PDB-5nr4: Crystal structure of Clasp2 TOG1 domain

ID or keywords:

Entry

Database: PDB / ID: 5nr4

Title

Crystal structure of Clasp2 TOG1 domain

Components

CLIP-associating protein 2

Keywords

STRUCTURAL PROTEIN / Microtubules / TOG domain / Tubulin

Function / homology

Function and homology information

presynaptic cytoskeleton organization / cortical microtubule plus-end / negative regulation of wound healing, spreading of epidermal cells / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / vesicle targeting / regulation of gastrulation / microtubule anchoring / microtubule organizing center organization / basal cortex / positive regulation of extracellular matrix disassembly ...presynaptic cytoskeleton organization / cortical microtubule plus-end / negative regulation of wound healing, spreading of epidermal cells / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / vesicle targeting / regulation of gastrulation / microtubule anchoring / microtubule organizing center organization / basal cortex / positive regulation of extracellular matrix disassembly / establishment of mitotic spindle localization / kinetochore microtubule / Role of ABL in ROBO-SLIT signaling / regulation of epithelial to mesenchymal transition / dystroglycan binding / negative regulation of focal adhesion assembly / negative regulation of microtubule depolymerization / microtubule nucleation / microtubule plus-end binding / regulation of microtubule-based process / microtubule organizing center / negative regulation of stress fiber assembly / exit from mitosis / regulation of axon extension / establishment or maintenance of cell polarity / positive regulation of epithelial cell migration / cytoplasmic microtubule / Golgi organization / cell leading edge / regulation of microtubule polymerization / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of exocytosis / mitotic spindle assembly / regulation of microtubule polymerization or depolymerization / axonal growth cone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein tyrosine kinase binding / mitotic spindle organization / protein localization to plasma membrane / spindle microtubule / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / trans-Golgi network / kinetochore / ruffle membrane / microtubule cytoskeleton organization / Separation of Sister Chromatids / actin filament binding / cell cortex / microtubule binding / microtubule / cell division / centrosome / glutamatergic synapse / Golgi apparatus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.198 Å

Authors

Sharma, A. / Olieric, N. / Weinert, T. / Olieric, V. / Steinmetz, M.O.

Citation

Journal: Dev. Cell / Year: 2018
Title: CLASP Suppresses Microtubule Catastrophes through a Single TOG Domain.
Authors: Aher, A. / Kok, M. / Sharma, A. / Rai, A. / Olieric, N. / Rodriguez-Garcia, R. / Katrukha, E.A. / Weinert, T. / Olieric, V. / Kapitein, L.C. / Steinmetz, M.O. / Dogterom, M. / Akhmanova, A.

History

Deposition	Apr 21, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 30, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 4, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jul 18, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.4	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5nr4.cif.gz	194.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5nr4.ent.gz	155.3 KB	Display	PDB format
PDBx/mmJSON format	5nr4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5nr4_validation.pdf.gz	441.2 KB	Display	wwPDB validaton report
Full document	5nr4_full_validation.pdf.gz	451.9 KB	Display
Data in XML	5nr4_validation.xml.gz	26.3 KB	Display
Data in CIF	5nr4_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nr/5nr4 ftp://data.pdbj.org/pub/pdb/validation_reports/nr/5nr4	HTTPS FTP

-
Related structure data

Similar structure data	6mq5-2 4g3a-1 3psk-2 6mq5-1 5d66-2 5ltv-3 4pq8-d 2eta-2 5lt9-1 3lqi-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#175 - Jul 2014 Microtubules similarity (2) #43 - Jul 2003 Src Tyrosine Kinase similarity (2) #205 - Jan 2017 Nuclear Pore Complex similarity (5) #245 - May 2020 Spliceosomes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: CLIP-associating protein 2

