PDB-5vh2: Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mu...

ID or keywords:

Entry

Database: PDB / ID: 5vh2

Title

Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D

Components

Cadherin-23

Keywords

CELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN

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: 2.84 Å

Authors

Termine, D.J. / Jaiganesh, A. / Sotomayor, M.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	R01-DC015271	United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	R00-DC012534	United States

Citation

Journal: Structure / Year: 2018
Title: Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness.
Authors: Jaiganesh, A. / De-la-Torre, P. / Patel, A.A. / Termine, D.J. / Velez-Cortes, F. / Chen, C. / Sotomayor, M.

History

Deposition	Apr 12, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 18, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 25, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2	Aug 1, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Sep 19, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 4, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_label_atom_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5vh2.cif.gz	323.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5vh2.ent.gz	264 KB	Display	PDB format
PDBx/mmJSON format	5vh2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5vh2_validation.pdf.gz	446.2 KB	Display	wwPDB validaton report
Full document	5vh2_full_validation.pdf.gz	448.9 KB	Display
Data in XML	5vh2_validation.xml.gz	28 KB	Display
Data in CIF	5vh2_validation.cif.gz	38.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vh/5vh2 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/5vh2	HTTPS FTP

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Related structure data

Related structure data	5i8dC 5tfkSC 5tflC 5tfmC 5uluC 5un2C 5uz8C 5vt8C 5vvmC 5w4tC 5wj8C 5wjmC 2whvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5czr-4 2wd0-2 5czr-3 5czr-2 2wd0-1 2wcp-d 5vt8-3 6s5y-6 4iff-1 5wj8-d 5czr-1 1avy-3 2whv-d 3mvs-d 6s5y-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5tfkSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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

B: Cadherin-23

C: Cadherin-23

D: Cadherin-23

hetero molecules

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

1

A: Cadherin-23

hetero molecules

defined by author&software
Evidence: gel filtration
24.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cadherin-23

hetero molecules

defined by author&software
24.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Cadherin-23

hetero molecules

defined by author&software
24.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Cadherin-23

hetero molecules

defined by author&software
24.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.738, 47.210, 113.044
Angle α, β, γ (deg.)	89.95, 90.02, 115.76
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASN	ASN	VAL	VAL	A	A	1179 - 1385	2 - 208
2	1	ASN	ASN	VAL	VAL	B	B	1179 - 1385	2 - 208
1	2	ASP	ASP	ASP	ASP	A	A	1180 - 1387	3 - 210
2	2	ASP	ASP	ASP	ASP	C	C	1180 - 1387	3 - 210
1	3	ASP	ASP	LEU	LEU	A	A	1180 - 1386	3 - 209
2	3	ASP	ASP	LEU	LEU	D	D	1180 - 1386	3 - 209
1	4	ASP	ASP	LEU	LEU	B	B	1180 - 1386	3 - 209
2	4	ASP	ASP	LEU	LEU	C	C	1180 - 1386	3 - 209
1	5	ASP	ASP	VAL	VAL	B	B	1180 - 1385	3 - 208
2	5	ASP	ASP	VAL	VAL	D	D	1180 - 1385	3 - 208
1	6	ASP	ASP	GLU	GLU	C	C	1180 - 1388	3 - 211
2	6	ASP	ASP	GLU	GLU	D	D	1180 - 1388	3 - 211

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Cadherin-23 / Otocadherin Mass: 24263.949 Da / Num. of mol.: 4 / Fragment: residues 1202-1412 / Mutation: S1339D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET-21a+ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-RIPL / References: UniProt: Q99PF4
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.8 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.05 M Tris pH 8.5 0.5 M NaCl 22% PEG 4000 / PH range: 8.1-8.7

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.542 Å

Detector

Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 14, 2016

Radiation

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

Radiation wavelength

Wavelength: 1.542 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.564
1	1	-h,-k,l	2	0.436

Reflection

Resolution: 2.84→50 Å / Num. obs: 19387 / % possible obs: 93.9 % / Redundancy: 1.6 % / R_merge(I) obs: 0.165 / Net I/σ(I): 4.3269

Reflection shell

Resolution: 2.84→2.89 Å / Redundancy: 1.6 % / R_merge(I) obs: 0.377 / Mean I/σ(I) obs: 2.05 / % possible all: 89.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2WHV, 5TFK

2whv

5tfk

Resolution: 2.84→33.99 Å / Cor.coef. F_o:F_c: 0.831 / Cor.coef. F_o:F_c free: 0.779 / SU B: 28.631 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.272	1084	6 %	RANDOM
R_work	0.238	-	-	-
obs	0.24	17103	92.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 23.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.28 Å²	-6.49 Å²	0.1 Å²
2-	-	-11.33 Å²	7.99 Å²
3-	-	-	11.62 Å²

Refinement step

Cycle: LAST / Resolution: 2.84→33.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6376	0	14	0	6390

