f67.cif.gz	106.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5f67.ent.gz	82 KB	Display	PDB format
PDBx/mmJSON format	5f67.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5f67_validation.pdf.gz	422.4 KB	Display	wwPDB validaton report
Full document	5f67_full_validation.pdf.gz	422.3 KB	Display
Data in XML	5f67_validation.xml.gz	13.3 KB	Display
Data in CIF	5f67_validation.cif.gz	19.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f6/5f67 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/5f67	HTTPS FTP

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Related structure data

Related structure data	3diwS S: Starting model for refinement
Similar structure data	4ud7-2 6mjt-2 2iqj-2 3cgy-3 1jzh-d 3uge-2 1xau-d 4hlb-d 3c0d-7 1nz6-1 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	#174 - Jun 2014 GFP-like Proteins similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (2) #250 - Oct 2020 Capsaicin Receptor TRPV1 similarity (1)

Deposited unit

A: Inactivation-no-after-potential D protein

C: TRP C terminal Tail

B: Inactivation-no-after-potential D protein

D: TRP C terminal Tail

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

1

A: Inactivation-no-after-potential D protein

C: TRP C terminal Tail

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

2

B: Inactivation-no-after-potential D protein

D: TRP C terminal Tail

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

Unit cell

Length a, b, c (Å)	57.420, 30.126, 61.454
Angle α, β, γ (deg.)	90.00, 90.50, 90.00
Int Tables number	3
Space group name H-M	P121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND (RESSEQ 351:447 )
2	1	1	CHAIN B AND (RESSEQ 351:447 )
1	1	2	CHAIN C AND (RESSEQ 1257:1275 )
2	1	2	CHAIN D AND (RESSEQ 1257:1275 )

NCS ensembles :

ID
1
2

#1: Protein	Inactivation-no-after-potential D protein / INAD Mass: 11676.411 Da / Num. of mol.: 2 / Fragment: PDZ 3 domain, residues 345-448 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: inaD, CG3504 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24008
#2: Protein/peptide	TRP C terminal Tail Mass: 1950.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P19334*PLUS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 36.93 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 2%(v/v) Polyethylene glycol 400, 0.1 M Imidazole pH 7.0, 24%(w/v) Polyethylene glycol monomethyl ether 5000 PH range: 6.5-7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 10, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97923 Å / Relative weight: 1
Reflection	Resolution: 1.76→50 Å / Num. all: 21237 / Num. obs: 21025 / % possible obs: 99 % / Redundancy: 3.1 % / R_merge(I) obs: 0.056 / Net I/σ(I): 34.9
Reflection shell	Resolution: 1.76→1.79 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.19 / Mean I/σ(I) obs: 9.5 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.7.3_928	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3DIW

3diw

Resolution: 1.76→41.77 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.188	1081	5.14 %
R_work	0.156	-	-
obs	0.158	21022	98.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.05 Å² / k_sol: 0.37 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.4711 Å²	0 Å²	-2.0733 Å²
2-	-	12.552 Å²	0 Å²
3-	-	-	-6.0809 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→41.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1727	0	0	266	1993

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1747
X-RAY DIFFRACTION	f_angle_d	1.116	2353
X-RAY DIFFRACTION	f_dihedral_angle_d	11.42	627
X-RAY DIFFRACTION	f_chiral_restr	0.092	279
X-RAY DIFFRACTION	f_plane_restr	0.005	299

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	731	X-RAY DIFFRACTION	POSITIONAL
1	2	B	731	X-RAY DIFFRACTION	POSITIONAL	0.041
2	1	C	130	X-RAY DIFFRACTION	POSITIONAL
2	2	D	130	X-RAY DIFFRACTION	POSITIONAL	0.015

