7RS5 | pdb_00007rs5

Cryo-EM structure of Kip3 (AMPPNP) bound to Taxol-Stabilized Microtubules

PDB DOI: https://doi.org/10.2210/pdb7RS5/pdb
EM Map EMD-24666: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Sus scrofa, Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2021-08-10 Released: 2022-08-17
Deposition Author(s): Hernandez-Lopez, R.A., Leschziner, A.E., Arellano-Santoyo, H., Pellman, D., Stokasimov, E., Wang, R.Y.-R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Multimodal tubulin binding by the yeast kinesin-8, Kip3, underlies its motility and depolymerization

Arellano-Santoyo, H., Hernandez-Lopez, R.A., Stokasimov, E., Wang, R.Y.R., Pellman, D., Leschziner, A.E.

(2021) bioRxiv

DOI: https://doi.org/10.1101/2021.10.12.464151

Macromolecule Content

Total Structure Weight: 1,280.61 kDa
Atom Count: 86,121
Modeled Residue Count: 10,791
Deposited Residue Count: 11,259
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1A chain	A D [auth C] G [auth E] J [auth G] M [auth I] A, D [auth C], G [auth E], J [auth G], M [auth I], P [auth L], S [auth N], V [auth P], Y [auth R]	451	Sus scrofa	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P02550 (Sus scrofa) Explore P02550 Go to UniProtKB: P02550
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02550
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 E [auth D] H [auth F] K [auth H] N [auth J] B, E [auth D], H [auth F], K [auth H], N [auth J], Q [auth M], T [auth O], W [auth Q], Z [auth S]	445	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
yeast kinesin-8/ Kip3	AA [auth h] C [auth K] F [auth a] I [auth b] L [auth c] AA [auth h], C [auth K], F [auth a], I [auth b], L [auth c], O [auth d], R [auth e], U [auth f], X [auth g]	355	Saccharomyces cerevisiae	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TA1 (Subject of Investigation/LOI) Query on TA1 Download:Ideal Coordinates CCD File SDF format, chain AC [auth S] SDF format, chain CB [auth J] SDF format, chain EA [auth B] SDF format, chain KA [auth D] SDF format, chain OB [auth O] SDF format, chain QA [auth F] SDF format, chain UB [auth Q] SDF format, chain WA [auth H] SDF format, chain IB [auth M] MOL2 format, chain AC [auth S] MOL2 format, chain CB [auth J] MOL2 format, chain EA [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain OB [auth O] MOL2 format, chain QA [auth F] MOL2 format, chain UB [auth Q] MOL2 format, chain WA [auth H] MOL2 format, chain IB [auth M] mmCIF format, chain AC [auth S] mmCIF format, chain CB [auth J] mmCIF format, chain EA [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain OB [auth O] mmCIF format, chain QA [auth F] mmCIF format, chain UB [auth Q] mmCIF format, chain WA [auth H] mmCIF format, chain IB [auth M]	AC [auth S] CB [auth J] EA [auth B] IB [auth M] KA [auth D] AC [auth S], CB [auth J], EA [auth B], IB [auth M], KA [auth D], OB [auth O], QA [auth F], UB [auth Q], WA [auth H]	TAXOL C₄₇ H₅₁ N O₁₄ RCINICONZNJXQF-MZXODVADSA-N		Interactions Focus chain AC [auth S] Focus chain CB [auth J] Focus chain EA [auth B] Focus chain IB [auth M] Focus chain KA [auth D] Focus chain OB [auth O] Focus chain QA [auth F] Focus chain UB [auth Q] Focus chain WA [auth H] Interactions & Density Focus chain AC [auth S] Focus chain CB [auth J] Focus chain EA [auth B] Focus chain IB [auth M] Focus chain KA [auth D] Focus chain OB [auth O] Focus chain QA [auth F] Focus chain UB [auth Q] Focus chain WA [auth H]
