[English] 日本語
Yorodumi
- PDB-6zwb: Z-SBTub3 photoswitch bound to tubulin-DARPin D1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zwb
TitleZ-SBTub3 photoswitch bound to tubulin-DARPin D1 complex
Components
  • Designed Ankyrin Repeat Protein (DARPIN) D1
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / photopharmacology / microtubule dynamics / cytoskeleton / tubulin polymerisation inhibitor / colchicine / antimitotic / azobenzene / cell division / spatiotemporal control
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 / nervous system development / mitotic cell cycle / microtubule / protein heterodimerization activity ...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 / nervous system development / mitotic cell cycle / microtubule / protein heterodimerization activity / GTPase activity / GTP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-QRN / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.747 Å
AuthorsWranik, M. / Weinert, T. / Olieric, N. / Gao, L. / Kraus, Y.C.M. / Bingham, R. / Ntouliou, E. / Ahlfeld, J. / Thorn-Seshold, O. / Steinmetz, M.O. / Standfuss, J.
CitationJournal: Cell Chem Biol / Year: 2021
Title: A Robust, GFP-Orthogonal Photoswitchable Inhibitor Scaffold Extends Optical Control over the Microtubule Cytoskeleton.
Authors: Gao, L. / Meiring, J.C.M. / Kraus, Y. / Wranik, M. / Weinert, T. / Pritzl, S.D. / Bingham, R. / Ntouliou, E. / Jansen, K.I. / Olieric, N. / Standfuss, J. / Kapitein, L.C. / Lohmuller, T. / ...Authors: Gao, L. / Meiring, J.C.M. / Kraus, Y. / Wranik, M. / Weinert, T. / Pritzl, S.D. / Bingham, R. / Ntouliou, E. / Jansen, K.I. / Olieric, N. / Standfuss, J. / Kapitein, L.C. / Lohmuller, T. / Ahlfeld, J. / Akhmanova, A. / Steinmetz, M.O. / Thorn-Seshold, O.
History
DepositionJul 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
F: Designed Ankyrin Repeat Protein (DARPIN) D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5497
Polymers118,2733
Non-polymers1,2764
Water11,980665
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-39 kcal/mol
Surface area36540 Å2
Unit cell
Length a, b, c (Å)73.869, 91.724, 83.006
Angle α, β, γ (deg.)90.000, 97.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
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 natural source / Source: (natural) 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 natural source / Source: (natural) 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: synthetic construct (others)

-
Non-polymers , 5 types, 669 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-QRN / 5-[2-(1,3-benzothiazol-2-yl)ethyl]-2-methoxy-phenol


Mass: 285.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15NO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3000, ammonium sulfate, bis-tris methane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2019
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.747→45.039 Å / Num. obs: 68165 / % possible obs: 61.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 23.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.054 / Rrim(I) all: 0.119 / Net I/σ(I): 9.2
Reflection shellResolution: 1.747→1.973 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3408 / CC1/2: 0.649 / Rpim(I) all: 0.424 / Rrim(I) all: 0.877 / % possible all: 10

