9DUQ | pdb_00009duq

HURP(65-174) bound to GMPCPP-stabilized microtubule

PDB DOI: https://doi.org/10.2210/pdb9DUQ/pdb
EM Map EMD-47173: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Homo sapiens, Sus scrofa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-03 Released: 2024-11-27
Deposition Author(s): Ma, M., Valdez, V., Petry, S., Zhang, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

HURP facilitates spindle assembly by stabilizing microtubules and working synergistically with TPX2.

Valdez, V.A., Ma, M., Gouveia, B., Zhang, R., Petry, S.

(2024) Nat Commun 15: 9689-9689

PubMed: 39516491 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-53630-6
Primary Citation Related Structures:
9DUQ

PubMed Abstract:
In vertebrate spindles, most microtubules are formed via branching microtubule nucleation, whereby microtubules nucleate along the side of pre-existing microtubules. Hepatoma up-regulated protein (HURP) is a microtubule-associated protein that has been implicated in spindle assembly, but its mode of action is yet to be defined. In this study, we show that HURP is necessary for RanGTP-induced branching microtubule nucleation in Xenopus egg extract. Specifically, HURP stabilizes the microtubule lattice to promote microtubule formation from γ-TuRC. This function is shifted to promote branching microtubule nucleation through enhanced localization to TPX2 condensates, which form the core of the branch site on microtubules. Lastly, we provide a high-resolution cryo-EM structure of HURP on the microtubule, revealing how HURP binding stabilizes the microtubule lattice. We propose a model in which HURP stabilizes microtubules during their formation, and TPX2 preferentially enriches HURP to microtubules to promote branching microtubule nucleation and thus spindle assembly.

Organizational Affiliation

Department of Molecular Biology, Princeton University, Princeton, NJ, USA.

