PDB-2whv: CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 (ALL CATION BINDING ...

ID or keywords:

Entry

Database: PDB / ID: 2whv

Title

CRYSTAL STRUCTURE OF MOUSE CADHERIN-23 EC1-2 (ALL CATION BINDING SITES OCCUPIED BY CALCIUM)

Components

CADHERIN-23

Keywords

CELL ADHESION / HEARING / DEAFNESS

Function / homology

Function and homology information

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

Biological species

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.36 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	May 7, 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	Jul 5, 2017	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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	2whv.cif.gz	64.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2whv.ent.gz	47.1 KB	Display	PDB format
PDBx/mmJSON format	2whv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2whv_validation.pdf.gz	431.9 KB	Display	wwPDB validaton report
Full document	2whv_full_validation.pdf.gz	432.4 KB	Display
Data in XML	2whv_validation.xml.gz	11.9 KB	Display
Data in CIF	2whv_validation.cif.gz	17.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wh/2whv ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2whv	HTTPS FTP

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Related structure data

Related structure data	2wbxC 2wcpSC 2wd0C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2wcp-d 2wd0-1 2wd0-2 4hlj-d 6bwn-d 5czr-2 5czr-1 5vh2-1 2gbo-d 5czr-3 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 (7)

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)	151.290, 151.290, 136.881
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

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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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99PF4

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Non-polymers , 5 types, 197 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#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.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 187 / 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: 6.28 Å³/Da / Density % sol: 80.43 % / Description: NONE
Crystal grow	pH: 6.5 Details: 0.1 M MES PH 6.5, 1.1 M CALCIUM CHLORIDE DIHYDRATE, 0.15 M POTASSIUM CHLORIDE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 3, 2009 / Details: MIRRORS
Radiation	Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.36→22.25 Å / Num. obs: 24907 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6 % / R_merge(I) obs: 0.09 / Net I/σ(I): 17.65
Reflection shell	Resolution: 2.36→2.4 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / % possible all: 97.1

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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 2WCP

2wcp

Resolution: 2.36→22.25 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.938 / SU B: 8.801 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL CADHERIN CATION BINDING SITES ARE OCCUPIED BY CALCIUM

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22139	1268	5.1 %	RANDOM
R_work	0.1996	-	-	-
obs	0.20072	23640	99.76 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.743 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.56 Å²	-0.28 Å²	0 Å²
2-	-	-0.56 Å²	0 Å²
3-	-	-	0.83 Å²

Refinement step

Cycle: LAST / Resolution: 2.36→22.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1626	0	15	187	1828

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	1707
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1113
X-RAY DIFFRACTION	r_angle_refined_deg	1.143	1.95	2342
X-RAY DIFFRACTION	r_angle_other_deg	0.793	3.001	2717
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.089	5	215
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.444	24.824	85
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.091	15	259
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.929	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	271
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	1929
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	343
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	0.508	1.5	1058
X-RAY DIFFRACTION	r_mcbond_other	0.099	1.5	416
X-RAY DIFFRACTION	r_mcangle_it	0.964	2	1743
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.401	3	649
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.336	4.5	596
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: 2.356→2.416 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.337	82	-
R_work	0.326	1674	-
obs	-	-	97.77 %

