5IYZ | pdb_00005iyz

Tubulin-MMAE complex

PDB DOI: https://doi.org/10.2210/pdb5IYZ/pdb

Classification: CELL CYCLE
Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-03-24 Released: 2016-08-17
Deposition Author(s): Waight, A.B., Bargsten, K., Doronina, S., Steinmetz, M.O., Sussman, D., Prota, A.E.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.202 (Depositor), 0.204 (DCC)
R-Value Work:
0.167 (Depositor), 0.172 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural Basis of Microtubule Destabilization by Potent Auristatin Anti-Mitotics.

Waight, A.B., Bargsten, K., Doronina, S., Steinmetz, M.O., Sussman, D., Prota, A.E.

(2016) PLoS One 11: e0160890-e0160890

PubMed: 27518442 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0160890
Primary Citation Related Structures:
5IYZ, 5J2T, 5J2U

PubMed Abstract:
The auristatin class of microtubule destabilizers are highly potent cytotoxic agents against several cancer cell types when delivered as antibody drug conjugates. Here we describe the high resolution structures of tubulin in complex with both monomethyl auristatin E and F and unambiguously define the trans-configuration of both ligands at the Val-Dil amide bond in their tubulin bound state. Moreover, we illustrate how peptidic vinca-site agents carrying terminal carboxylate residues may exploit an observed extended hydrogen bond network with the M-loop Arg278 to greatly improve the affinity of the corresponding analogs and to maintain the M-loop in an incompatible conformation for productive lateral tubulin-tubulin contacts in microtubules. Our results highlight a potential, previously undescribed molecular mechanism by which peptidic vinca-site agents maintain unparalleled potency as microtubule-destabilizing agents.

Organizational Affiliation

Department of Protein Sciences, Seattle Genetics, Inc., Bothell, WA, United States of America.

Macromolecule Content

Total Structure Weight: 265.9 kDa
Atom Count: 19,140
Modeled Residue Count: 2,185
Deposited Residue Count: 2,319
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Bos taurus	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 0 Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043 Go to UniProtKB: P63043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TUBULIN-TYROSINE LIGASE	F	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4Q5 Query on 4Q5 Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain M [auth B] MOL2 format, chain S [auth D] MOL2 format, chain M [auth B] mmCIF format, chain S [auth D] mmCIF format, chain M [auth B]	M [auth B], S [auth D]	N-methyl-L-valyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide C₃₉ H₆₇ N₅ O₇ DASWEROEPLKSEI-UIJRFTGLSA-N		Interactions Focus chain M [auth B] Focus chain S [auth D] Interactions & Density Focus chain M [auth B] Focus chain S [auth D]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C]	G [auth A], N [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth C]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain U [auth F] MOL2 format, chain U [auth F] mmCIF format, chain U [auth F]	U [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain U [auth F] Interactions & Density Focus chain U [auth F]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain Q [auth D] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth D]	J [auth B], Q [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Focus chain Q [auth D] Interactions & Density Focus chain J [auth B] Focus chain Q [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain I [auth A]	I [auth A], P [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth C] Interactions & Density Focus chain I [auth A] Focus chain P [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain T [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth F] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth F]	H [auth A], K [auth B], O [auth C], R [auth D], T [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain T [auth F]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 10
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002173 (4Q5) Query on PRD_002173	M [auth B], S [auth D]	N-methyl-L-valyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide	Peptide-like / Inhibitor		Interactions Focus chain M [auth B] Focus chain S [auth D] Interactions & Density Focus chain M [auth B] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.202 (Depositor), 0.204 (DCC)
R-Value Work: 0.167 (Depositor), 0.172 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.51	α = 90
b = 156.61	β = 90
c = 182.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_138659

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2016-08-24
Changes: Database references
Version 1.2: 2016-10-19
Changes: Database references
Version 1.3: 2016-12-21
Changes: Non-polymer description
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description