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 (%)
1.7597-1.8398	0.2773	128	0.2058	2399	X-RAY DIFFRACTION	97
1.8398-1.9368	0.2113	138	0.1624	2482	X-RAY DIFFRACTION	100
1.9368-2.0581	0.2111	121	0.1475	2518	X-RAY DIFFRACTION	100
2.0581-2.217	0.1827	156	0.1441	2474	X-RAY DIFFRACTION	100
2.217-2.4401	0.1791	130	0.1472	2510	X-RAY DIFFRACTION	100
2.4401-2.7931	0.2001	139	0.1605	2524	X-RAY DIFFRACTION	100
2.7931-3.5187	0.1498	123	0.1529	2520	X-RAY DIFFRACTION	99
3.5187-41.7826	0.1893	146	0.1569	2514	X-RAY DIFFRACTION	95

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	0.0161	-0.0106	0.0051	0.018	0.0014	0.008	0.0391	-0.1155	0.2653	0.1497	-0.0639	-0.0999	-0.2159	-0.2636	0.0001	0.161	0.0295	-0.0072	0.1677	0.0068	0.1586	20.0072	9.6829	35.2153
2	0.0847	-0.0255	0.0467	0.0102	-0.032	0.1054	-0.02	-0.0134	-0.0316	0.0182	0.0166	-0.0365	0.1147	0.1352	0.005	0.1114	-0.0157	0.0178	0.1153	0.0099	0.1005	25.8079	1.297	22.9593
3	0.0456	0.0135	0.0346	0.0849	-0.0145	0.0335	0.0561	0.144	-0.0798	0.0758	0.0144	0.0569	0.1262	-0.2486	0.0006	0.1374	-0.0233	0.0125	0.1364	0.0099	0.1285	11.4728	-0.2585	20.8989
4	0.2978	0.1538	0.0365	0.0821	0.0019	0.1661	0.0506	-0.084	-0.2635	-0.0238	-0.0221	-0.0144	0.2463	0.054	0.0641	0.1523	0.0426	0.0105	0.0989	-0.0016	0.1838	24.4074	-6.1931	18.3749
5	0.0466	0.0116	-0.0242	0.046	0.0012	0.0302	-0.0681	-0.0374	0.0176	0.0006	-0.0759	0.0218	-0.0687	-0.0965	-0.0027	0.1204	-0.0166	0.0054	0.1178	0.0261	0.1299	17.5593	4.9694	25.3932
6	0.0072	-0.0136	0.0035	0.0298	-0.0163	0.021	0.0613	-0.0487	0.0911	-0.0176	-0.0554	-0.0679	-0.1101	-0.2285	0.0001	0.1506	-0.0029	-0.0067	0.171	0.0038	0.114	16.6944	11.3017	24.6736
7	0.0248	0.0118	0.0192	0.0217	0.0671	0.2255	0.072	0.0551	0.1973	-0.1242	-0.1174	0.0147	-0.107	-0.0927	-0.0829	0.1308	-0.0002	0.0143	0.0799	0.0243	0.1851	17.4445	10.2557	14.962
8	0.1281	-0.0828	0.0284	0.0988	0.0025	0.0877	0.061	-0.008	0.1612	-0.0193	-0.0153	0.0575	0.0342	0.0495	0.0545	0.0841	-0.0051	0.0177	0.1382	0.014	0.0945	22.9728	2.642	24.2368
9	0.4479	-0.3072	0.0924	0.2363	-0.0785	0.028	0.1342	0.0894	-0.0054	-0.1732	0.127	-0.0066	0.0374	-0.0709	0.0552	0.2514	-0.0468	0.0461	0.527	-0.0558	0.1863	27.4611	-2.2949	3.2075
10	0.0185	-0.0014	-0.0091	0.0006	0.0033	0.0177	-0.0775	0.0107	-0.0111	-0.0306	-0.0575	-0.0318	0.0339	-0.0236	-0.0005	0.2242	0.0038	0.0213	0.1259	-0.0349	0.1769	19.7144	-10.2117	10.8595
11	1.0973	-0.4018	0.0988	0.147	-0.036	0.0091	-0.0504	0.1217	0.2149	-0.0538	0.0541	-0.0146	0.0791	-0.016	-0.0283	0.145	-0.0179	-0.01	0.1551	-0.0377	0.0787	19.7057	-4.9477	7.6617
12	0.0174	0.0006	-0.0148	0.0118	-0.0062	0.0149	0.0136	0.1132	-0.1593	-0.0743	-0.0083	-0.0557	0.1733	-0.2011	-0	0.1688	-0.0234	-0.009	0.182	0.0131	0.1558	-8.4235	-0.1453	-4.4996
13	0.1348	-0.0159	-0.0746	0.0287	-0.0091	0.1045	-0.0549	-0.0072	0.0465	-0.0229	0.0729	-0.0154	-0.191	0.0668	0.0155	0.1238	0.014	-0.0074	0.1279	0.0091	0.0992	-2.7921	8.2587	7.7796
