9M1M | pdb_00009m1m

Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx

PDB DOI: https://doi.org/10.2210/pdb9M1M/pdb
EM Map EMD-63576: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Homo sapiens, Sus scrofa
Expression System: Homo sapiens, Sus scrofa
Mutation(s): No

Deposited: 2025-02-26 Released: 2025-10-22
Deposition Author(s): Seong, Y.J., Kim, H.M., Byun, K.M., Park, Y.W., Roh, S.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.21 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural dissection of alpha beta-tubulin heterodimer assembly and disassembly by human tubulin-specific chaperones

Seong, Y.J., Kim, H.M., Byun, K.M., Park, Y.W., Roh, S.H.

(2025) Science

DOI: https://doi.org/10.1126/science.ady270

Macromolecule Content

Total Structure Weight: 353.95 kDa
Atom Count: 22,547
Modeled Residue Count: 2,854
Deposited Residue Count: 3,144
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin-specific chaperone C	A [auth C]	346	Homo sapiens	Mutation(s): 0 Gene Names: TBCC
UniProt & NIH Common Fund Data Resources
Find proteins for Q15814 (Homo sapiens) Explore Q15814 Go to UniProtKB: Q15814
PHAROS: Q15814 GTEx: ENSG00000124659
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15814
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin-specific chaperone D	B [auth D]	1,192	Homo sapiens	Mutation(s): 0 Gene Names: TBCD, KIAA0988, SSD1, TFCD, PP1096
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BTW9 (Homo sapiens) Explore Q9BTW9 Go to UniProtKB: Q9BTW9
PHAROS: Q9BTW9 GTEx: ENSG00000141556
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BTW9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin-specific chaperone E	C [auth E]	527	Homo sapiens	Mutation(s): 0 Gene Names: TBCE
UniProt & NIH Common Fund Data Resources
Find proteins for Q15813 (Homo sapiens) Explore Q15813 Go to UniProtKB: Q15813
PHAROS: Q15813
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15813
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor-like protein 2	D [auth G]	184	Homo sapiens	Mutation(s): 0 Gene Names: ARL2
UniProt & NIH Common Fund Data Resources
Find proteins for P36404 (Homo sapiens) Explore P36404 Go to UniProtKB: P36404
PHAROS: P36404 GTEx: ENSG00000213465
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36404
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	E [auth a]	451	Sus scrofa	Mutation(s): 0 Gene Names: TUBA1B EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2XVP4
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	F [auth b]	444	Sus scrofa	Mutation(s): 0 Gene Names: TUBB, TUBB5
UniProt
Find proteins for Q767L7 (Sus scrofa) Explore Q767L7 Go to UniProtKB: Q767L7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q767L7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain J [auth a] SDF format, chain L [auth b] MOL2 format, chain J [auth a] MOL2 format, chain L [auth b] mmCIF format, chain J [auth a] mmCIF format, chain L [auth b]	J [auth a], L [auth b]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain J [auth a] Focus chain L [auth b] Interactions & Density Focus chain J [auth a] Focus chain L [auth b]
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain G MOL2 format, chain G mmCIF format, chain G	G	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G Interactions & Density Focus chain G
AF3 (Subject of Investigation/LOI) Query on AF3 Download Ideal Coordinates CCD File SDF format, chain H [auth G] MOL2 format, chain H [auth G] mmCIF format, chain H [auth G]	H [auth G]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain H [auth G] Interactions & Density Focus chain H [auth G]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth G] SDF format, chain K [auth a] SDF format, chain M [auth b] MOL2 format, chain I [auth G] MOL2 format, chain K [auth a] MOL2 format, chain M [auth b] mmCIF format, chain I [auth G] mmCIF format, chain K [auth a] mmCIF format, chain M [auth b]	I [auth G], K [auth a], M [auth b]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth G] Focus chain K [auth a] Focus chain M [auth b] Interactions & Density Focus chain I [auth G] Focus chain K [auth a] Focus chain M [auth b]