PDB-4oyu: Crystal structure of the N-terminal domains of muskelin

ID or keywords:

Entry

Database: PDB / ID: 4oyu

Title

Crystal structure of the N-terminal domains of muskelin

Components

Muskelin

Keywords

PROTEIN BINDING /

Discoidin domain / LisH motif / Dimer

Function / homology

Function and homology information

: /

regulation of receptor internalization /

ubiquitin ligase complex / ruffle / cell-matrix adhesion /

cell cortex / regulation of cell shape / postsynapse / protein homodimerization activity /

nucleoplasm ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Delto, C. / Kuper, J. / Schindelin, H.

Citation

Journal: Structure / Year: 2015
Title: The LisH Motif of Muskelin Is Crucial for Oligomerization and Governs Intracellular Localization.
Authors: Delto, C.F. / Heisler, F.F. / Kuper, J. / Sander, B. / Kneussel, M. / Schindelin, H.

History

Deposition	Feb 13, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 18, 2015	Group: Database references / Derived calculations
Revision 1.2	Mar 25, 2015	Group: Derived calculations
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4oyu.cif.gz	239.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4oyu.ent.gz	199.9 KB	Display	PDB format
PDBx/mmJSON format	4oyu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oy/4oyu ftp://data.pdbj.org/pub/pdb/validation_reports/oy/4oyu	HTTPS FTP

-
Related structure data

Similar structure data	3kji-1 1pu8-d 1fqv-1 5tgq-1 1fqv-6 2vyt-d 2o25-2 2dd7-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Muskelin

B: Muskelin

hetero molecules

47.9 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)	63.060, 65.300, 101.390
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Muskelin / Mass: 23176.586 Da / Num. of mol.: 2 / Fragment: UNP residues 12-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mkln1, Msk / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q99PV3
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 45.38 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM BisTris pH 5.5, 200 mM sodium chloride and 32.5% (w/v) PEG 3350 PH range: 5.25-6.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95 Å / Relative weight: 1
Reflection	Resolution: 1.8→33.8 Å / Num. obs: 39509 / % possible obs: 100 % / Redundancy: 4.5 % / B_iso Wilson estimate: 25.82 Å² / Net I/σ(I): 17
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.7 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8_1069)	refinement
PHASER		phasing
SCALA		data scaling
MOSFLM		data reduction
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→33.8 Å / SU ML: 0.16 / σ(F): 0.86 / Phase error: 18.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.193	1979	5.02 %
R_work	0.156	-	-
obs	0.158	39448	100 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 41.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→33.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2979	0	98	270	3347

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3192
X-RAY DIFFRACTION	f_angle_d	1.422	4280
X-RAY DIFFRACTION	f_dihedral_angle_d	15.231	1215
X-RAY DIFFRACTION	f_chiral_restr	0.084	439
X-RAY DIFFRACTION	f_plane_restr	0.007	539

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 (%)
1.801-1.8238	0.2766	151	0.2221	2651	X-RAY DIFFRACTION	100
1.8238-1.8478	0.2169	108	0.2098	2658	X-RAY DIFFRACTION	100
1.8478-1.8731	0.2271	137	0.2061	2605	X-RAY DIFFRACTION	100
1.8731-1.8999	0.229	150	0.1903	2649	X-RAY DIFFRACTION	100
1.8999-1.9282	0.2324	113	0.1846	2656	X-RAY DIFFRACTION	100
1.9282-1.9584	0.2323	130	0.1779	2616	X-RAY DIFFRACTION	100
1.9584-1.9905	0.239	146	0.1859	2640	X-RAY DIFFRACTION	100
1.9905-2.0248	0.2175	138	0.1647	2681	X-RAY DIFFRACTION	100
2.0248-2.0616	0.1896	151	0.1553	2605	X-RAY DIFFRACTION	100
2.0616-2.1012	0.2056	165	0.1461	2607	X-RAY DIFFRACTION	100
2.1012-2.1441	0.1764	145	0.1498	2579	X-RAY DIFFRACTION	100
2.1441-2.1907	0.1776	125	0.1417	2681	X-RAY DIFFRACTION	100
2.1907-2.2417	0.2251	157	0.1471	2617	X-RAY DIFFRACTION	100
2.2417-2.2977	0.2038	144	0.1608	2617	X-RAY DIFFRACTION	100
2.2977-2.3599	0.1917	129	0.1531	2643	X-RAY DIFFRACTION	100
2.3599-2.4293	0.2212	145	0.1575	2636	X-RAY DIFFRACTION	100
2.4293-2.5077	0.2047	149	0.1542	2595	X-RAY DIFFRACTION	100
2.5077-2.5973	0.2192	129	0.1622	2664	X-RAY DIFFRACTION	100
2.5973-2.7012	0.2084	94	0.1562	2659	X-RAY DIFFRACTION	100
2.7012-2.8241	0.2263	150	0.155	2639	X-RAY DIFFRACTION	100
2.8241-2.9729	0.1851	170	0.1652	2591	X-RAY DIFFRACTION	100
2.9729-3.159	0.2011	144	0.1544	2638	X-RAY DIFFRACTION	100
3.159-3.4027	0.1963	149	0.1524	2623	X-RAY DIFFRACTION	100
3.4027-3.7448	0.1795	143	0.1368	2632	X-RAY DIFFRACTION	100
3.7448-4.2857	0.1962	131	0.1312	2625	X-RAY DIFFRACTION	100
4.2857-5.396	0.1168	132	0.139	2647	X-RAY DIFFRACTION	100
5.396-33.8102	0.2079	128	0.1935	2614	X-RAY DIFFRACTION	99

