PDB-7sb6: Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2

ID or keywords:

Entry

Database: PDB / ID: 7sb6

Title

Crystal Structure of Ancestral Mammalian Cadherin-23 EC1-2

Components

Cadherin 23

Keywords

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

Function / homology

:

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.588 Å

Authors

Nisler, C.R. / Narui, Y. / Sotomayor, M.

Funding support

France, 1items

Citation

Journal: Mol.Biol.Evol. / Year: 2023
Title: Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation.
Authors: Nisler, C.R. / Narui, Y. / Scheib, E. / Choudhary, D. / Bowman, J.D. / Mandayam Bharathi, H. / Lynch, V.J. / Sotomayor, M.

History

Deposition	Sep 23, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2022	Provider: repository / Type: Initial release
Revision 1.1	Mar 22, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 26, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7sb6.cif.gz	244.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7sb6.ent.gz	191.6 KB	Display	PDB format
PDBx/mmJSON format	7sb6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sb/7sb6 ftp://data.pdbj.org/pub/pdb/validation_reports/sb/7sb6	HTTPS FTP

-
Related structure data

Related structure data	7n4pC 7scmC 7sgxC 8e51C 2whvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cadherin 23

B: Cadherin 23

C: Cadherin 23

hetero molecules

72.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cadherin 23

hetero molecules

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

2

B: Cadherin 23

hetero molecules

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

3

C: Cadherin 23

hetero molecules

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

Unit cell

Length a, b, c (Å)	118.446, 168.834, 125.276
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

-
Protein , 1 types, 3 molecules ABC

#1: Protein	Cadherin 23 Mass: 23734.291 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIPL

-
Non-polymers , 5 types, 107 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: K
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.6 Å³/Da / Density % sol: 73.26 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 3.5 M Ammonium chloride 0.1 M MES pH 6.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.588→50 Å / Num. obs: 39416 / % possible obs: 99.9 % / Redundancy: 6.1 % / R_merge(I) obs: 0.091 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.588→2.63 Å / Redundancy: 5.8 % / R_merge(I) obs: 1.022 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 1925 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2WHV

2whv

Resolution: 2.588→48.529 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.918 / SU B: 17.672 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.282 / ESU R Free: 0.235
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2461	1913	4.862 %
R_work	0.204	37433	-
all	0.206	-	-
obs	-	39346	99.643 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 58.957 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.191 Å²	-0 Å²	0 Å²
2-	-	0.706 Å²	-0 Å²
3-	-	-	3.485 Å²

Refinement step

Cycle: LAST / Resolution: 2.588→48.529 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4776	0	35	87	4898

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	4899
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4512
X-RAY DIFFRACTION	r_angle_refined_deg	1.554	1.649	6690
X-RAY DIFFRACTION	r_angle_other_deg	1.222	1.574	10377
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.968	5	606
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.797	23.077	273
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.94	15	747
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.426	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	660
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5640
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1152
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	770
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.175	0.2	4008
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	2304
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	2492
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	102
X-RAY DIFFRACTION	r_metal_ion_refined	0.14	0.2	47
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.18	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.233	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.123	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.698	4.03	2433
X-RAY DIFFRACTION	r_mcbond_other	1.698	4.029	2432
X-RAY DIFFRACTION	r_mcangle_it	2.705	6.041	3036
X-RAY DIFFRACTION	r_mcangle_other	2.704	6.042	3037
X-RAY DIFFRACTION	r_scbond_it	1.962	4.33	2466
X-RAY DIFFRACTION	r_scbond_other	1.962	4.331	2467
X-RAY DIFFRACTION	r_scangle_it	3.205	6.388	3654
X-RAY DIFFRACTION	r_scangle_other	3.204	6.389	3655
X-RAY DIFFRACTION	r_lrange_it	5.489	46.179	4938
X-RAY DIFFRACTION	r_lrange_other	5.489	46.176	4938

