PDB-8d40: Crystal structure of human CELSR1 EC1-4

ID or keywords:

Entry

Database: PDB / ID: 8d40

Title

Crystal structure of human CELSR1 EC1-4

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: 3.554 Å

Authors

Tamilselvan, E. / Sotomayor, M.

Funding support

1items

Citation

Journal: to be published
Title: Crystal structure of human CELSR1 EC1-4
Authors: Tamilselvan, E. / Sotomayor, M.

History

Deposition	Jun 1, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8d40.cif.gz	335.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8d40.ent.gz	268.3 KB	Display	PDB format
PDBx/mmJSON format	8d40.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d4/8d40 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/8d40	HTTPS FTP

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Related structure data

Related structure data	3q2vS 3q2wS 5v5xS 5w4tS 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

102 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
Evidence: gel filtration
50.8 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
50.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	305.653, 90.356, 94.949
Angle α, β, γ (deg.)	90.000, 96.166, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Cadherin EGF LAG seven-pass G-type receptor 1 / Cadherin family member 9 / Flamingo homolog 2 / hFmi2 Mass: 50483.191 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
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H₂O
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: 6.46 Å³/Da / Density % sol: 80.96 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3 M Sodium Chloride, 0.1 M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9798 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9798 Å / Relative weight: 1
Reflection	Resolution: 3.55→47.244 Å / Num. obs: 31176 / % possible obs: 98.7 % / Redundancy: 5.7 % / CC_1/2: 0.993 / Net I/σ(I): 10.094
Reflection shell	Resolution: 3.55→3.61 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1550 / CC_1/2: 0.768 / % possible all: 98.2

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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: 5v5x, 5w4t, 3q2v, 3q2w

Resolution: 3.554→47.244 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.921 / SU B: 53.738 / SU ML: 0.336 / Cross valid method: FREE R-VALUE / ESU R: 1.258 / ESU R Free: 0.438
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2523	1483	4.82 %
R_work	0.2157	29283	-
all	0.217	-	-
obs	-	30766	98.209 %

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: 123.797 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-14.574 Å²	0 Å²	-7.28 Å²
2-	-	14.088 Å²	-0 Å²
3-	-	-	2.011 Å²

Refinement step

Cycle: LAST / Resolution: 3.554→47.244 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6647	0	18	8	6673

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	6784
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	6161
X-RAY DIFFRACTION	r_angle_refined_deg	1.932	1.64	9253
X-RAY DIFFRACTION	r_angle_other_deg	1.299	1.574	14168
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.505	5	845
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.694	22.903	403
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.291	15	1053
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.05	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	876
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7903
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1577
X-RAY DIFFRACTION	r_nbd_refined	0.272	0.2	1726
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.211	0.2	6600
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	3181
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	3715
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	124
X-RAY DIFFRACTION	r_metal_ion_refined	0.327	0.2	53
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.22	0.2	29
X-RAY DIFFRACTION	r_nbd_other	0.289	0.2	119
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.047	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.326	9.896	3392
X-RAY DIFFRACTION	r_mcbond_other	5.317	9.895	3391
X-RAY DIFFRACTION	r_mcangle_it	8.271	14.859	4233
X-RAY DIFFRACTION	r_mcangle_other	8.273	14.861	4234
X-RAY DIFFRACTION	r_scbond_it	5.777	10.537	3392
X-RAY DIFFRACTION	r_scbond_other	5.777	10.54	3393
X-RAY DIFFRACTION	r_scangle_it	9.218	15.576	5020
X-RAY DIFFRACTION	r_scangle_other	9.217	15.579	5021
X-RAY DIFFRACTION	r_lrange_it	15.352	193.221	27952
X-RAY DIFFRACTION	r_lrange_other	15.351	193.217	27951