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	3.0873	5.5955	0.392	10.1503	0.4783	6.337	-0.1107	-0.0949	0.4907	-0.1879	-0.1457	0.8839	-0.3361	-0.665	0.2564	0.021	0.0319	-0.0276	0.1154	-0.0344	0.1215	-94.609	25.438	-42.438
2	9.3707	0.6349	1.9718	0.3626	0.9733	2.6388	-0.2357	0.9264	0.8112	-0.1205	0.0716	0.0593	-0.3062	0.1726	0.1642	0.0587	-0.0709	-0.0418	0.2079	0.11	0.1344	-76.162	30.799	-40.426
3	1.4987	0.332	-2.3956	1.4805	-1.3399	5.1697	0.1888	0.1129	0.2263	-0.068	-0.0262	-0.0289	-0.212	-0.2655	-0.1626	0.0332	0.0155	0.033	0.0305	-0.0166	0.1748	-57.442	30.538	-32.199
4	1.7823	0.8965	-0.6317	1.7824	1.5759	2.9188	-0.0321	0.3672	0.9142	-0.1083	-0.0037	0.6997	-0.1172	-0.4019	0.0358	0.0859	-0.0187	-0.0055	0.1944	0.1866	0.66	-74.639	33.391	-34.044
5	10.1401	-2.5572	1.3035	1.8647	-0.6245	1.2195	-0.016	0.0686	-0.1681	-0.1185	0.1239	0.0614	0.1445	-0.0274	-0.1079	0.0304	-0.0223	-0.0052	0.0326	-0.0153	0.043	-71.932	22.587	-32.664
6	3.2408	0.7528	-1.9407	0.4917	-0.7472	2.7822	-0.0395	-0.0686	-0.2585	-0.0569	0.0359	-0.0444	0.2011	0.0416	0.0036	0.0208	-0.0022	-0.0122	0.015	-0.0148	0.1276	-60.83	24.376	-28.606
7	9.3991	1.7432	-0.4466	0.8922	-0.5099	0.4465	0.1694	0.406	-0.1872	-0.1291	-0.032	0.032	0.1382	-0.0078	-0.1374	0.0584	0.0129	-0.0342	0.0969	0.0153	0.1287	-61.398	21.883	-38.205
8	1.9276	2.2072	2.8194	5.8436	1.7859	6.5886	0.0301	0.0073	-0.0892	0.4292	0.0146	0.5652	0.1051	-0.315	-0.0447	0.1253	-0.0632	0.0357	0.1651	-0.0284	0.3678	-83.77	22.132	-34.474
9	8.6237	-0.5281	-1.2852	0.0635	-0.0405	0.7025	0.0978	0.2354	-0.1853	-0.0297	-0.0281	0.0111	0.0697	0.025	-0.0697	0.0201	0.013	0.0103	0.0204	-0.0061	0.1886	-53.808	25.333	-36.952
10	6.7845	-1.5353	-1.7277	1.4601	0.2489	1.9313	-0.1307	-0.4948	-0.4299	0.0337	0.0384	0.1112	0.2485	0.3612	0.0923	0.0361	0.0552	0.0129	0.2385	-0.0197	0.1516	-15.3	19.207	-40.412
11	9.2003	1.4314	-2.1137	1.2437	0.2674	0.8361	0.1799	-0.2527	0.4857	-0.0932	-0.0251	0.0406	-0.1156	0.0853	-0.1548	0.0233	0.0069	0.0346	0.1859	-0.0358	0.1712	-31.941	28.904	-37.193
12	9.4645	1.0467	4.3053	0.228	0.8233	9.7312	-0.112	-0.3653	0.4293	0.0542	0.0825	-0.0192	-0.5287	0.7688	0.0295	0.1253	0.0006	-0.0026	0.2709	-0.1268	0.2143	-15.125	30.147	-34.934
13	13.261	-0.3454	2.5944	2.5952	-1.0339	1.0925	-0.0179	0.0405	0.4459	-0.1472	-0.0348	-0.0919	-0.003	0.1301	0.0527	0.0227	-0.0217	0.021	0.0893	-0.0453	0.0535	-11.475	27.711	-41.386
14	9.497	-3.2952	-1.7932	2.7003	1.0831	2.6266	-0.2212	-1.2831	0.5458	0.3439	0.3391	-0.1525	-0.1808	0.5069	-0.1179	0.0996	-0.0262	0.0201	0.4002	-0.1101	0.1262	-19.634	26.912	-31.846
15	10.8106	-2.0679	-2.5549	0.5628	0.9372	1.8103	-0.4733	-1.3016	0.0326	0.1384	0.3232	0.0522	0.2416	0.527	0.1501	0.0359	0.0788	0.024	0.3542	-0.0351	0.0931	-23.236	24.076	-30.907
16	5.6971	4.4326	-3.9984	8.735	-0.0912	4.5493	-0.2384	-0.3641	-0.5904	0.0982	0.1981	-1.1356	0.3087	0.4364	0.0403	0.0629	0.1624	-0.0521	0.5386	-0.0503	0.3338	-0.205	14.612	-39.415

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	2	A	701
5	X-RAY DIFFRACTION	3	A	15 - 30
6	X-RAY DIFFRACTION	4	A	31 - 36
7	X-RAY DIFFRACTION	5	A	37 - 56
8	X-RAY DIFFRACTION	5	A	501
9	X-RAY DIFFRACTION	6	A	57 - 75
10	X-RAY DIFFRACTION	7	A	76 - 84
11	X-RAY DIFFRACTION	8	A	85 - 89
12	X-RAY DIFFRACTION	9	A	90 - 110
13	X-RAY DIFFRACTION	9	A	402 - 404
14	X-RAY DIFFRACTION	10	A	111 - 133
15	X-RAY DIFFRACTION	10	A	502
16	X-RAY DIFFRACTION	11	A	134 - 149
17	X-RAY DIFFRACTION	11	A	601
18	X-RAY DIFFRACTION	12	A	150 - 161
19	X-RAY DIFFRACTION	13	A	162 - 172
20	X-RAY DIFFRACTION	14	A	173 - 192
21	X-RAY DIFFRACTION	15	A	193 - 203
22	X-RAY DIFFRACTION	16	A	204 - 208
23	X-RAY DIFFRACTION	16	A	503

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