PDB-9f8g: Photostatin (photoswitchable azo-combretastatin) Z-PST27 bound to...

ID or keywords:

Entry

Database: PDB / ID: 9f8g

Title

Photostatin (photoswitchable azo-combretastatin) Z-PST27 bound to tubulin-DARPin D1 complex

Components

Designed Ankyrin Repeat Protein (DARPIN) D1
Tubulin alpha-1B chain
Tubulin beta-2B chain

Keywords

CELL CYCLE / tubulin polymerisation inhibitor / microtubule dynamics / antimitotics / photopharmacology / photoswitch / sensitisation

Function / homology

Function and homology information

positive regulation of axon guidance / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule / protein heterodimerization activity ...
Similarity search - Function

Biological species

Bos taurus (cattle)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Wranik, M. / Steinmetz, M.O.

Funding support

Switzerland, 1items

Citation

Journal: Chem Sci / Year: 2024
Title: A photo-SAR study of photoswitchable azobenzene tubulin-inhibiting antimitotics identifying a general method for near-quantitative photocontrol.
Authors: Reynders, M. / Garscia, M. / Muller-Deku, A. / Wranik, M. / Krauskopf, K. / de la Osa de la Rosa, L. / Schaffer, K. / Jotten, A. / Rode, A. / Stierle, V. / Kraus, Y. / Baumgartner, B. / Ali, ...

History

Deposition	May 6, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 4, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9f8g.cif.gz	603.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9f8g.ent.gz		Display	PDB format
PDBx/mmJSON format	9f8g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9f8g_validation.pdf.gz	990.4 KB	Display	wwPDB validaton report
Full document	9f8g_full_validation.pdf.gz	1001.9 KB	Display
Data in XML	9f8g_validation.xml.gz	44.6 KB	Display
Data in CIF	9f8g_validation.cif.gz	58.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f8/9f8g ftp://data.pdbj.org/pub/pdb/validation_reports/f8/9f8g	HTTPS FTP

-
Related structure data

Similar structure data	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 (19) #176 - Aug 2014 Dynein similarity (19) #241 - Jan 2020 Twenty Years of Molecules similarity (19)

Deposited unit

A: Tubulin alpha-1B chain

B: Tubulin beta-2B chain

F: Designed Ankyrin Repeat Protein (DARPIN) D1

hetero molecules

120 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	73.460, 91.115, 82.684
Angle α, β, γ (deg.)	90.00, 97.61, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Protein , 3 types, 3 molecules ABF

#1: Protein	Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain Mass: 50204.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: P81947
#2: Protein	Tubulin beta-2B chain Mass: 49999.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: TUBB2B / Production host: Bos taurus (cattle) / References: UniProt: Q6B856
#3: Protein	Designed Ankyrin Repeat Protein (DARPIN) D1 Mass: 18068.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia phage EcSzw-2 (virus) / Strain (production host): BL21

-
Non-polymers , 5 types, 171 molecules

#4: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#7: Chemical	ChemComp-A1IBN / 5-[(~{Z})-(3,5-diethyl-4-methoxy-phenyl)diazenyl]-2-methyl-phenol Mass: 298.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₂₂N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.96 % / Description: Monoclinic needles
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 21% PEG 3000 (w/v), 0.2 M ammonium sulfate and 0.1 M bis-tris methane

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.905→44.62 Å / Num. obs: 65942 / % possible obs: 78.16 % / Redundancy: 6.13 % / CC_1/2: 0.9903 / R_merge(I) obs: 0.135 / R_pim(I) all: 0.059 / R_rim(I) all: 0.148 / Net I/σ(I): 13.385
Reflection shell	Resolution: 1.905→2.032 Å / Redundancy: 3.69 % / R_merge(I) obs: 0.72 / Mean I/σ(I) obs: 1.837 / Num. unique obs: 3297 / CC_1/2: 0.6969 / R_pim(I) all: 0.439 / R_rim(I) all: 0.846 / % possible all: 22.34

