PDB-2wcp: CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2

ID or keywords:

Entry

Database: PDB / ID: 2wcp

Title

CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2

Components

CADHERIN-23

Keywords

CELL ADHESION / HEARING / DEAFNESS

Function / homology

Function and homology information

cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium ...
Similarity search - Function

Biological species

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.98 Å

Authors

Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P.

Citation

Journal: Neuron / Year: 2010
Title: Structural Determinants of Cadherin-23 Function in Hearing and Deafness.
Authors: Sotomayor, M. / Weihofen, W. / Gaudet, R. / Corey, D.P.

History

Deposition	Mar 13, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jun 6, 2012	Group: Other
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wcp.cif.gz	67.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2wcp.ent.gz	49.7 KB	Display	PDB format
PDBx/mmJSON format	2wcp.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2wcp_validation.pdf.gz	417.8 KB	Display	wwPDB validaton report
Full document	2wcp_full_validation.pdf.gz	418.8 KB	Display
Data in XML	2wcp_validation.xml.gz	6.9 KB	Display
Data in CIF	2wcp_validation.cif.gz	10.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wc/2wcp ftp://data.pdbj.org/pub/pdb/validation_reports/wc/2wcp	HTTPS FTP

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Related structure data

Related structure data	2wbxC 2wd0C 2whvC 1ff5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2whv-d 2wd0-1 6bwn-d 2wd0-2 5vh2-1 5vt8-3 4hlj-d 2gbo-d 3mvs-d 5czr-4 5apv-1 5vh2-2 5czr-3 6n22-d 5czr-2 4uy3-d 5wjm-d 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	#99 - Mar 2008 Cadherin similarity (8)

Deposited unit

A: CADHERIN-23

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	151.463, 151.463, 133.457
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-2052- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	CADHERIN-23 / OTOCADHERIN Mass: 23856.436 Da / Num. of mol.: 1 / Fragment: EC1-2, RESIDUES 24-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99PF4

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Non-polymers , 5 types, 271 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	N-TERMINAL METHIONINE IS A CLONING ARTIFACT. PROTEIN WAS CLONED WITH AN ADDITIONAL C-TERMINAL HIS- ...N-TERMINAL METHIONINE IS A CLONING ARTIFACT. PROTEIN WAS CLONED WITH AN ADDITIONAL C-TERMINAL HIS-TAG WHICH IS NOT SEEN IN ELECTRON DENSITY.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 6.14 Å³/Da / Density % sol: 80 % / Description: NONE
Crystal grow	pH: 8 / Details: 2.7M NACL,0.1M TRIS HCL,PH 8.0, 10% GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918
Detector	Type: ADSC CCD / Detector: CCD / Date: Oct 9, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.98→30 Å / Num. obs: 40718 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / R_merge(I) obs: 0.07 / Net I/σ(I): 13.2
Reflection shell	Resolution: 1.98→2.01 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0070	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FF5

1ff5

Resolution: 1.98→30 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.963 / SU B: 4.642 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.188	937	2.3 %	RANDOM
R_work	0.173	-	-	-
obs	0.176	39770	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 17.05 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1626	0	19	262	1907

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1773
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1158
X-RAY DIFFRACTION	r_angle_refined_deg	1.363	1.949	2448
X-RAY DIFFRACTION	r_angle_other_deg	0.828	3.001	2832
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.054	5	235
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.118	24.659	88
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.831	15	272
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.735	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	287
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2021
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	360
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.766	1.5	1091
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.349	2	1813
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.916	3	682
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.937	4.5	623
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.98→2.03 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.217	77	-
R_work	0.227	2857	-
obs	-	-	98.32 %

