PDB-7sz8: Crystal structure of human CELSR1 EC4-7

ID or keywords:

Entry

Database: PDB / ID: 7sz8

Title

Crystal structure of human CELSR1 EC4-7

Components

Cadherin EGF LAG seven-pass G-type receptor 1

Keywords

CELL ADHESION / planar cell polarity / signaling / Cadherin EGF LAG seven-pass G-type receptor 1

Function / homology

Function and homology information

orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis / planar dichotomous subdivision of terminal units involved in lung branching morphogenesis / lateral sprouting involved in lung morphogenesis / protein localization involved in establishment of planar polarity / establishment of body hair planar orientation / establishment of planar polarity of embryonic epithelium / establishment of planar polarity / apical protein localization / Wnt signaling pathway, planar cell polarity pathway / homophilic cell adhesion via plasma membrane adhesion molecules ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.337 Å

Authors

Tamilselvan, E. / Sotomayor, M.

Funding support

1items

Citation

Journal: to be published
Title: Crystal structure of human CELSR1 EC4-7
Authors: Tamilselvan, E. / Sotomayor, M.

History

Deposition	Nov 26, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 14, 2022	Provider: repository / Type: Initial release
Revision 2.0	May 10, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7sz8.cif.gz	321.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7sz8.ent.gz	252.1 KB	Display	PDB format
PDBx/mmJSON format	7sz8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7sz8_validation.pdf.gz	6.9 MB	Display	wwPDB validaton report
Full document	7sz8_full_validation.pdf.gz	6.9 MB	Display
Data in XML	7sz8_validation.xml.gz	31.2 KB	Display
Data in CIF	7sz8_validation.cif.gz	44.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sz/7sz8 ftp://data.pdbj.org/pub/pdb/validation_reports/sz/7sz8	HTTPS FTP

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Related structure data

Related structure data	5sznS 5t9tS 5v5xS 6c13S 6e6bS 6vg4S S: Starting model for refinement
Similar structure data	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	#184 - Apr 2015 Glucagon similarity (10) #99 - Mar 2008 Cadherin similarity (7) #126 - Jun 2010 Epidermal Growth Factor similarity (7) #92 - Aug 2007 Anabolic Steroids similarity (3) #75 - Mar 2006 Tissue Factor similarity (6) #182 - Feb 2015 Insulin receptor similarity (1) #17 - May 2001 Cyclooxygenase similarity (1)

Deposited unit

A: Cadherin EGF LAG seven-pass G-type receptor 1

B: Cadherin EGF LAG seven-pass G-type receptor 1

hetero molecules

99.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cadherin EGF LAG seven-pass G-type receptor 1

hetero molecules

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

2

B: Cadherin EGF LAG seven-pass G-type receptor 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.384, 76.943, 92.742
Angle α, β, γ (deg.)	89.834, 87.776, 76.235
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 2 molecules AB

#1: Protein	Cadherin EGF LAG seven-pass G-type receptor 1 / Cadherin family member 9 / Flamingo homolog 2 / hFmi2 Mass: 49165.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CELSR1, CDHF9, FMI2 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: Q9NYQ6

#1: Protein

Cadherin EGF LAG seven-pass G-type receptor 1 / Cadherin family member 9 / Flamingo homolog 2 / hFmi2

Mass: 49165.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: CELSR1, CDHF9, FMI2 / Plasmid: pET21a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: Q9NYQ6

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Non-polymers , 5 types, 177 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.83 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M magnesium chloride, 0.1 M MES pH 7.3, 30% PEG400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 8, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97911 Å / Relative weight: 1
Reflection	Resolution: 2.337→46.378 Å / Num. obs: 47823 / % possible obs: 85.3 % / Redundancy: 3.3 % / CC_1/2: 0.992 / Net I/σ(I): 15.375
Reflection shell	Resolution: 2.337→2.39 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 8.824 / Num. unique obs: 1953 / CC_1/2: 0.984 / % possible all: 82.5