B: CLIP-associating protein 2

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

1

A: CLIP-associating protein 2

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

2

B: CLIP-associating protein 2

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

Unit cell

Length a, b, c (Å)	66.083, 47.116, 74.152
Angle α, β, γ (deg.)	90.00, 115.83, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	CLIP-associating protein 2 / Cytoplasmic linker-associated protein 2 / Protein Orbit homolog 2 / hOrbit2 Mass: 25754.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLASP2, KIAA0627 / Production host: Escherichia coli (E. coli) / References: UniProt: O75122
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.02 Å³/Da / Density % sol: 39.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30mM Sodium fluoride; 30mM Sodium bromide; 30mM Sodium iodide; 100mM Tris(Base)/Bicine pH 8.5; 12.5% v/v MPD; 12.5% PEG1000; 12.5% PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 26, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.19→38.5 Å / Num. obs: 128081 / % possible obs: 99 % / Redundancy: 6.2 % / Net I/σ(I): 13.42

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_2420: ???)	refinement
XDS		data reduction
XSCALE		data scaling
SHELXCD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.198→38.491 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.21

	R_factor	Num. reflection	% reflection
R_free	0.2136	2003	1.57 %
R_work	0.2003	-	-
obs	0.2005	127811	98.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.198→38.491 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3360	0	0	770	4130

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3423
X-RAY DIFFRACTION	f_angle_d	1.273	4612
X-RAY DIFFRACTION	f_dihedral_angle_d	14.969	1294
X-RAY DIFFRACTION	f_chiral_restr	0.079	529
X-RAY DIFFRACTION	f_plane_restr	0.006	584

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 (%)
1.1976-1.2275	0.297	130	0.2954	8062	X-RAY DIFFRACTION	89
1.2275-1.2607	0.2986	133	0.2798	8831	X-RAY DIFFRACTION	98
1.2607-1.2978	0.2513	145	0.2594	8968	X-RAY DIFFRACTION	99
1.2978-1.3397	0.2665	148	0.249	9030	X-RAY DIFFRACTION	100
1.3397-1.3876	0.2452	142	0.2375	9068	X-RAY DIFFRACTION	100
1.3876-1.4431	0.2308	142	0.2312	9003	X-RAY DIFFRACTION	100
1.4431-1.5088	0.2249	144	0.2151	9045	X-RAY DIFFRACTION	100
1.5088-1.5884	0.2155	144	0.1997	9052	X-RAY DIFFRACTION	100
1.5884-1.6879	0.2192	147	0.1965	9118	X-RAY DIFFRACTION	100
1.6879-1.8182	0.2116	140	0.1932	9037	X-RAY DIFFRACTION	100
1.8182-2.0012	0.2072	152	0.1948	9068	X-RAY DIFFRACTION	100
2.0012-2.2907	0.1987	141	0.1839	9098	X-RAY DIFFRACTION	100
2.2907-2.8859	0.2141	146	0.1952	9155	X-RAY DIFFRACTION	100
2.8859-38.5113	0.1964	149	0.1853	9273	X-RAY DIFFRACTION	100