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	12.2274	-1.1123	2.1081	6.3478	-3.7674	3.4209	-0.0483	-0.2318	0.8316	0.3146	-0.1535	-0.3106	-0.2555	0.0051	0.2018	0.089	-0.0568	-0.0302	0.0611	-0.015	0.1571	25.563	94.328	41.053
2	2.8902	4.7878	2.798	9.6311	3.1824	3.992	0.5635	-0.6765	0.453	1.0215	-0.9195	0.7916	0.3889	-0.7633	0.356	0.1992	-0.1962	0.084	0.2576	-0.125	0.4025	11.455	81.569	39.916
3	3.0632	1.5984	-2.2786	3.6703	-2.2941	4.7357	0.0012	-0.0019	-0.0503	0.3564	0.1818	0.3838	0.0227	0.078	-0.183	0.0853	0.0041	0.0182	0.0458	0.0423	0.3698	2.073	65.211	31.527
4	1.4293	0.8244	0.3498	4.2956	0.1587	1.2551	0.0112	-0.1428	0.4102	0.2184	-0.1142	0.6036	-0.0603	-0.1393	0.103	0.0884	-0.0344	0.0298	0.1153	-0.0382	0.3803	8.539	81.754	33.613
5	2.2474	2.3333	0.3017	8.7	1.8902	1.2565	0.1643	-0.2149	-0.0428	0.1576	-0.1111	-0.2754	-0.0185	0.1329	-0.0532	0.0163	-0.0269	-0.0205	0.0592	0.0104	0.2438	16.521	73.69	31.999
6	2.4391	1.8897	-1.3919	3.0313	-0.9029	2.2357	-0.0159	-0.0343	-0.1989	0.0383	0.0218	-0.0444	0.1417	0.1648	-0.0059	0.0247	0.0034	-0.0219	0.0261	0.0001	0.2725	9.111	64.812	28.2
7	4.0065	4.7858	0.9421	10.2707	2.0981	0.4361	0.4301	-0.4406	-0.4943	0.8355	-0.4025	-0.1251	0.1469	-0.0504	-0.0275	0.1681	-0.126	-0.0479	0.1559	0.0225	0.291	11.507	64.275	37.817
8	6.4905	4.6881	1.7576	6.2883	-2.1439	10.2814	0.2002	0.15	-0.0769	-0.0613	-0.0681	-0.2658	-0.0183	0.3715	-0.1322	0.0404	0.0123	0.0205	0.0214	-0.0135	0.1143	22.58	83.651	33.637
9	1.8136	3.5542	-0.9908	7.4399	-1.6928	0.7754	0.1699	-0.1084	-0.1033	0.5212	-0.046	-0.1915	0.0636	0.0968	-0.1238	0.201	-0.0259	-0.0155	0.1265	0.0346	0.4502	4.902	59.3	36.159
10	1.8069	0.9943	-1.7478	9.2838	-3.7744	4.3359	-0.3256	0.0584	-0.2156	-0.8848	0.193	-0.545	0.569	-0.0612	0.1326	0.4362	-0.1476	-0.0127	0.0556	0.027	0.3771	-9.261	22.789	39.109
11	2.5242	4.9518	-0.6584	10.1815	-1.3266	0.2793	-0.0857	0.0985	0.4032	-0.1538	0.2717	0.6162	0.1518	-0.1142	-0.186	0.2163	-0.1083	-0.0603	0.0829	0.0524	0.3127	-9.183	42.235	36.201
12	3.7799	2.6308	-0.4276	9.6145	0.3704	7.61	-0.1541	0.5017	0.2407	-1.0692	0.4384	1.3066	0.8949	-0.9357	-0.2842	0.5101	-0.2815	-0.2282	0.2502	0.1508	0.5378	-18.44	28.391	33.321
13	6.2433	5.1273	0.5078	14.4971	2.198	1.6537	-0.1079	0.1475	0.1893	0.3096	0.1591	0.8915	0.3345	-0.1677	-0.0512	0.1954	-0.1038	-0.0402	0.0669	0.0642	0.1771	-18.166	23.82	39.788
14	1.3929	2.0456	-0.4494	10.7821	-1.6394	1.3726	-0.2046	0.4362	0.1896	-1.1605	0.2827	0.6894	0.4634	-0.3804	-0.0781	0.5158	-0.2041	-0.0924	0.2664	0.0786	0.3456	-13.413	30.664	30.299
15	0.9591	2.3417	-0.5482	15.7743	-1.9172	0.9361	-0.2387	0.1598	0.0056	-0.925	0.2813	0.0129	0.3393	-0.0974	-0.0425	0.2491	-0.0999	-0.0175	0.0617	0.0243	0.1123	-9.055	32.379	29.562
16	8.2313	12.1799	-2.9533	20.8085	-8.2913	11.1192	-0.6679	-0.2439	-1.6512	-1.6841	-0.4581	-1.9195	0.6157	1.5965	1.126	1.0126	-0.2586	-0.0129	0.4968	0.2975	0.8823	-12.123	7.539	37.82

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 4
2	X-RAY DIFFRACTION	2	A	5 - 14
3	X-RAY DIFFRACTION	2	A	401
4	X-RAY DIFFRACTION	3	A	15 - 30
5	X-RAY DIFFRACTION	4	A	31 - 36
6	X-RAY DIFFRACTION	5	A	37 - 56
7	X-RAY DIFFRACTION	6	A	57 - 75
8	X-RAY DIFFRACTION	7	A	76 - 84
9	X-RAY DIFFRACTION	8	A	85 - 89
10	X-RAY DIFFRACTION	9	A	90 - 110
11	X-RAY DIFFRACTION	9	A	402 - 403
12	X-RAY DIFFRACTION	9	A	501
13	X-RAY DIFFRACTION	10	A	111 - 133
14	X-RAY DIFFRACTION	11	A	134 - 149
15	X-RAY DIFFRACTION	12	A	150 - 161
16	X-RAY DIFFRACTION	13	A	162 - 172
17	X-RAY DIFFRACTION	14	A	173 - 192
18	X-RAY DIFFRACTION	15	A	193 - 203
19	X-RAY DIFFRACTION	16	A	204 - 208

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