-
Processing

Software

Name	Version	Classification
PHENIX	1.14-3260	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→44.62 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2256	1619	2.96 %
R_work	0.1871	-	-
obs	0.1883	54617	99.44 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.2→44.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7868	0	89	165	8122

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8657
X-RAY DIFFRACTION	f_angle_d	0.61	11878
X-RAY DIFFRACTION	f_dihedral_angle_d	13.564	1291
X-RAY DIFFRACTION	f_chiral_restr	0.042	1321
X-RAY DIFFRACTION	f_plane_restr	0.004	1577

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 (%)
2.2-2.26	0.2511	131	0.241	4265	X-RAY DIFFRACTION	97
2.26-2.34	0.2671	134	0.2336	4421	X-RAY DIFFRACTION	99
2.34-2.42	0.2734	134	0.2201	4373	X-RAY DIFFRACTION	100
2.42-2.52	0.2836	136	0.2149	4457	X-RAY DIFFRACTION	100
2.52-2.63	0.2143	134	0.1993	4400	X-RAY DIFFRACTION	100
2.63-2.77	0.228	136	0.2045	4437	X-RAY DIFFRACTION	100
2.77-2.95	0.2724	136	0.2095	4449	X-RAY DIFFRACTION	100
2.95-3.17	0.2287	134	0.2055	4418	X-RAY DIFFRACTION	100
3.17-3.49	0.2138	134	0.1917	4374	X-RAY DIFFRACTION	99
3.49-4	0.2009	136	0.1678	4446	X-RAY DIFFRACTION	100
4-5.03	0.1893	136	0.1441	4467	X-RAY DIFFRACTION	100
5.03-44.62	0.2313	138	0.184	4491	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	1.1635	0.7968	0.7332	2.561	-0.57	2.9421	0.1584	-0.0668	0.0013	0.0696	-0.0154	0.3047	0.1087	-0.8052	-0.0846	0.2573	0.0046	-0.0103	0.3898	0.0347	0.2355	-19.2667	-15.5193	31.6462
2	1.4127	0.499	0.5049	1.4546	0.2613	2.0723	0.0453	0.0751	-0.2982	-0.0207	-0.0116	0.0007	0.1862	-0.5606	-0.0599	0.2799	-0.0098	-0.0267	0.3367	0.0448	0.2307	-14.2198	-16.6047	21.3745
3	2.1232	0.1176	-0.0229	0.8796	0.346	2.1276	0.0402	0.0544	0.126	-0.1225	0.0046	-0.0433	-0.3382	-0.1233	-0.0204	0.3007	0.069	0.0296	0.175	0.0456	0.2124	-6.5797	-2.6314	21.5013
4	1.462	-0.2648	-0.1502	1.2986	0.4607	2.7152	0.0223	-0.1634	0.0443	-0.0856	0.0757	-0.0348	-0.2276	-0.1084	-0.0638	0.2952	0.0044	0.0031	0.2301	0.0355	0.2397	-4.1508	-9.1579	38.8208
5	1.1717	-0.5833	-0.4806	0.8838	1.1015	2.8046	0.0592	-0.3036	-0.1502	0.0161	-0.0612	-0.3623	0.0904	0.1941	-0.048	0.311	-0.0059	-0.0608	0.2556	0.0293	0.2881	0.628	-12.78	50.5379
6	2.1533	0.8771	-0.7539	1.9107	-0.4911	2.325	0.189	-0.3606	-0.0407	0.1859	-0.0253	-0	-0.2152	0.0206	-0.0761	0.3341	0.0499	-0.0197	0.3303	-0.0254	0.181	-8.9409	-4.8757	55.0114
7	1.5792	-0.4444	-0.3706	1.0704	-0.2541	2.0859	0.0489	-0.1707	-0.1428	0.1234	-0.1051	-0.1521	-0.1142	-0.1226	-0.0727	0.3407	0.0784	-0.0343	0.3546	0.0025	0.2523	-7.4665	-7.7403	49.6678
8	1.1002	0.1376	-0.518	0.1334	-0.3497	1.3325	0.1814	-0.0521	0.1753	0.0792	0.033	-0.0239	-0.4174	0.1453	-0.1739	0.3905	-0.0319	0.0744	0.2052	-0.0263	0.302	8.3855	3.2634	28.6875
9	2.5857	0.9424	-0.4872	2.123	-0.9934	2.4176	-0.0181	-0.0771	-0.6349	-0.007	0.0261	0.5699	0.1999	-0.3472	0.0663	0.297	-0.0423	-0.024	0.3452	-0.0695	0.7299	9.0998	-32.1783	2.9988