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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: 5t9t, 5szn, 5v5x, 6c13, 6e6b, 6vg4

Resolution: 2.337→46.378 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.886 / SU B: 16.6 / SU ML: 0.193 / Cross valid method: FREE R-VALUE / ESU R: 0.396 / ESU R Free: 0.291
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2794	1974	4.84 %
R_work	0.2133	38811	-
all	0.217	-	-
obs	-	40785	84.627 %

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: 37.087 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.333 Å²	2.056 Å²	-3.349 Å²
2-	-	-4.996 Å²	3.032 Å²
3-	-	-	8.536 Å²

Refinement step

Cycle: LAST / Resolution: 2.337→46.378 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6472	0	20	157	6649

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	6613
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	5964
X-RAY DIFFRACTION	r_angle_refined_deg	1.752	1.645	9052
X-RAY DIFFRACTION	r_angle_other_deg	1.23	1.575	13721
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.649	5	834
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.649	23.316	377
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.195	15	996
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.575	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	905
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7726
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1518
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	1119
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	5628
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	3053
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	3447
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.172	0.2	214
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.095	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.168	0.2	63
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.174	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	88
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.068	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	0.958	2.212	3342
X-RAY DIFFRACTION	r_mcbond_other	0.957	2.212	3341
X-RAY DIFFRACTION	r_mcangle_it	1.596	3.313	4171
X-RAY DIFFRACTION	r_mcangle_other	1.596	3.314	4172
X-RAY DIFFRACTION	r_scbond_it	0.929	2.312	3271
X-RAY DIFFRACTION	r_scbond_other	0.929	2.312	3272
X-RAY DIFFRACTION	r_scangle_it	1.53	3.433	4880
X-RAY DIFFRACTION	r_scangle_other	1.53	3.433	4881
X-RAY DIFFRACTION	r_lrange_it	2.959	25.395	6761
X-RAY DIFFRACTION	r_lrange_other	2.916	25.336	6728

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 (%)
2.337-2.397	0.329	127	0.271	2491	X-RAY DIFFRACTION	73.498
2.397-2.463	0.326	138	0.257	2933	X-RAY DIFFRACTION	87.8684
2.463-2.534	0.321	119	0.256	2920	X-RAY DIFFRACTION	90.3389
2.534-2.612	0.316	147	0.25	2863	X-RAY DIFFRACTION	92.1899
2.612-2.698	0.333	133	0.229	2792	X-RAY DIFFRACTION	91.6353
2.698-2.792	0.308	142	0.223	2607	X-RAY DIFFRACTION	89.1664
2.792-2.898	0.265	138	0.206	2230	X-RAY DIFFRACTION	80.6814
2.898-3.016	0.282	148	0.223	2483	X-RAY DIFFRACTION	90.5368
3.016-3.15	0.303	99	0.235	2381	X-RAY DIFFRACTION	91.3444
3.15-3.303	0.333	117	0.24	2179	X-RAY DIFFRACTION	87.3336
3.303-3.482	0.27	88	0.229	2015	X-RAY DIFFRACTION	85.2452
3.482-3.693	0.281	79	0.222	1859	X-RAY DIFFRACTION	81.9797
3.693-3.947	0.296	106	0.196	1594	X-RAY DIFFRACTION	77.5901
3.947-4.263	0.237	94	0.185	1330	X-RAY DIFFRACTION	67.4242
4.263-4.669	0.225	78	0.174	1333	X-RAY DIFFRACTION	75.3739
4.669-5.218	0.268	47	0.164	1259	X-RAY DIFFRACTION	76.3743
5.218-6.022	0.249	67	0.186	1225	X-RAY DIFFRACTION	84.3893
6.022-7.368	0.306	37	0.18	1056	X-RAY DIFFRACTION	86.8149
7.368-10.387	0.19	34	0.165	772	X-RAY DIFFRACTION	81.005
10.387-46.378	0.216	36	0.209	489	X-RAY DIFFRACTION	96.1538