Macromolecule Content

Total Structure Weight: 932.26 kDa
Atom Count: 64,539
Modeled Residue Count: 8,127
Deposited Residue Count: 8,208
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large-associated protein 5	A [auth r] AA [auth z] T [auth s] U [auth t] V [auth u] A [auth r], AA [auth z], T [auth s], U [auth t], V [auth u], W [auth v], X [auth w], Y [auth x], Z [auth y]	46	Homo sapiens	Mutation(s): 0 Gene Names: DLGAP5, DLG7, KIAA0008
UniProt & NIH Common Fund Data Resources
Find proteins for Q15398 (Homo sapiens) Explore Q15398 Go to UniProtKB: Q15398
PHAROS: Q15398 GTEx: ENSG00000126787
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15398
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D, F, H, J B, D, F, H, J, L, N, P, R	427	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554 Go to UniProtKB: P02554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	C [auth A] E [auth C] G [auth E] I [auth G] K [auth I] C [auth A], E [auth C], G [auth E], I [auth G], K [auth I], M [auth K], O [auth M], Q [auth O], S [auth Q]	439	Sus scrofa	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain XA [auth K] SDF format, chain TA [auth I] SDF format, chain PA [auth G] SDF format, chain LA [auth E] SDF format, chain JB [auth Q] SDF format, chain HA [auth C] SDF format, chain FB [auth O] SDF format, chain DA [auth A] SDF format, chain BB [auth M] MOL2 format, chain XA [auth K] MOL2 format, chain TA [auth I] MOL2 format, chain PA [auth G] MOL2 format, chain LA [auth E] MOL2 format, chain JB [auth Q] MOL2 format, chain HA [auth C] MOL2 format, chain FB [auth O] MOL2 format, chain DA [auth A] MOL2 format, chain BB [auth M] mmCIF format, chain XA [auth K] mmCIF format, chain TA [auth I] mmCIF format, chain PA [auth G] mmCIF format, chain LA [auth E] mmCIF format, chain JB [auth Q] mmCIF format, chain HA [auth C] mmCIF format, chain FB [auth O] mmCIF format, chain DA [auth A] mmCIF format, chain BB [auth M]	BB [auth M] DA [auth A] FB [auth O] HA [auth C] JB [auth Q] BB [auth M], DA [auth A], FB [auth O], HA [auth C], JB [auth Q], LA [auth E], PA [auth G], TA [auth I], XA [auth K]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain BB [auth M] Focus chain DA [auth A] Focus chain FB [auth O] Focus chain HA [auth C] Focus chain JB [auth Q] Focus chain LA [auth E] Focus chain PA [auth G] Focus chain TA [auth I] Focus chain XA [auth K] Interactions & Density Focus chain BB [auth M] Focus chain DA [auth A] Focus chain FB [auth O] Focus chain HA [auth C] Focus chain JB [auth Q] Focus chain LA [auth E] Focus chain PA [auth G] Focus chain TA [auth I] Focus chain XA [auth K]
G2P Query on G2P Download:Ideal Coordinates CCD File SDF format, chain ZA [auth N] SDF format, chain VA [auth L] SDF format, chain RA [auth J] SDF format, chain NA [auth H] SDF format, chain JA [auth F] SDF format, chain HB [auth R] SDF format, chain FA [auth D] SDF format, chain DB [auth P] SDF format, chain BA [auth B] MOL2 format, chain ZA [auth N] MOL2 format, chain VA [auth L] MOL2 format, chain RA [auth J] MOL2 format, chain NA [auth H] MOL2 format, chain JA [auth F] MOL2 format, chain HB [auth R] MOL2 format, chain FA [auth D] MOL2 format, chain DB [auth P] MOL2 format, chain BA [auth B] mmCIF format, chain ZA [auth N] mmCIF format, chain VA [auth L] mmCIF format, chain RA [auth J] mmCIF format, chain NA [auth H] mmCIF format, chain JA [auth F] mmCIF format, chain HB [auth R] mmCIF format, chain FA [auth D] mmCIF format, chain DB [auth P] mmCIF format, chain BA [auth B]	BA [auth B] DB [auth P] FA [auth D] HB [auth R] JA [auth F] BA [auth B], DB [auth P], FA [auth D], HB [auth R], JA [auth F], NA [auth H], RA [auth J], VA [auth L], ZA [auth N]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ GXTIEXDFEKYVGY-KQYNXXCUSA-N		Interactions Focus chain BA [auth B] Focus chain DB [auth P] Focus chain FA [auth D] Focus chain HB [auth R] Focus chain JA [auth F] Focus chain NA [auth H] Focus chain RA [auth J] Focus chain VA [auth L] Focus chain ZA [auth N] Interactions & Density Focus chain BA [auth B] Focus chain DB [auth P] Focus chain FA [auth D] Focus chain HB [auth R] Focus chain JA [auth F] Focus chain NA [auth H] Focus chain RA [auth J] Focus chain VA [auth L] Focus chain ZA [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain YA [auth K] SDF format, chain WA [auth L] SDF format, chain UA [auth I] SDF format, chain SA [auth J] SDF format, chain QA [auth G] SDF format, chain OA [auth H] SDF format, chain MA [auth E] SDF format, chain KB [auth Q] SDF format, chain KA [auth F] SDF format, chain IB [auth R] SDF format, chain IA [auth C] SDF format, chain GB [auth O] SDF format, chain GA [auth D] SDF format, chain EB [auth P] SDF format, chain EA [auth A] SDF format, chain CB [auth M] SDF format, chain CA [auth B] SDF format, chain AB [auth N] MOL2 format, chain YA [auth K] MOL2 format, chain WA [auth L] MOL2 format, chain UA [auth I] MOL2 format, chain SA [auth J] MOL2 format, chain QA [auth G] MOL2 format, chain OA [auth H] MOL2 format, chain MA [auth E] MOL2 format, chain KB [auth Q] MOL2 format, chain KA [auth F] MOL2 format, chain IB [auth R] MOL2 format, chain IA [auth C] MOL2 format, chain GB [auth O] MOL2 format, chain GA [auth D] MOL2 format, chain EB [auth P] MOL2 format, chain EA [auth A] MOL2 format, chain CB [auth M] MOL2 format, chain CA [auth B] MOL2 format, chain AB [auth N] mmCIF format, chain YA [auth K] mmCIF format, chain WA [auth L] mmCIF format, chain UA [auth I] mmCIF format, chain SA [auth J] mmCIF format, chain QA [auth G] mmCIF format, chain OA [auth H] mmCIF format, chain MA [auth E] mmCIF format, chain KB [auth Q] mmCIF format, chain KA [auth F] mmCIF format, chain IB [auth R] mmCIF format, chain IA [auth C] mmCIF format, chain GB [auth O] mmCIF format, chain GA [auth D] mmCIF format, chain EB [auth P] mmCIF format, chain EA [auth A] mmCIF format, chain CB [auth M] mmCIF format, chain CA [auth B] mmCIF format, chain AB [auth N]	AB [auth N] CA [auth B] CB [auth M] EA [auth A] EB [auth P] AB [auth N], CA [auth B], CB [auth M], EA [auth A], EB [auth P], GA [auth D], GB [auth O], IA [auth C], IB [auth R], KA [auth F], KB [auth Q], MA [auth E], OA [auth H], QA [auth G], SA [auth J], UA [auth I], WA [auth L], YA [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth N] Focus chain CA [auth B] Focus chain CB [auth M] Focus chain EA [auth A] Focus chain EB [auth P] Focus chain GA [auth D] Focus chain GB [auth O] Focus chain IA [auth C] Focus chain IB [auth R] Focus chain KA [auth F] Focus chain KB [auth Q] Focus chain MA [auth E] Focus chain OA [auth H] Focus chain QA [auth G] Focus chain SA [auth J] Focus chain UA [auth I] Focus chain WA [auth L] Focus chain YA [auth K] Interactions & Density Focus chain AB [auth N] Focus chain CA [auth B] Focus chain CB [auth M] Focus chain EA [auth A] Focus chain EB [auth P] Focus chain GA [auth D] Focus chain GB [auth O] Focus chain IA [auth C] Focus chain IB [auth R] Focus chain KA [auth F] Focus chain KB [auth Q] Focus chain MA [auth E] Focus chain OA [auth H] Focus chain QA [auth G] Focus chain SA [auth J] Focus chain UA [auth I] Focus chain WA [auth L] Focus chain YA [auth K]