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NM5

5nm5


Resolution: 1.747→45.039 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 2000 2.93 %
Rwork0.185 66146 -
obs0.1864 68146 61.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 371.86 Å2 / Biso mean: 44.3475 Å2 / Biso min: 7.84 Å2
Refinement stepCycle: final / Resolution: 1.747→45.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7873 0 113 665 8651
Biso mean--29.52 50.78 -
Num. residues----1023
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.747-1.79020.313830.33961232
1.7902-1.83860.1845160.28324906
1.8386-1.89280.3315250.298586011
1.8928-1.95380.3403410.2616134918
1.9538-2.02370.313610.2567200726
2.0237-2.10470.2849910.2479301039
2.1047-2.20050.30411520.2514503766
2.2005-2.31650.26672170.2469714393
2.3165-2.46160.26452320.2227678100
2.4616-2.65170.23352310.20667669100
2.6517-2.91850.24752330.20367706100
2.9185-3.34070.25422290.1834757398
3.3407-4.20840.19552340.14897733100
4.2084-45.0390.20032350.1451776899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.0492-0.49210.40831.40070.32381.36450.0985-0.0919-0.032-0.0007-0.0006-0.17750.12810.6384-0.02540.10580.0052-0.01160.2638-0.05090.1227124.724819.731111.2658
21.4487-0.1423-0.11570.7819-0.21381.51070.0027-0.115-0.02780.03130.0287-0.0151-0.1730.2167-0.0140.1422-0.05860.00370.0631-0.0410.072112.560628.354319.9385
31.26090.0899-0.26151.0459-0.08511.50680.0290.12810.04910.0287-0.0610.0839-0.13230.04220.01580.1868-0.0247-0.00330.1117-0.04720.116110.134226.09232.1352
41.1251-0.2958-0.63080.2140.24031.39480.06550.2807-0.1043-0.1025-0.06010.087-0.1465-0.0698-0.0060.1949-0.0243-0.01810.1206-0.02140.1201107.378227.6313-6.9047
50.97640.5406-0.7631.9303-1.12681.19890.1613-0.06050.1917-0.0128-0.0219-0.0007-0.3167-0.0245-0.06750.29530.0040.06510.0649-0.01840.166796.195740.997317.1799
62.0249-0.329-0.04641.0190.00561.0020.0584-0.8786-0.47480.3311-0.1258-0.4130.33410.3458-0.08010.04580.0858-0.09260.23810.17970.366892.77856.70946.2615
72.0664-0.1998-0.35050.8752-0.02180.93410.0241-0.34730.21490.0402-0.0363-0.1454-0.15150.17850.03640.1151-0.036-0.04450.18370.02150.178584.537419.716544.1611
81.1307-0.098-0.22951.4897-0.38191.2371-0.041-0.0036-0.3077-0.151-0.007-0.14660.14380.0260.03740.1130.00340.00110.11880.01680.205581.723911.430431.7229
92.13490.606-0.45530.3258-0.16183.3036-0.1480.4424-0.5945-0.11910.2407-0.16530.5498-0.2455-0.10110.2325-0.0572-0.0180.2811-0.05970.306875.19747.163122.4881
101.13990.1599-0.22121.0229-0.07331.0894-0.00230.4081-0.1866-0.2573-0.0249-0.14020.155-0.1782-0.00080.1599-0.00980.00660.161-0.03720.155979.63215.816123.1287
112.02510.2102-0.57690.625-0.71133.03470.3212-0.26140.55740.0728-0.1357-0.0572-0.51680.1445-0.04330.2363-0.02070.04980.1322-0.01870.284372.175429.90342.8026
122.6563-0.7798-0.83472.8390.4364.385-0.1432-0.20310.2793-0.00640.1056-0.2494-0.46930.6562-0.00390.2978-0.0202-0.05290.50320.01290.153455.345723.698570.3698
134.89460.2724-2.60931.73972.18674.5460.1939-0.1606-0.14910.7060.22960.23150.25020.38090.07630.57090.21840.09720.48620.14030.239952.125415.496373.5123
141.04330.0503-0.17852.05450.09861.4085-0.0656-0.17990.03390.1845-0.0383-0.1278-0.04820.2970.02130.14850.0094-0.01170.23390.01380.130351.775323.294463.7852
151.7669-0.0494-0.61022.14280.89273.3803-0.1383-0.3368-0.44520.1290.08070.11110.3966-0.09490.07110.23510.02210.06390.25190.14520.24446.660812.939664.1119
162.2416-0.4691-0.22461.037-0.02852.0482-0.026-0.2724-0.19090.11250.03510.09730.01270.028-0.01930.1055-0.00470.00140.16080.00590.089249.202219.336153.6749
171.1622-0.0153-0.06980.8116-0.02780.89870.05290.14830.03280.01690.02010.0714-0.1333-0.129-0.08350.11350.0046-0.02040.1701-0.00840.112850.719222.018545.4457
189.4016-0.0592-2.67770.77150.10983.4738-0.02750.0284-0.8848-0.13740.07530.05220.4804-0.053-0.02460.1817-0.0612-0.01140.1932-0.04510.226749.676410.71442.446
192.3071.724-1.19864.8884-1.90872.19420.05980.0178-0.0119-0.0721-0.17850.0201-0.2288-0.10650.09080.14810.0076-0.06660.23910.03170.085648.772924.47737.0425
202.9891-0.312-0.06710.48190.20480.7659-0.13440.1554-0.0154-0.48370.0683-0.1387-0.14490.17330.02910.2274-0.0128-0.02050.2513-0.02470.196557.592519.099632.3501
218.8751-0.57794.26332.05070.02532.09590.08930.4421-0.8381-0.42850.00060.38890.2964-0.2189-0.01550.2155-0.0227-0.01010.3016-0.05040.285853.362110.946832.5215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 72 )A1 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 197 )A73 - 197
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 273 )A198 - 273
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 401 )A274 - 401
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 437 )A402 - 437
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 127 )B1 - 127
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 199 )B128 - 199
8X-RAY DIFFRACTION8chain 'B' and (resid 200 through 273 )B200 - 273
9X-RAY DIFFRACTION9chain 'B' and (resid 274 through 311 )B274 - 311
10X-RAY DIFFRACTION10chain 'B' and (resid 312 through 401 )B312 - 401
11X-RAY DIFFRACTION11chain 'B' and (resid 402 through 441 )B402 - 441
12X-RAY DIFFRACTION12chain 'F' and (resid 13 through 24 )F13 - 24
13X-RAY DIFFRACTION13chain 'F' and (resid 25 through 35 )F25 - 35
14X-RAY DIFFRACTION14chain 'F' and (resid 36 through 59 )F36 - 59
15X-RAY DIFFRACTION15chain 'F' and (resid 60 through 69 )F60 - 69
16X-RAY DIFFRACTION16chain 'F' and (resid 70 through 101 )F70 - 101
17X-RAY DIFFRACTION17chain 'F' and (resid 102 through 125 )F102 - 125
18X-RAY DIFFRACTION18chain 'F' and (resid 126 through 134 )F126 - 134
19X-RAY DIFFRACTION19chain 'F' and (resid 135 through 148 )F135 - 148
20X-RAY DIFFRACTION20chain 'F' and (resid 149 through 158 )F149 - 158
21X-RAY DIFFRACTION21chain 'F' and (resid 159 through 167 )F159 - 167

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more