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	1.9786	-2.2573	1.7627	5.8018	-2.7602	3.1546	0.1192	0.2661	0.1607	-0.5179	-0.0304	0.2645	-0.098	-0.0315	-0.0888	0.1449	-0.0311	0.0262	0.2359	-0.0052	0.1454	-12.9263	101.6674	-36.2821
2	1.3021	-1.4875	0.6853	5.7064	-1.275	0.4272	0.0264	0.0093	-0.0685	-0.062	0.0258	0.2566	0.0266	-0.032	-0.0522	0.0824	-0.02	0.0494	0.1719	-0.0404	0.0501	5.5121	56.957	-19.9803
3	1.3504	-1.8805	0.2626	5.0999	-1.4495	0.8301	-0.0005	-0.0478	-0.0266	0.1615	0.0376	0.0603	0.0414	0.0332	-0.0371	0.0641	-0.0268	0.0091	0.1489	-0.0618	0.0276	17.0849	11.519	-7.0028
4	4.3211	-2.7655	1.4372	3.9415	-1.5269	1.808	-0.0886	-0.2064	-0.0284	0.2578	0.0529	-0.0153	0.0164	-0.0112	0.0357	0.2296	0.0288	0.0152	0.229	-0.0575	0.0218	42.7988	-25.9208	13.0054
5	3.0393	-3.103	2.0081	4.6832	-3.0677	2.5956	-0.0495	0.021	0.2135	0.1063	-0.0773	-0.4449	0.0076	0.1386	0.1269	0.4001	0.0033	-0.0489	0.3032	-0.0304	0.108	48.8231	-10.7033	26.492
6	1.2669	-0.2936	0.5297	3.8404	-1.2896	1.747	-0.0725	-0.0024	-0.0003	0.1637	0.0035	-0.2883	0.0123	0.2025	0.069	0.1014	-0.0055	0.0042	0.1855	-0.0528	0.0397	30.8409	29.6536	-0.0582
7	0.8588	-0.5976	0.7629	4.2112	-2.0992	1.6857	0.0555	0.0342	-0.003	0.1362	-0.0131	-0.0892	0.0596	0.0116	-0.0424	0.0557	-0.0364	0.0036	0.1386	-0.047	0.0437	21.6987	74.135	-16.5705
8	1.9196	-1.7733	0.6802	5.0888	-1.8749	2.2468	-0.1576	0.073	0.1739	0.0004	0.0317	0.0973	-0.4431	-0.1857	0.1258	0.2127	0.0078	-0.0038	0.2213	-0.0426	0.1137	3.2358	116.1792	-36.0173

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	338 - 463
2	X-RAY DIFFRACTION	1	ALL	A	801 - 803
3	X-RAY DIFFRACTION	2	ALL	A	464 - 565
4	X-RAY DIFFRACTION	2	ALL	A	804 - 805
5	X-RAY DIFFRACTION	3	ALL	A	566 - 668
6	X-RAY DIFFRACTION	3	ALL	A	806 - 808
7	X-RAY DIFFRACTION	4	ALL	A	669 - 773
8	X-RAY DIFFRACTION	4	ALL	A	809
9	X-RAY DIFFRACTION	5	ALL	B	337 - 463
10	X-RAY DIFFRACTION	5	ALL	B	801 - 803
11	X-RAY DIFFRACTION	6	ALL	B	464 - 565
12	X-RAY DIFFRACTION	6	ALL	B	804 - 805
13	X-RAY DIFFRACTION	7	ALL	B	566 - 668
14	X-RAY DIFFRACTION	7	ALL	B	806 - 808
15	X-RAY DIFFRACTION	8	ALL	B	669 - 773
16	X-RAY DIFFRACTION	8	ALL	B	809

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