PDB-5lnp: Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic...

ID or keywords:

Entry

Database: PDB / ID: 5lnp

Title

Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from monomeric fraction

Components

(Segment polarity protein dishevelled homolog DVL-2) x 2

Keywords

SIGNALING PROTEIN / Dishevelled / DEP domain / WNT signalling

Function / homology

Function and homology information

Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / clathrin-coated endocytic vesicle / WNT5:FZD7-mediated leishmania damping / frizzled binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Renko, M. / Gammons, M.V. / Bienz, M.

Citation

Journal: Mol.Cell / Year: 2016
Title: Wnt Signalosome Assembly by DEP Domain Swapping of Dishevelled.
Authors: Gammons, M.V. / Renko, M. / Johnson, C.M. / Rutherford, T.J. / Bienz, M.

History

Deposition	Aug 5, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 19, 2016	Group: Database references
Revision 1.2	May 1, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lnp.cif.gz	159.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5lnp.ent.gz	128 KB	Display	PDB format
PDBx/mmJSON format	5lnp.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/ln/5lnp ftp://data.pdbj.org/pub/pdb/validation_reports/ln/5lnp	HTTPS FTP

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Related structure data

Related structure data	5suyC 5suzC C: citing same article (ref.)
Similar structure data	5suy-d 3nas-d 5u06-d 1x2w-2 5hpt-3 2oct-1 6b3p-d 4x5r-d 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	#60 - Dec 2004 Ubiquitin similarity (8) #88 - Apr 2007 Clathrin similarity (1) #245 - May 2020 Spliceosomes similarity (3) #122 - Feb 2010 Enhanceosome similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (3) #56 - Aug 2004 Caspases similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (2) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#60 - Dec 2004
Ubiquitin
similarity (8)
#88 - Apr 2007
Clathrin
similarity (1)
#245 - May 2020
Spliceosomes
similarity (3)
#122 - Feb 2010
Enhanceosome
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (3)
#56 - Aug 2004
Caspases
similarity (1)
#141 - Sep 2011
O-GlcNAc Transferase
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (2)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)

Deposited unit

A: Segment polarity protein dishevelled homolog DVL-2

B: Segment polarity protein dishevelled homolog DVL-2

C: Segment polarity protein dishevelled homolog DVL-2

D: Segment polarity protein dishevelled homolog DVL-2

hetero molecules

43.5 kDa, 4 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)	61.583, 60.181, 66.292
Angle α, β, γ (deg.)	90.00, 117.71, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Segment polarity protein dishevelled homolog DVL-2 / Dishevelled-2 / DSH homolog 2 Mass: 10862.361 Da / Num. of mol.: 3 / Fragment: DEP domain, UNP residues 416-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Plasmid: pETM-41 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14641
#2: Protein	Segment polarity protein dishevelled homolog DVL-2 / Dishevelled-2 / DSH homolog 2 Mass: 10846.361 Da / Num. of mol.: 1 / Fragment: DEP domain, UNP residues 416-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Plasmid: pETM-41 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14641
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.5 Å³/Da / Density % sol: 50.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES, pH=6.5 0.1 M NaCl 0.1 M Li2SO4 23 % PEG400

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04-1 / Wavelength: 0.92819 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.92819 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.533
1	1	-H, -K, H+L	2	0.467

Reflection

Resolution: 1.99→42.02 Å / Num. obs: 29398 / % possible obs: 99 % / Redundancy: 6.8 % / R_merge(I) obs: 0.064 / Net I/σ(I): 17.3

Reflection shell

Resolution: 1.99→2.06 Å / Redundancy: 6.6 % / R_merge(I) obs: 0.636 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2884

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: unpublished model

Resolution: 1.99→42.02 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.927 / SU B: 7.387 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24552	1561	5.3 %	RANDOM
R_work	0.19351	-	-	-
obs	0.1963	27828	99.12 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 36.899 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	15.28 Å²	0 Å²	8.21 Å²
2-	-	10.18 Å²	0 Å²
3-	-	-	-25.46 Å²

Refinement step

Cycle: 1 / Resolution: 1.99→42.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2993	0	5	33	3031

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	3069
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2912
X-RAY DIFFRACTION	r_angle_refined_deg	1.743	1.947	4149
X-RAY DIFFRACTION	r_angle_other_deg	1.046	3	6682
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.126	5	373
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.48	22.353	136
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.494	15	514
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.241	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	454
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3407
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	737
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	1.491	2.685	1504
X-RAY DIFFRACTION	r_mcbond_other	1.484	2.684	1503
X-RAY DIFFRACTION	r_mcangle_it	2.36	4.016	1873
X-RAY DIFFRACTION	r_mcangle_other	2.36	4.017	1874
X-RAY DIFFRACTION	r_scbond_it	1.506	2.933	1565
X-RAY DIFFRACTION	r_scbond_other	1.496	2.929	1562
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.372	4.311	2271
X-RAY DIFFRACTION	r_long_range_B_refined	3.973	21.331	3261
X-RAY DIFFRACTION	r_long_range_B_other	3.972	21.331	3261
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.989→2.04 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	102	-
R_work	0.21	1972	-
obs	-	-	97.1 %

