PDB-8whh: Crystal structure of Se-Met derivative CLASP2 in complex with CLIP170

ID or keywords:

Entry

Database: PDB / ID: 8whh

Title

Crystal structure of Se-Met derivative CLASP2 in complex with CLIP170

Components

CLIP-associating protein 2
CLIP1 protein

Keywords

PROTEIN BINDING / Complex

Function / homology

Function and homology information

presynaptic cytoskeleton organization / cortical microtubule plus-end / negative regulation of wound healing, spreading of epidermal cells / vesicle targeting / microtubule anchoring / basal cortex / positive regulation of extracellular matrix disassembly / Role of ABL in ROBO-SLIT signaling / microtubule organizing center organization / kinetochore microtubule ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.801 Å

Authors

Jin, G. / Wei, Z.

Funding support

China, 4items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	31971131	China
National Natural Science Foundation of China (NSFC)	32170697	China
National Natural Science Foundation of China (NSFC)	32370743	China
National Natural Science Foundation of China (NSFC)	32371009	China

Citation

Journal: Nat Commun / Year: 2024
Title: CLASP-mediated competitive binding in protein condensates directs microtubule growth.
Authors: Jia, X. / Lin, L. / Guo, S. / Zhou, L. / Jin, G. / Dong, J. / Xiao, J. / Xie, X. / Li, Y. / He, S. / Wei, Z. / Yu, C.

History

Deposition	Sep 23, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Aug 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8whh.cif.gz	530.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8whh.ent.gz	443.8 KB	Display	PDB format
PDBx/mmJSON format	8whh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8whh_validation.pdf.gz	478.1 KB	Display	wwPDB validaton report
Full document	8whh_full_validation.pdf.gz	486.6 KB	Display
Data in XML	8whh_validation.xml.gz	41.8 KB	Display
Data in CIF	8whh_validation.cif.gz	57.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wh/8whh ftp://data.pdbj.org/pub/pdb/validation_reports/wh/8whh	HTTPS FTP

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Related structure data

Related structure data	8whiC 8whjC 8whkC 8whlC 8whmC C: citing same article (ref.)
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	#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

E: CLIP1 protein

F: CLIP1 protein

B: CLIP-associating protein 2

C: CLIP-associating protein 2

D: CLIP-associating protein 2

G: CLIP1 protein

H: CLIP1 protein

157 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: CLIP-associating protein 2

G: CLIP1 protein

H: CLIP1 protein

A: CLIP-associating protein 2

defined by author
Evidence: gel filtration, Two heterotetramers in one ASU are formed by chains B/C/E/F and chains A/D/G/H, respectively. To generate the proper heterotetramers, the symmetry mates of chains A and C in ...Evidence: gel filtration, Two heterotetramers in one ASU are formed by chains B/C/E/F and chains A/D/G/H, respectively. To generate the proper heterotetramers, the symmetry mates of chains A and C in the coordinate should be used.
78.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: CLIP1 protein

F: CLIP1 protein

B: CLIP-associating protein 2

C: CLIP-associating protein 2

defined by author
78.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.115, 100.826, 226.065
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	CLIP-associating protein 2 / Cytoplasmic linker-associated protein 2 / Protein Orbit homolog 2 / hOrbit2 Mass: 26678.258 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLASP2, KIAA0627 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75122
#2: Protein	CLIP1 protein Mass: 12689.077 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLIP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6P5Z9
Has ligand of interest	N
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: 3.13 Å³/Da / Density % sol: 60.76 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v PEG 3,350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.987 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.987 Å / Relative weight: 1

Reflection

Resolution: 3.8→50 Å / Num. obs: 37419 / % possible obs: 100 % / Redundancy: 7.8 % / CC_1/2: 0.994 / CC star: 0.999 / R_merge(I) obs: 0.128 / R_pim(I) all: 0.049 / R_rim(I) all: 0.137 / Χ²: 0.623 / Net I/σ(I): 3.1 / Num. measured all: 291365