14	0.0884	-0.0306	-0.016	0.0408	-0.0471	0.1288	0.047	-0.1585	0.0857	-0.0348	0.0333	0.0835	-0.0704	-0.2231	0.0113	0.1261	0.0203	-0.0094	0.1201	0.0156	0.1474	-17.1604	9.7932	9.7347
15	0.0883	-0.0079	-0.0254	0.0354	-0.0056	0.08	-0.0485	0.044	0.1957	-0.0041	-0.0028	-0.041	-0.2374	0.1013	0.0019	0.1606	-0.0335	-0.015	0.1015	0.0137	0.1873	-4.2619	15.7499	12.3583
16	0.0691	0.0284	-0.0333	0.025	0.021	0.1036	-0.0399	0.1384	0.026	0.0353	-0.0046	-0.064	0.0495	-0.2422	-0.0003	0.1242	0.0057	-0.001	0.1315	0.0093	0.1162	-11.5893	0.3937	5.7773
17	0.0208	-0.0165	-0.0262	0.0252	0.0596	0.156	0.009	-0.0614	-0.1795	0.0256	-0.0452	0.0111	0.0483	-0.0993	-0.1095	0.1352	-0.0049	-0.0015	0.0756	0.0283	0.1667	-11.2359	-0.6982	15.7487
18	0.0413	0.0474	0.0017	0.0537	0.0018	-0.0002	0.0483	-0.0209	-0.1562	0.0024	-0.0054	0.0291	-0.0163	0.1018	0.0013	0.0966	0.0033	-0.0139	0.1235	0.0176	0.1079	-5.0117	6.1929	6.936
19	0.1265	-0.0214	-0.0052	0.0464	0.0044	0.0023	0.0326	-0.0761	0.02	0.0423	0.0229	-0.0212	-0.0327	-0.0124	0.0207	0.2971	0.0402	-0.0671	0.5459	-0.0673	0.1806	-1.3179	11.8518	27.5085
20	0.0088	0.0002	0.0078	0.0004	0.0025	0.0192	-0.0773	0.033	0.0281	-0.0501	-0.0067	0.0044	0.0212	-0.0176	-0.0003	0.2209	0.0212	-0.0362	0.1782	-0.0192	0.1554	-9.0341	19.78	19.8376
21	0.4858	0.3285	0.1118	0.2545	0.0766	0.026	-0.1172	-0.065	-0.1652	0.1623	0.1634	-0.0758	0.0469	-0.0548	0.0083	0.1462	0.0418	0.0382	0.1782	-0.0412	0.0952	-9.0618	14.5255	23.0529

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESSEQ 351:360)
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESSEQ 361:376)
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESSEQ 377:396)
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESSEQ 397:411)
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESSEQ 412:416)
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESSEQ 417:425)
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESSEQ 426:435)
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESSEQ 436:448)
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESSEQ 1257:1261)
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESSEQ 1262:1266)
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESSEQ 1267:1275)
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESSEQ 351:360)
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESSEQ 361:376)
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESSEQ 377:396)
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESSEQ 397:411)
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESSEQ 412:425)
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESSEQ 426:435)
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESSEQ 436:447)
19	X-RAY DIFFRACTION	19	CHAIN 'D' AND (RESSEQ 1257:1261)
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESSEQ 1262:1266)
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESSEQ 1267:1275)

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