PDB-2wp3: Crystal structure of the Titin M10-Obscurin like 1 Ig complex

ID or keywords:

Entry

Database: PDB / ID: 2wp3

Title

Crystal structure of the Titin M10-Obscurin like 1 Ig complex

Components

OBSCURIN-LIKE PROTEIN 1
TITIN

Keywords

TRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX / SARCOMERE / IMMUNOGLOBULIN DOMAIN / LIMB-GIRDLE MUSCULAR DYSTROPHY / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / KELCH REPEAT / CARDIOMYOPATHY / CALMODULIN-BINDING

Function / homology

Function and homology information

3M complex / sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / protein localization to Golgi apparatus / detection of muscle stretch / muscle alpha-actinin binding / protein kinase A signaling ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.48 Å

Authors

Pernigo, S. / Fuzukawa, A. / Gautel, M. / Steiner, R.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Insight Into M-Band Assembly and Mechanics from the Titin-Obscurin-Like-1 Complex.
Authors: Pernigo, S. / Fukuzawa, A. / Bertz, M. / Holt, M. / Rief, M. / Steiner, R.A. / Gautel, M.

History

Deposition	Aug 2, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 16, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 24, 2011	Group: Derived calculations
Revision 1.3	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wp3.cif.gz	61.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2wp3.ent.gz	45.2 KB	Display	PDB format
PDBx/mmJSON format	2wp3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wp3_validation.pdf.gz	454.2 KB	Display	wwPDB validaton report
Full document	2wp3_full_validation.pdf.gz	455.2 KB	Display
Data in XML	2wp3_validation.xml.gz	13 KB	Display
Data in CIF	2wp3_validation.cif.gz	18.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wp/2wp3 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wp3	HTTPS FTP

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Related structure data

Related structure data	2wwkC 2wwmC 1bpv 1g1c 1nct 1ncu 1tit 1tiu 1tki 1tnm 1tnn 1waa 1ya5 2a38 2bk8 2cpc 2f8v 2j8h 2j8o C: citing same article (ref.)
Similar structure data	4o92-d 2wwm-1 6f4q-1 2vqh-d 6xc1-d 6gki-1 5z8i-d 4qnd-1 1w97-d 6i9n-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	#185 - May 2015 Titin similarity (11) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (3) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

O: OBSCURIN-LIKE PROTEIN 1

T: TITIN

hetero molecules

22.6 kDa, 2 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)	61.674, 61.674, 42.347
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	OBSCURIN-LIKE PROTEIN 1 Mass: 11125.619 Da / Num. of mol.: 1 / Fragment: IG1, RESIDUES 1-106 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 / References: UniProt: O75147
#2: Protein	TITIN / CONNECTIN / RHABDOMYSARCOMA ANTIGEN MU-RMS-40.14 Mass: 10981.231 Da / Num. of mol.: 1 / Fragment: M10, RESIDUES 34252-34350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	INITIAL GSS ARE FROM THE EXPRESSION VECTOR

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.5 % / Description: NONE
Crystal grow	pH: 7 Details: PROTEIN COMPLEX AT 13 MG/ML 2M AMM SULPHATE, 0.1 M BIS-TRIS PH 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9745
Detector	Type: ADSC CCD / Detector: CCD / Date: Jan 21, 2009 / Details: MIRRORS
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9745 Å / Relative weight: 1
Reflection	Resolution: 1.48→53.38 Å / Num. obs: 30142 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / B_iso Wilson estimate: 19.38 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shell	Resolution: 1.48→1.56 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 4.6 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0070	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY SOLVED STRUCTURE FROM IN-HOUSE DATA

Resolution: 1.48→33.19 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.953 / SU B: 4.202 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21741	1470	5 %	RANDOM
R_work	0.1755	-	-	-
obs	0.17754	28138	98.37 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 12.578 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.5 Å²	-0.75 Å²	0 Å²
2-	-	-1.5 Å²	0 Å²
3-	-	-	2.25 Å²

Refinement step

Cycle: LAST / Resolution: 1.48→33.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1459	0	29	233	1721

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	1632
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1108
X-RAY DIFFRACTION	r_angle_refined_deg	1.78	1.988	2235
X-RAY DIFFRACTION	r_angle_other_deg	0.924	3.001	2726
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.431	5	221
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.562	24.154	65
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.112	15	257
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.203	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	256
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	1833
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	304
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	1.072	1.5	1047
X-RAY DIFFRACTION	r_mcbond_other	0.338	1.5	420
X-RAY DIFFRACTION	r_mcangle_it	1.742	2	1702
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.723	3	585
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.27	4.5	525
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.479→1.517 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.32	98	-
R_work	0.313	1991	-
obs	-	-	93.8 %