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	2.3864	0.6452	0.1467	0.2133	-0.1671	1.1288	0.0246	-0.0675	-0.1001	0.0331	-0.0351	-0.0245	-0.16	0.0488	0.0105	0.0722	-0.0018	-0.0754	0.0624	-0.0091	0.1103	-13.823	8.9248	-26.5264
2	1.4337	0.1369	-2.9738	1.298	-2.3531	9.5013	-0.0032	0.0523	0.0961	0.0091	0.0429	-0.0929	-0.0048	-0.1674	-0.0397	0.0131	-0.0176	-0.0262	0.0601	0.0138	0.0762	-2.3223	5.5171	-2.4539
3	1.6832	1.2261	0.4373	1.036	-0.1985	2.1768	-0.0502	0.1387	0.0785	0.0086	0.0158	0.0544	-0.1562	0.2005	0.0343	0.0448	-0.0404	-0.055	0.1437	0.0161	0.0927	15.1665	10.7338	11.8534
4	0.739	-0.3867	0.1951	1.6381	0.5399	0.3388	0.0089	0.117	-0.1381	-0.0977	0.0159	0.087	-0.0427	0.066	-0.0248	0.047	-0.0102	-0.0593	0.0853	-0.0083	0.1054	9.8754	2.414	5.732
5	1.2375	-1.0982	0.6984	1.5734	-0.2952	0.786	0.0257	0.0879	-0.1436	-0.0109	-0.0534	0.0486	-0.0875	0.0459	0.0276	0.0543	0.0012	-0.0792	0.0851	-0.0142	0.132	12.4387	8.6591	20.9895
6	0.7777	-0.3279	-1.8316	0.3138	0.1167	6.7695	0.0204	-0.0261	0.0436	-0.0152	0.0074	-0.0336	-0.0244	0.0816	-0.0278	0.0129	-0.0107	-0.0129	0.044	-0.0069	0.0697	-0.3274	6.5054	-1.4075
7	1.4161	-0.6789	0.9004	0.3502	-0.2454	2.3737	-0.0473	-0.2588	-0.0537	-0.0004	0.1001	0.0165	-0.2412	-0.1799	-0.0528	0.0703	0.03	-0.054	0.1249	0.0077	0.0863	-17.3223	8.9078	-17.7028
8	1.4603	-0.2112	0.627	2.1409	-1.2104	0.8646	0.0758	-0.3896	-0.2115	-0.0177	-0.0854	-0.1568	0.0305	-0.1009	0.0096	0.0462	0.0222	-0.0463	0.1577	0.0358	0.0881	-12.9782	3.6632	-13.1845
9	3.0295	-0.4612	-1.8522	0.7347	0.1925	1.1493	0.0001	0.065	0.0435	-0.067	0.0097	0.0142	0.0099	-0.0395	-0.0098	0.0415	-0.0025	-0.0342	0.094	0.0091	0.0932	-12.9666	20.7347	27.7721
10	0.1469	-0.1811	1.129	0.6482	-1.5472	8.7405	0.0001	0.0328	-0.0014	-0.0202	-0.0133	-0.0117	-0.0025	0.2314	0.0132	0.0143	0.0139	-0.0235	0.075	0.0064	0.0689	0.0525	23.3768	4.5751
11	1.6451	-0.3103	-1.7998	1.0107	0.6866	2.1776	-0.1501	-0.2943	-0.029	0.0374	0.0431	0.0024	0.2131	0.2836	0.107	0.0642	0.0034	0.008	0.1027	0.0084	0.1095	17.5069	18.5267	-11.4921
12	0.0376	-0.1406	-0.2004	1.8479	0.6253	1.5482	-0.0205	-0.0386	0.0218	0.0979	-0.0546	-0.0014	-0.0207	0.2098	0.0752	0.0453	0.0203	-0.0643	0.1296	-0.0161	0.1116	12.015	26.0306	-5.9496
13	2.9678	-0.1057	-1.6093	0.8173	0.4929	1.1414	-0.0275	-0.0209	-0.033	0.0494	-0.0465	-0	0.065	-0.0245	0.074	0.0634	-0.006	-0.0056	0.0724	-0.0007	0.1138	12.2126	20.111	-18.7769
14	1.1939	0.4343	-1.5083	0.3016	-0.4832	1.963	-0.207	0.0699	-0.2231	0.0244	-0.0326	-0.1597	0.3247	-0.0628	0.2395	0.1228	-0.0151	-0.0273	0.1302	0.0005	0.094	-8.7442	18.6244	16.2042
15	0.5531	0.2777	-1.1197	1.6101	-0.0755	2.4309	0.0147	0.1579	0.0369	-0.0339	-0.0076	0.1683	-0.0441	-0.3368	-0.007	0.0378	-0.012	-0.0617	0.1351	0.0299	0.1114	-16.8837	24.1871	15.8776
16	2.4966	-0.231	1.2477	1.2638	0.5796	1.5392	-0.061	0.2656	0.1401	-0.0293	-0.0377	0.0834	-0.0138	-0.0048	0.0988	0.0171	-0.0157	-0.0392	0.0895	0.0178	0.0975	-10.7612	26.3916	11.8202

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	415 - 441
2	X-RAY DIFFRACTION	2	A	442 - 449
3	X-RAY DIFFRACTION	3	A	450 - 488
4	X-RAY DIFFRACTION	4	A	489 - 508
5	X-RAY DIFFRACTION	5	B	415 - 439
6	X-RAY DIFFRACTION	6	B	440 - 449
7	X-RAY DIFFRACTION	7	B	450 - 493
8	X-RAY DIFFRACTION	8	B	494 - 508
9	X-RAY DIFFRACTION	9	C	415 - 439
10	X-RAY DIFFRACTION	10	C	440 - 449
11	X-RAY DIFFRACTION	11	C	450 - 490
12	X-RAY DIFFRACTION	12	C	491 - 509
13	X-RAY DIFFRACTION	13	D	415 - 442
14	X-RAY DIFFRACTION	14	D	443 - 471
15	X-RAY DIFFRACTION	15	D	472 - 492
16	X-RAY DIFFRACTION	16	D	493 - 507

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