GTP (Subject of Investigation/LOI) Query on GTP Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain TA [auth G] SDF format, chain XB [auth R] SDF format, chain ZA [auth I] SDF format, chain RB [auth P] SDF format, chain NA [auth E] SDF format, chain LB [auth N] SDF format, chain HA [auth C] SDF format, chain FB [auth L] MOL2 format, chain BA [auth A] MOL2 format, chain TA [auth G] MOL2 format, chain XB [auth R] MOL2 format, chain ZA [auth I] MOL2 format, chain RB [auth P] MOL2 format, chain NA [auth E] MOL2 format, chain LB [auth N] MOL2 format, chain HA [auth C] MOL2 format, chain FB [auth L] mmCIF format, chain BA [auth A] mmCIF format, chain TA [auth G] mmCIF format, chain XB [auth R] mmCIF format, chain ZA [auth I] mmCIF format, chain RB [auth P] mmCIF format, chain NA [auth E] mmCIF format, chain LB [auth N] mmCIF format, chain HA [auth C] mmCIF format, chain FB [auth L]	BA [auth A] FB [auth L] HA [auth C] LB [auth N] NA [auth E] BA [auth A], FB [auth L], HA [auth C], LB [auth N], NA [auth E], RB [auth P], TA [auth G], XB [auth R], ZA [auth I]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain BA [auth A] Focus chain FB [auth L] Focus chain HA [auth C] Focus chain LB [auth N] Focus chain NA [auth E] Focus chain RB [auth P] Focus chain TA [auth G] Focus chain XB [auth R] Focus chain ZA [auth I] Interactions & Density Focus chain BA [auth A] Focus chain FB [auth L] Focus chain HA [auth C] Focus chain LB [auth N] Focus chain NA [auth E] Focus chain RB [auth P] Focus chain TA [auth G] Focus chain XB [auth R] Focus chain ZA [auth I]
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain BC [auth h] SDF format, chain DB [auth d] SDF format, chain FA [auth K] SDF format, chain JB [auth e] SDF format, chain LA [auth a] SDF format, chain RA [auth b] SDF format, chain VB [auth g] SDF format, chain XA [auth c] SDF format, chain PB [auth f] MOL2 format, chain BC [auth h] MOL2 format, chain DB [auth d] MOL2 format, chain FA [auth K] MOL2 format, chain JB [auth e] MOL2 format, chain LA [auth a] MOL2 format, chain RA [auth b] MOL2 format, chain VB [auth g] MOL2 format, chain XA [auth c] MOL2 format, chain PB [auth f] mmCIF format, chain BC [auth h] mmCIF format, chain DB [auth d] mmCIF format, chain FA [auth K] mmCIF format, chain JB [auth e] mmCIF format, chain LA [auth a] mmCIF format, chain RA [auth b] mmCIF format, chain VB [auth g] mmCIF format, chain XA [auth c] mmCIF format, chain PB [auth f]	BC [auth h] DB [auth d] FA [auth K] JB [auth e] LA [auth a] BC [auth h], DB [auth d], FA [auth K], JB [auth e], LA [auth a], PB [auth f], RA [auth b], VB [auth g], XA [auth c]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain BC [auth h] Focus chain DB [auth d] Focus chain FA [auth K] Focus chain JB [auth e] Focus chain LA [auth a] Focus chain PB [auth f] Focus chain RA [auth b] Focus chain VB [auth g] Focus chain XA [auth c] Interactions & Density Focus chain BC [auth h] Focus chain DB [auth d] Focus chain FA [auth K] Focus chain JB [auth e] Focus chain LA [auth a] Focus chain PB [auth f] Focus chain RA [auth b] Focus chain VB [auth g] Focus chain XA [auth c]
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain BB [auth J] SDF format, chain DA [auth B] SDF format, chain NB [auth O] SDF format, chain TB [auth Q] SDF format, chain VA [auth H] SDF format, chain ZB [auth S] SDF format, chain PA [auth F] SDF format, chain JA [auth D] SDF format, chain HB [auth M] MOL2 format, chain BB [auth J] MOL2 format, chain DA [auth B] MOL2 format, chain NB [auth O] MOL2 format, chain TB [auth Q] MOL2 format, chain VA [auth H] MOL2 format, chain ZB [auth S] MOL2 format, chain PA [auth F] MOL2 format, chain JA [auth D] MOL2 format, chain HB [auth M] mmCIF format, chain BB [auth J] mmCIF format, chain DA [auth B] mmCIF format, chain NB [auth O] mmCIF format, chain TB [auth Q] mmCIF format, chain VA [auth H] mmCIF format, chain ZB [auth S] mmCIF format, chain PA [auth F] mmCIF format, chain JA [auth D] mmCIF format, chain HB [auth M]	BB [auth J] DA [auth B] HB [auth M] JA [auth D] NB [auth O] BB [auth J], DA [auth B], HB [auth M], JA [auth D], NB [auth O], PA [auth F], TB [auth Q], VA [auth H], ZB [auth S]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain BB [auth J] Focus chain DA [auth B] Focus chain HB [auth M] Focus chain JA [auth D] Focus chain NB [auth O] Focus chain PA [auth F] Focus chain TB [auth Q] Focus chain VA [auth H] Focus chain ZB [auth S] Interactions & Density Focus chain BB [auth J] Focus chain DA [auth B] Focus chain HB [auth M] Focus chain JA [auth D] Focus chain NB [auth O] Focus chain PA [auth F] Focus chain TB [auth Q] Focus chain VA [auth H] Focus chain ZB [auth S]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain EB [auth d] SDF format, chain GA [auth K] SDF format, chain GB [auth L] SDF format, chain IA [auth C] SDF format, chain KB [auth e] SDF format, chain MA [auth a] SDF format, chain QB [auth f] SDF format, chain SA [auth b] SDF format, chain SB [auth P] SDF format, chain UA [auth G] SDF format, chain YA [auth c] SDF format, chain YB [auth R] SDF format, chain WB [auth g] SDF format, chain OA [auth E] SDF format, chain MB [auth N] SDF format, chain CC [auth h] SDF format, chain AB [auth I] MOL2 format, chain CA [auth A] MOL2 format, chain EB [auth d] MOL2 format, chain GA [auth K] MOL2 format, chain GB [auth L] MOL2 format, chain IA [auth C] MOL2 format, chain KB [auth e] MOL2 format, chain MA [auth a] MOL2 format, chain QB [auth f] MOL2 format, chain SA [auth b] MOL2 format, chain SB [auth P] MOL2 format, chain UA [auth G] MOL2 format, chain YA [auth c] MOL2 format, chain YB [auth R] MOL2 format, chain WB [auth g] MOL2 format, chain OA [auth E] MOL2 format, chain MB [auth N] MOL2 format, chain CC [auth h] MOL2 format, chain AB [auth I] mmCIF format, chain CA [auth A] mmCIF format, chain EB [auth d] mmCIF format, chain GA [auth K] mmCIF format, chain GB [auth L] mmCIF format, chain IA [auth C] mmCIF format, chain KB [auth e] mmCIF format, chain MA [auth a] mmCIF format, chain QB [auth f] mmCIF format, chain SA [auth b] mmCIF format, chain SB [auth P] mmCIF format, chain UA [auth G] mmCIF format, chain YA [auth c] mmCIF format, chain YB [auth R] mmCIF format, chain WB [auth g] mmCIF format, chain OA [auth E] mmCIF format, chain MB [auth N] mmCIF format, chain CC [auth h] mmCIF format, chain AB [auth I]	AB [auth I] CA [auth A] CC [auth h] EB [auth d] GA [auth K] AB [auth I], CA [auth A], CC [auth h], EB [auth d], GA [auth K], GB [auth L], IA [auth C], KB [auth e], MA [auth a], MB [auth N], OA [auth E], QB [auth f], SA [auth b], SB [auth P], UA [auth G], WB [auth g], YA [auth c], YB [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain CA [auth A] Focus chain CC [auth h] Focus chain EB [auth d] Focus chain GA [auth K] Focus chain GB [auth L] Focus chain IA [auth C] Focus chain KB [auth e] Focus chain MA [auth a] Focus chain MB [auth N] Focus chain OA [auth E] Focus chain QB [auth f] Focus chain SA [auth b] Focus chain SB [auth P] Focus chain UA [auth G] Focus chain WB [auth g] Focus chain YA [auth c] Focus chain YB [auth R] Interactions & Density Focus chain AB [auth I] Focus chain CA [auth A] Focus chain CC [auth h] Focus chain EB [auth d] Focus chain GA [auth K] Focus chain GB [auth L] Focus chain IA [auth C] Focus chain KB [auth e] Focus chain MA [auth a] Focus chain MB [auth N] Focus chain OA [auth E] Focus chain QB [auth f] Focus chain SA [auth b] Focus chain SB [auth P] Focus chain UA [auth G] Focus chain WB [auth g] Focus chain YA [auth c] Focus chain YB [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta
RECONSTRUCTION	FREALIGN

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-17

Deposition Author(s):

Hernandez-Lopez, R.A.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-08-17
Type: Initial release
Version 1.1: 2023-03-08
Changes: Database references, Refinement description
Version 1.2: 2024-06-05
Changes: Data collection, Refinement description