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.02	6466
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5952
X-RAY DIFFRACTION	r_angle_refined_deg	1.475	1.961	8792
X-RAY DIFFRACTION	r_angle_other_deg	0.806	3	13774
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.579	5	822
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.138	25.497	302
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.534	15	1060
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.766	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1052
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	7278
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1270
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	0.1	3306
X-RAY DIFFRACTION	r_mcbond_other	0	0.1	3305
X-RAY DIFFRACTION	r_mcangle_it	0	0.15	4122
X-RAY DIFFRACTION	r_mcangle_other	0	0.15	4123
X-RAY DIFFRACTION	r_scbond_it	0	0.1	3160
X-RAY DIFFRACTION	r_scbond_other	0	0.1	3158
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0	0.15	4670
X-RAY DIFFRACTION	r_long_range_B_refined	0	1.907	25817
X-RAY DIFFRACTION	r_long_range_B_other	0	1.907	25816
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	12586	0.06
1	2	B	12586	0.06
2	1	A	12002	0.07
2	2	C	12002	0.07
3	1	A	12328	0.08
3	2	D	12328	0.08
4	1	B	11958	0.08
4	2	C	11958	0.08
5	1	B	12232	0.08
5	2	D	12232	0.08
6	1	C	12104	0.08
6	2	D	12104	0.08

LS refinement shell

Resolution: 2.82→2.89 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	86	-
R_work	0.274	1012	-
obs	-	-	75.36 %

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	0.7479	-0.5917	-0.3261	1.2067	0.6732	0.3758	-0.0814	0.128	-0.0736	0.0109	0.1379	-0.0844	0.008	0.0842	-0.0565	0.1928	0.0131	-0.0602	0.2216	-0.0436	0.278	82.763	163.696	-10.73
2	0.7361	-1.1948	0.567	3.0901	-0.5293	0.7031	0.054	-0.0711	-0.0904	0.0185	-0.0976	-0.0004	0.1167	-0.0248	0.0435	0.1756	0.006	0.0116	0.2783	-0.0023	0.403	63.091	124.502	13.066
3	0.8887	0.5116	-0.0588	0.5283	-0.1089	0.0286	0.04	-0.0318	-0.0099	-0.1409	-0.0688	-0.0647	0.0505	0.0094	0.0288	0.1338	0.0087	-0.0103	0.1715	-0.0593	0.3322	72.79	136.998	45.804
4	0.925	-1.0701	0.1546	1.2828	-0.5161	2.9017	-0.1306	-0.1869	0.1862	0.2007	0.2032	-0.1883	-0.0494	0.1158	-0.0727	0.2184	-0.0384	0.0184	0.2649	-0.0605	0.3539	92.301	176.027	69.52
5	0.5512	-0.7459	-0.4669	1.0534	0.526	0.6802	-0.0682	-0.0358	0.1069	0.1555	0.0997	-0.1814	-0.07	-0.0324	-0.0315	0.1129	0.0404	-0.0023	0.1177	-0.0772	0.3455	98.633	147.689	58.141
6	0.2526	0.5321	0.2828	2.6459	0.9246	1.8309	-0.0664	0.1624	-0.1376	-0.1698	0.1897	-0.0868	0.2935	0.1087	-0.1233	0.1593	0.0078	0.0157	0.2011	-0.0686	0.2955	78.672	108.857	35.475
7	0.5457	-0.2488	-0.3033	1.246	-1.5601	2.7185	-0.1797	0.0855	-0.0986	0.0852	0.2399	0.116	0.111	-0.4365	-0.0601	0.2541	0.0063	0.0108	0.3027	-0.0769	0.2738	76.98	109.891	1.959
8	0.7138	-0.5248	0.3038	0.5568	-0.057	0.3042	-0.0439	0.0005	0.0539	-0.0423	-0.0338	0.0749	-0.0408	0.0174	0.0778	0.2873	0.0447	0.021	0.3302	-0.0444	0.3021	97.428	149.346	-21.038

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1179 - 1284
2	X-RAY DIFFRACTION	1	A	1401 - 1402
3	X-RAY DIFFRACTION	2	A	1285 - 1387
4	X-RAY DIFFRACTION	2	A	1403
5	X-RAY DIFFRACTION	3	B	1179 - 1284
6	X-RAY DIFFRACTION	3	B	1401 - 1403
7	X-RAY DIFFRACTION	4	B	1285 - 1386
8	X-RAY DIFFRACTION	4	B	1404
9	X-RAY DIFFRACTION	5	C	1180 - 1284
10	X-RAY DIFFRACTION	5	C	1401 - 1402
11	X-RAY DIFFRACTION	6	C	1285 - 1388
12	X-RAY DIFFRACTION	6	C	1403
13	X-RAY DIFFRACTION	7	D	1180 - 1284
14	X-RAY DIFFRACTION	7	D	1401 - 1402
15	X-RAY DIFFRACTION	8	D	1285 - 1388
16	X-RAY DIFFRACTION	8	D	1403

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