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	3.8077	2.0297	-0.1685	5.0254	-0.4335	2.3724	-0.1037	-0.205	0.0618	0.2573	-0.1812	0.0252	-0.1489	0.0836	0.1589	0.2984	-0.0201	0.0513	0.2526	-0.0073	0.2218	21.0911	-7.8239	51.4476
2	1.4357	0.4454	-0.0132	3.8238	-0.7052	1.6157	-0.0209	-0.1661	-0.2211	0.347	-0.1008	-0.1011	0.0153	0.2618	0.0567	0.3115	-0.0092	-0.0025	0.2347	0.0117	0.1708	28.6204	-12.3668	48.9594
3	3.898	-2.8516	1.1253	2.0893	-0.8198	0.3256	-0.0474	-0.3937	-0.2735	0.3649	0.2471	0.1236	0.1719	0.0829	-0.061	0.4153	0	0.0955	0.3523	0.0513	0.3696	13.94	-18.6802	46.7393
4	4.396	1.7306	-0.5225	1.7974	-0.3031	0.9445	-0.0026	0.0758	0.0678	0.0092	0.0293	0.0513	-0.1853	-0.0115	-0.0211	0.1194	-0.0045	0.0001	0.1416	-0.0059	0.1313	21.8936	-7.0527	41.2939
5	1.608	0.6868	-0.1996	1.4114	-0.1812	0.9522	0.0273	-0.1008	-0.1049	0.0934	-0.0701	0.0401	0.053	-0.0045	0.0437	0.1078	-0.0026	0.0091	0.1127	-0.0035	0.126	24.8309	-12.37	35.4816
6	2.8207	1.6603	0.4208	1.9323	0.4064	0.7701	0.005	0.0372	-0.2468	0.0475	-0.0222	-0.1929	0.1161	0.0474	0.037	0.0922	0.0082	0.0065	0.1104	0.0014	0.1443	31.5747	-14.3611	29.559
7	1.2387	0.9484	-0.3211	1.4995	-0.4687	0.5587	-0.0261	0.0633	0.116	-0.0033	0.0274	0.261	-0.0153	-0.188	0.0056	0.1156	0.0052	0.0093	0.143	-0.0111	0.1382	22.3433	-9.2584	21.4091
8	0.435	0.4724	-0.0505	2.497	0.2202	0.434	0.0324	0.0118	-0.1012	0.0841	-0.0588	-0.0786	0.1195	0.0537	0.0343	0.1134	0.0088	0.0065	0.0989	0.0026	0.1209	31.87	-12.8613	19.6452
9	4.4212	-5.0941	0.577	7.7103	-3.3009	3.8516	0.0018	0.139	-0.1336	-0.1526	0.0697	0.2801	0.2075	-0.1639	-0.0135	0.1893	0.0012	0.0059	0.2255	0.0311	0.229	20.7351	-21.1001	13.7723
10	0.2182	0.0284	0.2331	1.0873	0.3592	0.6526	-0.0353	0.0101	-0.057	0.0231	0.0278	-0.0264	0.0393	0.0472	0.0103	0.0967	0.013	0.0096	0.1116	0.0041	0.0907	31.5501	-10.4636	10.2615
11	0.4852	-0.2853	0.0099	1.8047	-0.3263	0.6407	-0.0004	0.0002	-0.1088	-0.0274	-0.0199	-0.0413	0.0788	0.0352	0.0173	0.1296	-0.0017	0.0157	0.1089	0.0024	0.1062	32.0337	-12.5254	0.0673
12	0.3215	0.0881	0.2698	0.0357	0.0339	0.5738	0.2366	-0.54	-0.0887	0.1942	-0.1116	0.0644	0.1619	-0.34	0.2307	0.3702	-0.341	-0.0447	0.6983	-0.0866	0.105	40.865	15.7606	58.7463
13	0.6672	0.3765	0.1696	0.841	0.0822	0.54	0.3375	-0.5034	-0.2711	0.2426	-0.3088	-0.0664	0.1766	-0.0878	-0.007	0.1848	-0.0926	-0.0304	0.2822	0.0146	0.1553	40.1105	12.1734	45.3552
14	0.6048	0.0575	0.1941	0.6308	0.0413	1.169	-0.0069	-0.0248	0.0203	-0.0026	-0.0462	-0.0218	-0.0524	0.0775	0.0537	0.098	0.0049	-0.008	0.1	0.0061	0.1012	39.8483	14.9334	27.7737
15	1.0851	-0.2951	-0.0472	1.8514	-0.1579	0.94	-0.0688	-0.0915	-0.0574	-0.0635	-0.0444	-0.1542	0.1809	0.2653	0.1017	0.1657	0.0515	0.0275	0.1731	0.0252	0.1091	41.1222	13.2823	11.4693

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 33 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 45 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 46 through 64 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 65 through 102 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 103 through 122 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 123 through 141 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 142 through 159 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 160 through 165 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 166 through 199 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 200 through 229 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 10 through 64 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 65 through 122 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 123 through 199 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 200 through 229 )

-
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