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	7.078	3.4465	3.9314	3.4999	2.06	2.6159	-0.2896	0.5369	0.1642	-0.2625	0.0276	0.6052	0.1973	-0.0648	0.6049	0.3387	-0.1213	-0.0147	0.3084	0.0183	0.268	-2.6201	12.1716	8.9687
2	2.6149	0.1881	0.4651	3.2868	0.3067	2.0297	-0.3197	0.4118	0.0416	-0.352	0.2944	-0.1116	-0.2984	0.3317	-0.0035	0.2661	-0.1366	-0.0081	0.2933	0.019	0.1993	9.4232	17.9114	13.235
3	3.3679	-1.8431	3.482	6.1384	-2.6259	3.9103	-0.3525	1.0256	0.7811	-0.658	-0.1173	-2.0871	-0.2703	1.3788	0.4641	0.4335	-0.1848	0.1609	0.8319	-0.1442	0.9149	20.5471	13.1618	6.8449
4	4.7368	1.9285	0.4642	4.4684	0.2882	2.8691	-0.1004	0.2576	-0.5641	-0.1222	0.1979	-0.3877	0.2153	0.3838	0.0202	0.2019	-0.0442	-0.0086	0.2211	-0.0312	0.2612	6.8676	7.0853	14.574
5	2.8382	-1.1933	0.2107	3.016	-3.2804	4.4462	-0.3309	-0.2007	0.3156	0.332	0.2009	-0.1758	-0.3712	0.7496	0.1835	0.2842	-0.0144	-0.0288	0.3055	-0.0561	0.4078	-9.654	1.1803	28.6608
6	3.6843	-0.6604	-0.1437	2.0841	0.3151	3.8317	0.0939	-0.2146	-0.2395	0.3616	-0.1707	-0.1881	-0.2071	0.1858	-0.0277	0.2548	-0.0994	-0.0212	0.1982	0.0053	0.1343	2.6425	21.4018	65.8279
7	4.6302	0.5686	-0.5142	0.5886	-1.1335	3.3029	0.3611	-0.1851	0.5221	0.4972	-0.3004	0.2125	-0.842	0.0329	0.0386	0.4493	-0.0977	0.0555	0.2175	-0.0513	0.2554	-1.396	27.5138	63.7173
8	4.7951	1.405	-0.4417	4.706	-0.7172	4.518	0.2136	0.0217	0.3084	0.209	-0.1252	0.5168	-0.277	-0.4257	-0.001	0.157	-0.0242	0.0404	0.2208	-0.0164	0.2088	-8.3414	21.9104	61.438
9	2.3293	-0.8729	2.6512	3.1852	-0.1569	4.0845	0.0818	0.1769	-0.04	-0.2327	-0.2148	-0.2563	-0.4995	0.0502	0.1943	0.2835	-0.0384	0.0714	0.2826	-0.0378	0.3527	-12.7684	5.0287	47.3375

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 11 THROUGH 23 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 24 THROUGH 73 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 74 THROUGH 86 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 87 THROUGH 157 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 158 THROUGH 188 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 10 THROUGH 41 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 42 THROUGH 86 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 87 THROUGH 157 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 158 THROUGH 188 )

-
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

-
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

-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

-
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