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.8-3.87	8	1.212	1873	0.838	0.955	0.453	1.295	0.472	100
3.87-3.94	8	1.041	1857	0.806	0.945	0.387	1.111	0.707	100
3.94-4.01	8.1	0.891	1887	0.915	0.977	0.33	0.951	0.472	100
4.01-4.09	8	0.656	1869	0.953	0.988	0.246	0.701	0.467	100
4.09-4.18	8.1	0.611	1871	0.955	0.988	0.228	0.653	0.475	100
4.18-4.28	8	0.538	1868	0.947	0.986	0.201	0.574	0.488	100
4.28-4.39	7.9	0.447	1862	0.945	0.986	0.168	0.478	0.485	100
4.39-4.5	7.9	0.378	1878	0.962	0.99	0.142	0.405	0.514	100
4.5-4.64	7.9	0.354	1872	0.969	0.992	0.133	0.379	0.528	100
4.64-4.79	7.8	0.309	1875	0.982	0.995	0.118	0.331	0.509	100
4.79-4.96	7.7	0.274	1863	0.987	0.997	0.105	0.294	0.549	99.9
4.96-5.16	7.1	0.234	1865	0.99	0.997	0.093	0.252	0.578	99.8
5.16-5.39	6.9	0.25	1872	0.986	0.996	0.101	0.27	0.568	99.9
5.39-5.67	7.2	0.295	1869	0.969	0.992	0.118	0.318	0.498	100
5.67-6.03	8.1	0.277	1891	0.982	0.995	0.103	0.295	0.544	100
6.03-6.49	8.1	0.2	1838	0.988	0.997	0.074	0.213	0.561	100
6.49-7.15	8.1	0.116	1894	0.996	0.999	0.043	0.124	0.641	100
7.15-8.18	7.9	0.077	1850	0.998	0.999	0.029	0.083	0.798	99.9
8.18-10.29	7.1	0.055	1876	0.998	1	0.022	0.059	1.123	99.9
10.29-50	7.6	0.054	1889	0.997	0.999	0.022	0.058	1.553	99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data scaling
HKL-2000		data reduction
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.801→49.427 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2663	1858	4.99 %
R_work	0.2168	-	-
obs	0.2193	37252	99.56 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.801→49.427 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10075	0	0	0	10075

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10187
X-RAY DIFFRACTION	f_angle_d	0.821	13774
X-RAY DIFFRACTION	f_dihedral_angle_d	10.795	3874
X-RAY DIFFRACTION	f_chiral_restr	0.032	1679
X-RAY DIFFRACTION	f_plane_restr	0.004	1768

