[English] 日本語
Yorodumi
- PDB-6x1f: Tubulin-RB3_SLD-TTL in complex with compound 5m -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x1f
TitleTubulin-RB3_SLD-TTL in complex with compound 5m
Components
  • Stathmin-4
  • Tubulin Tyrosine Ligase
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE/INHIBITOR / MICROTUBULE INHIBITOR / COLCHICINE / CELL CYCLE / CANCER / CELL CYCLE-INHIBITOR COMPLEX
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. ...Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-Y5M / Tubulin beta chain / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsWhite, S.W. / Yun, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA148706 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: X-ray Crystallography-Guided Design, Antitumor Efficacy, and QSAR Analysis of Metabolically Stable Cyclopenta-Pyrimidinyl Dihydroquinoxalinone as a Potent Tubulin Polymerization Inhibitor.
Authors: Banerjee, S. / Mahmud, F. / Deng, S. / Ma, L. / Yun, M.K. / Fakayode, S.O. / Arnst, K.E. / Yang, L. / Chen, H. / Wu, Z. / Lukka, P.B. / Parmar, K. / Meibohm, B. / White, S.W. / Wang, Y. / Li, W. / Miller, D.D.
History
DepositionMay 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,98720
Polymers261,3056
Non-polymers3,68214
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.480, 157.923, 182.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein Tubulin Tyrosine Ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

-
Non-polymers , 8 types, 294 molecules

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


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: 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
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-Y5M / 7-methoxy-4-(2-methyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-3,4-dihydroquinoxalin-2(1H)-one


Mass: 310.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N4O2 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG 4000, 5% glycerol, 0.1M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 84115 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 41.02 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.045 / Net I/σ(I): 17.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4130 / CC1/2: 0.592 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6BR1

6br1


Resolution: 2.7→48.24 Å / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 24.5364 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2408 2000 2.47 %
Rwork0.1903 78919 -
obs0.1915 80919 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17142 0 230 280 17652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002117781
X-RAY DIFFRACTIONf_angle_d0.532324115
X-RAY DIFFRACTIONf_chiral_restr0.0412619
X-RAY DIFFRACTIONf_plane_restr0.00373118
X-RAY DIFFRACTIONf_dihedral_angle_d17.832410629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.3132910.28253605X-RAY DIFFRACTION62.24
2.77-2.840.34331290.26375083X-RAY DIFFRACTION87.8
2.84-2.930.28811440.25055687X-RAY DIFFRACTION97.8
2.93-3.020.331470.24395770X-RAY DIFFRACTION99.68
3.02-3.130.26311460.23965771X-RAY DIFFRACTION99.81
3.13-3.250.2881470.22165802X-RAY DIFFRACTION99.95
3.25-3.40.26131480.20855833X-RAY DIFFRACTION100
3.4-3.580.23881470.19215825X-RAY DIFFRACTION99.98
3.58-3.810.25481480.17955819X-RAY DIFFRACTION100
3.81-4.10.21351480.16245856X-RAY DIFFRACTION99.8
4.1-4.510.19931480.1475876X-RAY DIFFRACTION100
4.51-5.160.19161500.14575896X-RAY DIFFRACTION99.9
5.16-6.50.25761510.18795943X-RAY DIFFRACTION99.89
6.5-48.240.20691560.18296153X-RAY DIFFRACTION99.4
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)
10.947614352238-0.06749352610280.1956462359812.310526671171.282404557892.190606042930.0400812305240.0237050720492-0.101314310458-0.04700779208060.258141749409-0.2437501660130.3164957022230.317228320209-0.2430806961290.2592187684270.036283130142-0.03777432678210.2946573448-0.1469441991420.30762806351425.5885558799-83.4422847871-61.5825997301
20.7248683666920.4692040530430.3409293324831.748768136471.125091710212.245257763920.0540876446582-0.013503446723-0.142553879680.0767871163907-0.01375501576310.06162995233760.254888009412-0.0796848743047-0.09570265465960.1126065408340.0115679936182-0.02740170031420.23769304421-0.07715087917890.28163819038615.6770217763-57.7731605213-29.2847504522
30.8103739596890.163422443288-0.09863207207941.323612031370.432215852371.54448336315-0.0835487380807-0.144168243468-0.03862961251320.132288604160.02015179552830.0803404601090.0227603728621-0.09501635628910.03169689624360.1371932934440.0645507666966-0.003652849161140.223678909849-0.03702507263650.22221999617612.9776795601-29.26731260773.62512645366
41.47063247427-0.1136374708040.3475345060971.546603069180.4066466929021.99746652957-0.467492904466-0.8192444397570.261398515690.5050092862190.3790887547930.0761422667555-0.467901041197-0.2917090842910.067902120270.644180326920.301037374937-0.1379078124520.648880932625-0.3190699616570.2849055043618.18788771811.8931483665331.3855193837
50.3081815415760.2181016524130.3295966163160.9083362982360.7175179934091.12815149645-0.04993265981910.0634252561235-0.0423214040603-0.315908235530.544627035111-0.589776907252-0.4084151756390.709665163632-0.3104659077460.220003136391-0.0241336757165-0.04210427601850.551409750791-0.2515931473090.47977442064739.718121318-41.1772039601-20.3513085684
61.33423816772-0.1765662053991.512053094911.1291753447-0.2923780240822.00490043151-0.3523696605890.3673728034160.544376421735-0.3993328129720.113918982159-0.0536106553411-0.6782066042790.2597927704830.01190974655470.793625612025-0.117022638159-0.1668088600230.3964270251460.1005065784120.5224968277244.12508986141-56.0732674692-91.5486460299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 437)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 428)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 440)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 431)
5X-RAY DIFFRACTION5(chain 'E' and resid 6 through 141)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 380)

+
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://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