10	1.779	0.1504	-0.2914	1.2615	-0.0834	1.5202	0.0058	0.4171	-0.1649	-0.1839	-0.0681	0.2875	0.0804	-0.18	0.0349	0.2652	0.012	-0.0853	0.3323	-0.0883	0.394	19.7522	-20.7587	-5.8067
11	1.3316	-0.3443	0.3849	2.1037	-0.1694	0.92	-0.1108	-0.0731	-0.4675	0.1883	0.0105	0.2925	0.2072	-0.1318	0.1047	0.2748	-0.0035	0.0161	0.2532	-0.0344	0.4259	19.7539	-25.9421	9.8987
12	2.2853	-0.1111	-1.1058	0.9255	-0.1598	1.9129	0.0629	-0.3031	-0.0821	0.0785	-0.0463	0.1542	-0.007	0.1245	-0.0359	0.173	-0.0189	-0.0331	0.2179	-0.02	0.2379	28.1914	-16.3217	11.9452
13	3.7549	1.288	-0.5671	5.5809	-0.9574	3.9107	-0.1313	0.3859	0.3904	-0.2805	0.1049	0.5345	-0.7621	-0.6524	0.0295	0.4454	-0.0366	-0.0532	0.6405	-0.0855	0.2519	50.2635	-11.3751	-29.2345
14	2.9668	1.6236	-1.5806	3.1621	-1.371	4.5902	0.0722	0.2535	-0.6689	-1.237	-0.0014	-0.4138	0.3427	-0.125	-0.1722	0.8264	-0.0479	0.0658	0.6794	-0.1606	0.446	54.1164	-19.737	-32.4267
15	1.9286	0.1711	-0.3581	0.7042	-0.2177	2.1458	-0.0504	0.1295	-0.1637	-0.0217	0.0424	-0.062	0.0623	-0.0289	0.0239	0.1787	0.0077	-0.0034	0.2447	-0.0161	0.2043	55.3664	-15.6157	-13.1102
16	3.0901	-0.682	-0.1034	4.6854	0.5774	3.2067	0.1384	-0.2916	-0.0156	0.1572	-0.1191	0.0102	-0.2624	0.1563	0.0744	0.2467	-0.0047	-0.0394	0.3164	-0.0067	0.2121	56.5926	-10.5891	3.8221
17	2.7958	0.4301	0.587	4.3539	-0.8071	3.2854	-0.0223	-0.0418	-0.0406	0.4424	0.1371	-0.17	-0.107	0.0589	0.0028	0.2935	-0.0057	-0.034	0.3678	0.0147	0.2633	49.4162	-19.9377	8.6114

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 102 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 103 through 197 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 198 through 273 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 274 through 311 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 312 through 337 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 338 through 372 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 373 through 436 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 57 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 58 through 213 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 214 through 257 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 258 through 431 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 13 through 24 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 25 through 35 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 36 through 134 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 135 through 148 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 149 through 167 )

-
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://pdbjlvh1.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

-
Protein , 3 types, 3 molecules ABF

-
Non-polymers , 5 types, 171 molecules

-
Details

-
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

-Protein , 3 types, 3 molecules ABF

-Non-polymers , 5 types, 171 molecules

-Details

-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

-
Protein , 3 types, 3 molecules ABF

-
Non-polymers , 5 types, 171 molecules

-
Details

-
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