7Q1F | pdb_00007q1f

CPAP:TUBULIN:IE5 ALPHAREP COMPLEX

PDB DOI: https://doi.org/10.2210/pdb7Q1F/pdb

Classification: CELL CYCLE
Organism(s): Ovis aries, synthetic construct, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-19 Released: 2022-04-20
Deposition Author(s): Campanacci, V., Gigant, b.
Funding Organization(s): Fondation ARC, Centre National de la Recherche Scientifique (CNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.220 (Depositor), 0.224 (DCC)
R-Value Work:
0.188 (Depositor), 0.193 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural convergence for tubulin binding of CPAP and vinca domain microtubule inhibitors.

Campanacci, V., Urvoas, A., Ammar Khodja, L., Aumont-Nicaise, M., Noiray, M., Lachkar, S., Curmi, P.A., Minard, P., Gigant, B.

(2022) Proc Natl Acad Sci U S A 119: e2120098119-e2120098119

PubMed: 35507869 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2120098119
Primary Citation Related Structures:
7Q1E, 7Q1F, 7Z0F, 7Z0G

PubMed Abstract:
Microtubule dynamics is regulated by various cellular proteins and perturbed by small-molecule compounds. To what extent the mechanism of the former resembles that of the latter is an open question. We report here structures of tubulin bound to the PN2-3 domain of CPAP, a protein controlling the length of the centrioles. We show that an α-helix of the PN2-3 N-terminal region binds and caps the longitudinal surface of the tubulin β subunit. Moreover, a PN2-3 N-terminal stretch lies in a β-tubulin site also targeted by fungal and bacterial peptide-like inhibitors of the vinca domain, sharing a very similar binding mode with these compounds. Therefore, our results identify several characteristic features of cellular partners that bind to this site and highlight a structural convergence of CPAP with small-molecule inhibitors of microtubule assembly.

Organizational Affiliation

Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.

Macromolecule Content

Total Structure Weight: 321.46 kDa
Atom Count: 20,262
Modeled Residue Count: 2,561
Deposited Residue Count: 2,870
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A, F [auth R]	451	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, G [auth S]	445	Ovis aries	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IE5 ALPHAREP	C, D, H [auth T], I [auth U]	232	synthetic construct	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein J	E [auth P], J [auth V]	75	Homo sapiens	Mutation(s): 0 Gene Names: CENPJ, CPAP, LAP, LIP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC77 (Homo sapiens) Explore Q9HC77 Go to UniProtKB: Q9HC77
PHAROS: Q9HC77 GTEx: ENSG00000151849
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HC77
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain R MOL2 format, chain K [auth A] MOL2 format, chain R mmCIF format, chain K [auth A] mmCIF format, chain R	K [auth A], R	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain K [auth A] Focus chain R Interactions & Density Focus chain K [auth A] Focus chain R
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain U [auth S] MOL2 format, chain N [auth B] MOL2 format, chain U [auth S] mmCIF format, chain N [auth B] mmCIF format, chain U [auth S]	N [auth B], U [auth S]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain N [auth B] Focus chain U [auth S] Interactions & Density Focus chain N [auth B] Focus chain U [auth S]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain V [auth S] SDF format, chain W [auth S] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain V [auth S] MOL2 format, chain W [auth S] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain V [auth S] mmCIF format, chain W [auth S]	O [auth B], P [auth B], V [auth S], W [auth S]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth S] Focus chain W [auth S] Interactions & Density Focus chain O [auth B] Focus chain P [auth B] Focus chain V [auth S] Focus chain W [auth S]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain T [auth R] MOL2 format, chain M [auth A] MOL2 format, chain T [auth R] mmCIF format, chain M [auth A] mmCIF format, chain T [auth R]	M [auth A], T [auth R]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth A] Focus chain T [auth R] Interactions & Density Focus chain M [auth A] Focus chain T [auth R]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth R] MOL2 format, chain L [auth A] MOL2 format, chain S [auth R] mmCIF format, chain L [auth A] mmCIF format, chain S [auth R]	L [auth A], S [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain S [auth R] Interactions & Density Focus chain L [auth A] Focus chain S [auth R]