8CLG

Epothilone A and Colchicine bound to tubulin (T2R-TTL) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted EPClick on this verticalbar to view detailsBest fitted LOCClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.

Wranik, M.Kepa, M.W.Beale, E.V.James, D.Bertrand, Q.Weinert, T.Furrer, A.Glover, H.Gashi, D.Carrillo, M.Kondo, Y.Stipp, R.T.Khusainov, G.Nass, K.Ozerov, D.Cirelli, C.Johnson, P.J.M.Dworkowski, F.Beale, J.H.Stubbs, S.Zamofing, T.Schneider, M.Krauskopf, K.Gao, L.Thorn-Seshold, O.Bostedt, C.Bacellar, C.Steinmetz, M.O.Milne, C.Standfuss, J.

(2023) Nat Commun 14: 7956-7956

  • DOI: https://doi.org/10.1038/s41467-023-43523-5
  • Primary Citation of Related Structures:  
    8CL5, 8CL6, 8CL7, 8CL8, 8CL9, 8CLB, 8CLC, 8CLD, 8CLE, 8CLF, 8CLG, 8CLH

  • PubMed Abstract: 

    Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we describe a multi-reservoir, high viscosity extruder as a step towards automation of sample delivery at XFELs. Compared to a standard single extruder, sample exchange time was halved and the workload of users was greatly reduced. In-built temperature control of samples facilitated optimal extrusion and supported sample stability. After commissioning the device with lysozyme crystals, we collected time-resolved data using crystals of a membrane-bound, light-driven sodium pump. Static data were also collected from the soluble protein tubulin that was soaked with a series of small molecule drugs. Using these data, we identify low occupancy (as little as 30%) ligands using a minimal amount of data from a serial crystallography experiment, a result that could be exploited for structure-based drug design.


  • Organizational Affiliation

    Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland. maximilian.wranik@psi.ch.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain
A, C
440Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81947
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta-2B chain
B, D
431Bos taurusMutation(s): 0 
UniProt
Find proteins for Q6B856 (Bos taurus)
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UniProt GroupQ6B856
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Stathmin-4123synthetic constructMutation(s): 0 
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
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UniProt GroupP63043
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin-Tyrosine Ligase351synthetic constructMutation(s): 0 
EC: 6.3.2.25
UniProt
Find proteins for A0A8V0Z8P0 (Gallus gallus)
Explore A0A8V0Z8P0 
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UniProt GroupA0A8V0Z8P0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
G [auth A],
P [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP
Query on ACP

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V [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
EP (Subject of Investigation/LOI)
Query on EP

Download Ideal Coordinates CCD File 
L [auth B],
S [auth D]
EPOTHILONE A
C26 H39 N O6 S
HESCAJZNRMSMJG-KKQRBIROSA-N
GDP
Query on GDP

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N [auth B],
T [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
LOC (Subject of Investigation/LOI)
Query on LOC

Download Ideal Coordinates CCD File 
M [auth B]N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide
C22 H25 N O6
IAKHMKGGTNLKSZ-INIZCTEOSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
K [auth B],
R [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B],
Q [auth C],
U [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
LOC BindingDB:  8CLG IC50: min: 1700, max: 2620 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.76α = 90
b = 160.76β = 90
c = 180.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted EPClick on this verticalbar to view detailsBest fitted LOCClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_179351
Swiss National Science FoundationSwitzerland310030_207462
Swiss National Science FoundationSwitzerland310030_192566

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release