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 (%)
2.588-2.655	0.393	117	0.365	2674	X-RAY DIFFRACTION	96.2082
2.655-2.728	0.331	124	0.34	2659	X-RAY DIFFRACTION	99.5707
2.728-2.807	0.332	144	0.307	2593	X-RAY DIFFRACTION	99.9635
2.807-2.893	0.345	132	0.269	2516	X-RAY DIFFRACTION	100
2.893-2.988	0.312	126	0.242	2458	X-RAY DIFFRACTION	100
2.988-3.093	0.272	130	0.249	2346	X-RAY DIFFRACTION	100
3.093-3.209	0.288	125	0.241	2301	X-RAY DIFFRACTION	99.9176
3.209-3.34	0.29	126	0.234	2211	X-RAY DIFFRACTION	100
3.34-3.489	0.245	100	0.223	2120	X-RAY DIFFRACTION	100
3.489-3.659	0.281	98	0.215	2046	X-RAY DIFFRACTION	100
3.659-3.856	0.24	108	0.205	1928	X-RAY DIFFRACTION	100
3.856-4.09	0.199	98	0.193	1840	X-RAY DIFFRACTION	100
4.09-4.372	0.231	82	0.15	1735	X-RAY DIFFRACTION	100
4.372-4.721	0.148	83	0.138	1610	X-RAY DIFFRACTION	100
4.721-5.171	0.212	78	0.15	1498	X-RAY DIFFRACTION	99.9366
5.171-5.779	0.236	61	0.17	1370	X-RAY DIFFRACTION	100
5.779-6.669	0.186	61	0.17	1199	X-RAY DIFFRACTION	100
6.669-8.158	0.234	58	0.163	1031	X-RAY DIFFRACTION	100
8.158-11.497	0.218	39	0.158	826	X-RAY DIFFRACTION	100
11.497-48.529	0.243	23	0.239	472	X-RAY DIFFRACTION	97.0588

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	1.8462	0.0667	-1.1448	2.3264	-1.2478	5.8962	0.1377	-0.6298	-0.0148	0.2559	-0.0286	-0.3587	0.2504	0.977	-0.1091	0.122	0.0081	-0.0669	0.295	-0.0442	0.0989	11.2822	13.1517	173.5105
2	1.0152	-0.8324	0.2017	2.3075	2.444	9.2425	0.0314	0.0642	0.0476	-0.4306	0.392	-0.3278	-0.4476	0.888	-0.4234	0.1926	-0.1104	0.1061	0.1313	-0.076	0.0776	12.698	10.789	126.1697
3	7.1645	-2.0751	-0.9064	4.0531	0.7072	1.9521	0.0006	0.169	0.2486	-0.2326	-0.0292	0.2378	-0.1151	-0.2405	0.0286	0.1087	-0.0191	-0.0228	0.0472	0.0158	0.0534	8.4524	31.3234	117.9721
4	10.3483	1.6909	-2.0201	2.6016	-1.2928	2.1819	-0.0732	0.412	-0.7991	-0.1117	-0.1205	-0.4772	0.2718	0.4851	0.1936	0.1745	0.0279	0.07	0.2254	-0.0551	0.2325	55.1986	28.7532	110.3769
5	10.9637	1.2939	-1.0013	1.8476	-0.7002	1.2505	0.0385	-0.398	0.1481	0.1701	-0.0592	-0.2429	-0.0288	0.0937	0.0207	0.1604	-0.007	0.0079	0.102	0.0029	0.1595	45.2083	34.4419	135.6388
6	8.782	-1.1295	-0.4504	2.7673	0.5366	0.4347	-0.1635	-0.901	0.024	-0.1034	0.171	0.3003	-0.1179	0.0866	-0.0074	0.079	0.0544	0.0238	0.2394	0.0619	0.0749	-1.6249	34.4342	143.5865

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 101
2	X-RAY DIFFRACTION	1	ALL	A	301 - 302
3	X-RAY DIFFRACTION	1	ALL	A	304
4	X-RAY DIFFRACTION	2	ALL	A	102 - 203
5	X-RAY DIFFRACTION	2	ALL	A	303
6	X-RAY DIFFRACTION	3	ALL	B	1 - 101
7	X-RAY DIFFRACTION	3	ALL	B	301 - 302
8	X-RAY DIFFRACTION	3	ALL	B	304
9	X-RAY DIFFRACTION	4	ALL	B	102 - 203
10	X-RAY DIFFRACTION	4	ALL	B	303
11	X-RAY DIFFRACTION	5	ALL	C	1 - 101
12	X-RAY DIFFRACTION	5	ALL	C	301 - 302
13	X-RAY DIFFRACTION	5	ALL	C	304
14	X-RAY DIFFRACTION	6	ALL	C	102 - 203
15	X-RAY DIFFRACTION	6	ALL	C	303

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 5 types, 107 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 3 molecules ABC

-Non-polymers , 5 types, 107 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 5 types, 107 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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