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	3.2386	-0.7845	0.722	1.3849	0.3293	5.401	-0.0685	-0.0218	0.033	0.4167	0.0592	0.2532	-0.4375	-0.1411	0.0092	0.2181	0.036	0.0723	0.0643	0.0033	0.1183	-27.9095	11.945	2.0119
2	3.9355	1.4465	0.7325	8.9982	-0.2356	1.525	0.0072	-0.4444	0.1768	0.2486	-0.0719	-0.1972	-0.0439	-0.0292	0.0648	0.1268	-0.0327	0.0048	0.1012	0.0042	0.0421	-26.7975	-8.3513	5.713
3	1.9635	2.4874	-0.0544	4.4448	-3.3318	8.2395	0.0791	-0.0821	0.0162	0.1643	0.0351	0.073	-0.1582	-0.3769	-0.1142	0.054	0.0265	-0.0238	0.0647	-0.0104	0.1308	-33.565	12.02	-1.4899
4	2.6899	3.0835	2.6964	9.3624	2.5221	3.5107	-0.2286	0.4989	0.114	-0.2567	0.0839	-0.4036	-0.0833	0.4413	0.1447	0.1203	-0.0312	-0.0193	0.164	0.0574	0.1119	-27.2552	-2.9708	-8.9777
5	1.5099	-0.249	0.8761	9.9551	-0.6546	0.6013	-0.0441	-0.1075	0.2147	0.3482	-0.124	0.4764	0.0381	-0.114	0.1682	0.1415	-0.0735	0.0702	0.0718	-0.0785	0.155	-34.7645	-5.7215	-2.2875
6	0.5078	-1.1105	-0.2473	9.3653	-0.8037	0.7975	0.0611	0.0893	-0.0788	-0.4297	-0.2183	-0.2144	0.1153	0.0789	0.1572	0.0682	0.0223	-0.0265	0.0601	0.0139	0.1084	-24.4247	0.9354	-5.313
7	4.2904	-0.2469	1.4262	8.6773	-8.8198	9.3768	0.0077	-0.3261	-0.4286	-0.1652	-0.0479	-0.2376	0.3267	-0.0427	0.0402	0.2933	0.0074	-0.0732	0.0556	0.0124	0.2302	-21.8463	-14.4637	4.0035
8	3.2933	-1.1964	3.4804	4.6131	-4.4666	9.507	0.1495	-0.1187	-0.3469	0.0547	0.1619	0.0375	0.3284	-0.2813	-0.3115	0.0378	0.0015	-0.018	0.0193	0.0106	0.0387	-11.9522	-0.593	6.4432
9	2.6701	-1.8652	1.5824	5.5406	-3.9889	5.8231	0.0253	0.2778	0.1791	-0.2438	-0.1815	0.0354	-0.031	0.2025	0.1561	0.0308	-0.0037	-0.0242	0.0365	0.0207	0.0386	-18.6846	11.6654	-2.2714
10	5.73	2.1888	-3.424	8.3281	-5.1041	7.2889	0.1051	-0.3193	0.0116	0.7129	-0.0123	-0.2279	-0.5241	0.1724	-0.0927	0.0667	0.0026	-0.0133	0.0198	-0.0063	0.0197	-7.3763	8.1313	8.1048
11	9.4777	-6.7335	-0.9737	10.3862	5.7056	4.5919	-0.0978	-0.0646	0.5254	-0.1121	0.1716	-0.3921	-0.1633	0.138	-0.0738	0.039	-0.0449	0.0006	0.0706	-0.008	0.0307	-5.4067	17.811	2.8097
12	3.1698	1.7155	0.0013	9.4742	-2.6436	2.5019	-0.0213	-0.1809	0.3033	0.303	0.0818	0.2007	-0.1869	-0.1001	-0.0605	0.0172	0.0122	0.0014	0.0205	-0.0167	0.031	-15.321	16.6394	4.0684
13	5.1438	-2.1073	1.3893	8.1341	-3.7662	4.4773	0.0318	0.7673	0.3795	-0.7012	-0.1652	-0.0918	-0.0959	0.1849	0.1334	0.1268	-0.0159	-0.0126	0.1182	0.0589	0.0298	-11.0147	15.1787	-7.4477
14	2.9199	-1.9302	3.9519	3.5402	-4.1071	10.4707	0.0386	0.1651	-0.0418	-0.145	0.0028	-0.0361	0.0567	0.0728	-0.0414	0.0084	-0.0026	0.0035	0.0165	-0.0052	0.0027	-9.725	5.7811	-0.298

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	O	8 - 17
2	X-RAY DIFFRACTION	2	O	18 - 32
3	X-RAY DIFFRACTION	3	O	33 - 42
4	X-RAY DIFFRACTION	4	O	43 - 55
5	X-RAY DIFFRACTION	5	O	56 - 74
6	X-RAY DIFFRACTION	6	O	75 - 95
7	X-RAY DIFFRACTION	7	O	96 - 104
8	X-RAY DIFFRACTION	8	T	1 - 14
9	X-RAY DIFFRACTION	9	T	15 - 30
10	X-RAY DIFFRACTION	10	T	31 - 42
11	X-RAY DIFFRACTION	11	T	43 - 47
12	X-RAY DIFFRACTION	12	T	48 - 67
13	X-RAY DIFFRACTION	13	T	68 - 79
14	X-RAY DIFFRACTION	14	T	80 - 99

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