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 (%)
3.8014-3.9042	0.342	144	0.3153	2738	X-RAY DIFFRACTION	99
3.9042-4.019	0.3014	144	0.2757	2723	X-RAY DIFFRACTION	100
4.019-4.1487	0.3124	148	0.2675	2714	X-RAY DIFFRACTION	100
4.1487-4.2969	0.2807	141	0.2532	2719	X-RAY DIFFRACTION	100
4.2969-4.4688	0.2476	142	0.2285	2698	X-RAY DIFFRACTION	100
4.4688-4.672	0.2681	146	0.2159	2740	X-RAY DIFFRACTION	100
4.672-4.9182	0.2728	145	0.216	2739	X-RAY DIFFRACTION	100
4.9182-5.226	0.3275	143	0.2249	2691	X-RAY DIFFRACTION	99
5.226-5.629	0.2772	142	0.2532	2728	X-RAY DIFFRACTION	100
5.629-6.1944	0.3789	147	0.266	2755	X-RAY DIFFRACTION	100
6.1944-7.0885	0.2845	139	0.2354	2725	X-RAY DIFFRACTION	100
7.0885-8.9223	0.2415	136	0.1894	2727	X-RAY DIFFRACTION	100
8.9223-49.427	0.2192	141	0.1701	2697	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	0.9808	-0.6958	-0.6035	0.8543	1.1321	1.781	-0.0071	-0.6903	0.3045	-1.0769	0.1837	-0.3464	0.0792	1.1047	-0.3869	2.6049	0.9137	0.2824	3.5803	-1.1831	0.4124	43.2571	60.8342	-3.9753
2	4.1809	2.4751	-2.9071	7.2146	-3.8003	5.532	0.5155	-3.7116	0.5412	-0.8372	-0.3194	0.759	1.9864	0.0009	0.3583	1.7057	0.166	-0.0528	2.266	0.414	1.0655	51.2658	55.1991	-7.6686
3	8.134	0.3792	-3.2205	5.9599	1.0506	6.4435	-0.7497	-0.4877	-0.5766	0.2199	0.4765	-0.1688	0.2614	0.3563	0.3176	1.1611	0.2849	0.0599	1.5062	0.097	0.8542	47.463	59.061	-19.9498
4	6.9616	2.2104	-0.7656	6.4757	-3.4507	3.3499	-0.2239	0.0684	-0.0694	-0.2144	-0.0189	0.3043	0.2425	0.7059	0.2947	1.1185	0.183	0.0154	0.8041	-0.0556	0.9937	51.7673	59.648	-44.4914
5	-0.7445	-0.1699	0.3535	0.8038	-2.6445	4.5851	-0.5552	0.1284	-0.0227	-0.6509	0.2426	-0.1939	1.272	-1.3924	0.2772	1.8668	-0.0279	0.027	1.7555	0.3972	1.3206	29.9669	56.7375	-8.8166
6	0.0554	0.1988	0.8858	1.8407	-4.0448	6.7179	-0.0101	-0.0222	-0.2236	0.864	-0.3828	0.01	-1.5719	1.3849	0.4296	1.8232	0.355	0.2787	1.4033	0.2659	1.2304	29.8219	58.2362	-8.3225
7	6.6325	-3.1859	-1.4632	7.6817	-0.2891	5.82	1.2344	2.8181	0.2328	0.4386	-3.0752	1.6849	-0.7033	1.0415	1.4137	1.4779	-0.0992	-0.2307	2.8428	-0.0336	0.7784	5.727	40.2281	11.3812
8	8.497	0.2867	2.5543	5.5757	1.402	5.0916	-0.4774	1.8979	0.6939	0.0091	0.1708	-0.0907	-0.2826	-0.2859	0.362	1.0637	-0.0483	-0.0769	1.2513	0.1578	0.9455	4.9237	41.0141	30.7705
9	8.008	-3.593	0.7372	5.5272	-5.4725	8.1282	-0.225	-0.6579	0.2454	1.6279	-0.3335	0.5107	-0.6668	0.5504	0.5032	1.1938	-0.203	0.1138	0.7695	-0.2459	1.1639	12.089	41.2346	54.3466
10	7.8784	3.8356	4.4413	3.5178	4.4775	6.2655	-0.4077	-0.5696	1.0231	0.0018	-1.1977	2.0812	-0.9715	-0.921	0.8486	0.6963	0.7499	0.6764	2.3931	0.3528	2.974	-25.3867	46.7706	13.315
11	2.2431	3.2047	-2.2667	6.0911	-6.0438	7.4305	1.3122	1.9374	0.0297	1.0244	0.9415	2.3716	-0.3749	-2.4291	-1.7584	1.6842	-0.1288	-0.0337	3.2457	0.477	1.8156	-34.4244	40.5506	11.3216
12	6.4298	1.958	-1.8626	7.8797	-3.1214	6.4553	-1.0171	1.7418	-0.6328	0.0253	0.5044	0.5135	-0.6409	-0.9776	0.5488	0.968	0.1114	0.1739	1.4783	-0.2377	1.6723	-28.6399	33.37	20.0527
13	5.5343	-0.8616	-2.3208	3.8609	-2.314	4.5945	0.5317	0.0881	-1.6552	0.423	0.47	2.0648	0.715	0.5512	-0.7614	1.6949	-0.2566	0.3344	1.0364	-0.4734	1.87	-33.2357	27.6976	31.0758
14	5.4088	-0.0479	1.6747	6.6263	-2.0866	3.8211	-1.0108	2.1133	-1.8606	-2.5325	2.2717	1.247	-0.6974	0.5252	-0.8202	0.9923	-0.3843	0.6545	1.0843	-0.7076	2.9563	-36.1897	20.8181	32.3324
15	3.769	4.9891	1.411	6.6352	2.6023	6.9077	-0.2025	-0.4665	-3.0238	-1.4582	1.9959	-0.4913	-0.4646	1.9884	-0.6984	1.9864	0.4462	-0.1276	1.5726	-0.4207	2.4638	-33.2131	14.9885	41.052
