7LXB

HeLa-tubulin in complex with cryptophycin 52

  • Classification: CELL CYCLE
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-03-03 Released: 2021-09-08 
  • Deposition Author(s): Eren, E.
  • Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conformational changes in tubulin upon binding cryptophycin-52 reveal its mechanism of action.

Eren, E.Watts, N.R.Sackett, D.L.Wingfield, P.T.

(2021) J Biol Chem 297: 101138-101138

  • DOI: 10.1016/j.jbc.2021.101138
  • Primary Citation of Related Structures:  
    7LXB, 7M18, 7M20

  • PubMed Abstract: 
  • Cryptophycin-52 (Cp-52) is potentially the most potent anti-cancer drug known, with IC50 values in the low pM range, but its binding site on tubulin and mechanism of action are unknown. Here, we have determined the binding site of Cp-52, and its parent compound, Cryptophycin-1 (Cp-1), on Hela tubulin, to 3 ...

    Cryptophycin-52 (Cp-52) is potentially the most potent anti-cancer drug known, with IC50 values in the low pM range, but its binding site on tubulin and mechanism of action are unknown. Here, we have determined the binding site of Cp-52, and its parent compound, Cryptophycin-1 (Cp-1), on Hela tubulin, to 3.3 Å and 3.4 Å resolution, respectively, by cryo-EM and characterized this binding further by molecular dynamics simulations. The binding site was determined to be located at the tubulin inter-dimer interface and to partially overlap that of Maytansine, another cytotoxic tubulin inhibitor. Binding induces curvature both within and between tubulin dimers that is incompatible with the microtubule lattice. Conformational changes occur in both α- and β-tubulin, particularly in helices H8 and H10, with distinct differences between α and β monomers and between Cp-52- and Cp-1-bound tubulin. From these results, we have determined: (i) the mechanism of action of inhibition of both microtubule polymerization and depolymerization, (ii) how the affinity of Cp-52 for tubulin may be enhanced, and (iii) where linkers for targeted delivery can be optimally attached to this molecule.


    Organizational Affiliation

    Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: wingfiep@mail.nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chain
A, C, E, G, I, K, M, O
A, C, E, G, I, K, M, O
451Homo sapiensMutation(s): 0 
Gene Names: TUBA1B
UniProt & NIH Common Fund Data Resources
Find proteins for P68363 (Homo sapiens)
Explore P68363 
Go to UniProtKB:  P68363
PHAROS:  P68363
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68363
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-3 chain
B, D, F, H, J, L, N, P
B, D, F, H, J, L, N, P
450Homo sapiensMutation(s): 0 
Gene Names: TUBB3TUBB4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13509 (Homo sapiens)
Explore Q13509 
Go to UniProtKB:  Q13509
PHAROS:  Q13509
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13509
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YGY (Subject of Investigation/LOI)
Query on YGY

Download Ideal Coordinates CCD File 
AA [auth H],
DA [auth J],
GA [auth L],
JA [auth N],
MA [auth P],
AA [auth H],
DA [auth J],
GA [auth L],
JA [auth N],
MA [auth P],
R [auth B],
U [auth D],
X [auth F]
Cryptophycin 52
C36 H45 Cl N2 O8
LSXOBYNBRKOTIQ-HZMFLOLBSA-N
 Ligand Interaction
GTP
Query on GTP

Download Ideal Coordinates CCD File 
CA [auth I],
FA [auth K],
IA [auth M],
LA [auth O],
Q [auth A],
CA [auth I],
FA [auth K],
IA [auth M],
LA [auth O],
Q [auth A],
T [auth C],
W [auth E],
Z [auth G]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GDP
Query on GDP

Download Ideal Coordinates CCD File 
BA [auth H],
EA [auth J],
HA [auth L],
KA [auth N],
NA [auth P],
BA [auth H],
EA [auth J],
HA [auth L],
KA [auth N],
NA [auth P],
S [auth B],
V [auth D],
Y [auth F]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-03-03 
  • Released Date: 2021-09-08 
  • Deposition Author(s): Eren, E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesIntramural Research

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2021-09-15
    Changes: Database references
  • Version 1.2: 2021-10-06
    Changes: Database references