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 (%)
3.554-3.646	0.364	85	0.364	2050	X-RAY DIFFRACTION	92.0655
3.646-3.746	0.373	106	0.342	2093	X-RAY DIFFRACTION	98.8759
3.746-3.854	0.313	94	0.317	2056	X-RAY DIFFRACTION	99.0327
3.854-3.973	0.345	110	0.285	2015	X-RAY DIFFRACTION	99.1601
3.973-4.103	0.306	111	0.252	1911	X-RAY DIFFRACTION	99.4589
4.103-4.247	0.247	80	0.228	1876	X-RAY DIFFRACTION	99.2893
4.247-4.407	0.261	103	0.191	1797	X-RAY DIFFRACTION	99.1649
4.407-4.587	0.25	90	0.175	1739	X-RAY DIFFRACTION	99.3482
4.587-4.791	0.228	88	0.173	1604	X-RAY DIFFRACTION	94.1046
4.791-5.024	0.236	84	0.167	1581	X-RAY DIFFRACTION	97.5395
5.024-5.296	0.216	87	0.17	1512	X-RAY DIFFRACTION	99.6262
5.296-5.616	0.225	79	0.192	1451	X-RAY DIFFRACTION	99.8695
5.616-6.004	0.199	63	0.19	1388	X-RAY DIFFRACTION	99.7937
6.004-6.484	0.242	69	0.194	1267	X-RAY DIFFRACTION	100
6.484-7.101	0.274	59	0.198	1174	X-RAY DIFFRACTION	99.7573
7.101-7.937	0.201	48	0.183	1070	X-RAY DIFFRACTION	99.6435
7.937-9.161	0.196	39	0.178	948	X-RAY DIFFRACTION	98.4048
9.161-11.21	0.239	39	0.205	763	X-RAY DIFFRACTION	94.2421
11.21-15.81	0.234	33	0.215	639	X-RAY DIFFRACTION	99.4083
15.81-47.244	0.211	16	0.251	349	X-RAY DIFFRACTION	93.8303

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	7.2031	-2.2566	-1.3707	1.7784	-0.2077	1.4037	-0.0378	-0.5978	0.0749	0.1147	0.1474	-0.0065	-0.0305	-0.0724	-0.1096	0.3568	0.0591	0.0113	0.2511	-0.1177	0.1547	-106.2056	0.914	32.4445
2	8.4104	-3.563	-2.7671	1.5447	1.1241	0.9906	-0.1836	-0.2754	-0.0086	0.0509	0.0553	-0.0855	0.0232	0.1381	0.1282	0.4112	0.1083	0.1081	0.3013	-0.0128	0.3709	-59.9856	-16.3669	22.7357
3	8.3463	-4.427	1.2409	5.6536	-0.3601	1.7097	0.2469	-0.5557	-0.3304	-0.0039	-0.0601	0.0684	0.1319	-0.3058	-0.1868	0.2401	-0.0079	0.0752	0.1039	0.0637	0.0686	-22.2106	-46.5585	11.8913
4	7.6628	-1.2533	1.3858	2.1907	-0.9405	0.6003	0.0477	0.011	-1.1858	-0.1641	0.1438	0.0558	0.2578	0.09	-0.1915	0.5529	0.2605	-0.0551	0.216	-0.0916	0.4366	20.3414	-71.3086	17.9483
5	8.2726	0.8036	4.8411	0.6544	0.8954	6.2771	0.0163	0.2841	0.0256	-0.0035	0.2105	0.226	0.0126	0.0404	-0.2268	0.44	0.0058	0.0704	0.0977	0.0921	0.168	-101.9536	-88.0684	9.2548
6	8.6729	3.3871	5.9236	1.3509	2.2729	5.1654	-0.1367	0.2047	-0.0261	-0.0446	0.0382	-0.0658	-0.2211	0.3223	0.0985	0.4504	-0.061	0.0198	0.331	-0.1573	0.3207	-62.6133	-74.5254	37.3517
7	8.4782	4.1691	5.2789	7.0388	3.803	5.0659	0.2143	0.3597	-0.1465	0.1135	-0.0554	0.0439	0.3229	-0.245	-0.1589	0.2369	-0.0611	0.101	0.1422	0.0046	0.0764	-34.5577	-50.3696	70.1321
8	7.0396	1.5229	1.9061	2.5839	0.9649	2.0366	-0.2217	-0.038	0.5716	-0.0315	0.1051	-0.0355	-0.398	0.3907	0.1166	0.2879	-0.0629	0.1133	0.1103	0.0076	0.1473	4.4625	-27.4483	90.9504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	19 - 129
2	X-RAY DIFFRACTION	1	ALL	A	501 - 502
3	X-RAY DIFFRACTION	2	ALL	A	130 - 235
4	X-RAY DIFFRACTION	2	ALL	A	503 - 505
5	X-RAY DIFFRACTION	3	ALL	A	236 - 341
6	X-RAY DIFFRACTION	3	ALL	A	506 - 508
7	X-RAY DIFFRACTION	4	ALL	A	342 - 460
8	X-RAY DIFFRACTION	4	ALL	A	509
9	X-RAY DIFFRACTION	5	ALL	B	18 - 129
10	X-RAY DIFFRACTION	5	ALL	B	501 - 502
11	X-RAY DIFFRACTION	6	ALL	B	130 - 235
12	X-RAY DIFFRACTION	6	ALL	B	503 - 505
13	X-RAY DIFFRACTION	7	ALL	B	236 - 341
14	X-RAY DIFFRACTION	7	ALL	B	506 - 508
15	X-RAY DIFFRACTION	8	ALL	B	342 - 460
16	X-RAY DIFFRACTION	8	ALL	B	509

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