16	4.5523	0.5244	-1.582	4.8152	0.5884	5.9449	-0.2215	1.069	-1.3042	-0.2936	0.4295	-1.9882	1.4475	-1.1894	-0.4385	1.5956	0.001	0.3611	0.8031	0.0573	1.8192	-43.8603	13.4438	42.7863
17	0.9738	-0.7477	1.2118	2.009	-3.3373	5.5423	1.0876	-0.6392	-0.9853	-0.1962	-0.1029	0.8662	1.1123	-0.0849	-0.6808	0.2533	-0.4396	-1.3909	2.1069	0.8401	2.5466	16.8413	54.456	-2.095
18	8.4806	-5.8519	1.0771	5.4067	-2.0147	1.7776	0.2737	-3.3233	-3.546	-0.6021	0.6188	2.9906	0.4377	-0.0522	-1.0381	1.1844	-0.3286	-0.0309	2.2192	0.7138	2.8228	10.9048	54.4099	-7.6833
19	2.6133	-3.3561	-1.1235	9.5341	-3.1393	6.5991	-0.7839	-2.83	2.5518	0.9385	0.8627	0.2968	-0.1534	1.9924	0.2979	1.5224	-0.7761	-0.1949	2.6545	-0.2266	1.6081	17.9512	63.7504	-8.7458
20	0.0559	-0.1743	-0.1736	3.113	-5.4826	1.9952	-1.1983	-2.2681	2.4237	-0.1251	1.1883	1.2655	2.1133	-0.9701	0.3749	0.7102	0.1568	0.2059	1.912	-0.0495	2.4436	7.6768	62.2161	-13.4356
21	5.0532	0.1742	2.3698	4.0936	0.9739	5.8231	0.9768	-0.9743	-1.2413	0.3279	0.1231	-0.1321	0.0593	-0.0662	-1.1357	1.6174	0.0615	-0.2031	1.0692	0.0144	1.6662	9.8091	67.6505	-20.1862
22	3.1423	0.1944	0.548	3.3165	-1.9449	5.0868	-0.0747	-0.1976	1.3956	-0.8647	0.4369	-0.5288	-1.8832	-0.5216	-0.1484	1.3868	-0.1321	-0.3007	1.1995	-0.2465	2.026	7.1007	82.1211	-31.3787
23	3.8825	-1.8581	-5.2275	4.3333	3.1067	7.1404	-0.8491	-1.0178	3.0309	-0.9291	0.5978	-0.2115	-3.1997	0.5078	0.9562	2.3467	0.0548	-1.6185	1.9183	0.1852	2.1177	-7.0529	86.4181	-36.8403
24	0.07	0.3838	-0.5321	0.6307	-3.176	8.1197	-0.3174	-0.0871	-0.0329	0.5595	0.3064	0.0478	-1.0054	-0.7064	-0.2247	2.0923	0.4485	0.0471	1.4287	0.194	1.4118	-12.9592	43.1825	13.9196
25	0.4661	-0.1085	0.1251	3.3894	-5.0948	7.7064	-0.504	0.0976	0.1321	-0.672	-0.205	-0.2788	1.315	-0.3496	0.4276	1.497	-0.2211	-0.2095	1.0901	-0.0549	1.2654	-13.0324	40.9236	15.0539

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1256 through 1271 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1272 through 1292 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1293 through 1371 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1372 through 1477 )
5	X-RAY DIFFRACTION	5	chain 'E' and (resid 349 through 451 )
6	X-RAY DIFFRACTION	6	chain 'F' and (resid 349 through 450 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1257 through 1291 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1292 through 1408 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1409 through 1477 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1257 through 1271 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1272 through 1292 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1293 through 1351 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1352 through 1391 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1392 through 1408 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1409 through 1431 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1432 through 1477 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1256 through 1265 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1266 through 1292 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1293 through 1310 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 1311 through 1331 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1332 through 1370 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1371 through 1462 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 1463 through 1477 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 349 through 453 )
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 348 through 450 )

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