BMRB Entry 31025

Name: TPX2 Minimal Active Domain on Microtubules
Published: 2023-06-27

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PDB ID: 8cx6
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31025
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

TPX2 Minimal Active Domain on Microtubules

Deposition date:

2022-05-19

Original release date:

2023-06-27

Authors:

Guo, C.; Alfaro-Aco, R.; Russell, R.; Zhang, C.; Petry, S.; Polenova, T.

Citation:

Citation: Guo, C.; Alfaro-Aco, R.; Zhang, C.; Russell, R.; Petry, S.; Polenova, T.. "Structural basis of protein condensation on microtubules underlying branching microtubule nucleation" Nat. Commun. 14, 3682-3682 (2023).
PubMed: 37344496

Assembly members:

Assembly members:
entity_1, polymer, 240 residues, 28443.770 Da.

Natural source:

Natural source: Common Name: African clawed frog Taxonomy ID: 8355 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Xenopus laevis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: VPVIKATRMPHYGVPFKPKL VEQRQVDVCPFSFCDRDKER QLQKEKRLDELRKDEVPKFK AQPLPQFDNIRLPEKKVKMP TQQEPFDLEIEKRGASKLQR WQQQIQEELKQQKEMVVFKA RPNTVVHQEPFVPKKENRSL TESLSGSIVQEGFELATAKR AKERQEFDKCLAETEAQKSL LEEEIRKRREEEEKEEISQL RQELVHKAKPIRKYRAVEVK ASDVPLTVPRSPNFSDRFKC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	507
15N chemical shifts	173
1H chemical shifts	171

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 240 residues - 28443.770 Da.

1	VAL	PRO	VAL	ILE	LYS	ALA	THR	ARG	MET	PRO
2	HIS	TYR	GLY	VAL	PRO	PHE	LYS	PRO	LYS	LEU
3	VAL	GLU	GLN	ARG	GLN	VAL	ASP	VAL	CYS	PRO
4	PHE	SER	PHE	CYS	ASP	ARG	ASP	LYS	GLU	ARG
5	GLN	LEU	GLN	LYS	GLU	LYS	ARG	LEU	ASP	GLU
6	LEU	ARG	LYS	ASP	GLU	VAL	PRO	LYS	PHE	LYS
7	ALA	GLN	PRO	LEU	PRO	GLN	PHE	ASP	ASN	ILE
8	ARG	LEU	PRO	GLU	LYS	LYS	VAL	LYS	MET	PRO
9	THR	GLN	GLN	GLU	PRO	PHE	ASP	LEU	GLU	ILE
10	GLU	LYS	ARG	GLY	ALA	SER	LYS	LEU	GLN	ARG
11	TRP	GLN	GLN	GLN	ILE	GLN	GLU	GLU	LEU	LYS
12	GLN	GLN	LYS	GLU	MET	VAL	VAL	PHE	LYS	ALA
13	ARG	PRO	ASN	THR	VAL	VAL	HIS	GLN	GLU	PRO
14	PHE	VAL	PRO	LYS	LYS	GLU	ASN	ARG	SER	LEU
15	THR	GLU	SER	LEU	SER	GLY	SER	ILE	VAL	GLN
16	GLU	GLY	PHE	GLU	LEU	ALA	THR	ALA	LYS	ARG
17	ALA	LYS	GLU	ARG	GLN	GLU	PHE	ASP	LYS	CYS
18	LEU	ALA	GLU	THR	GLU	ALA	GLN	LYS	SER	LEU
19	LEU	GLU	GLU	GLU	ILE	ARG	LYS	ARG	ARG	GLU
20	GLU	GLU	GLU	LYS	GLU	GLU	ILE	SER	GLN	LEU
21	ARG	GLN	GLU	LEU	VAL	HIS	LYS	ALA	LYS	PRO
22	ILE	ARG	LYS	TYR	ARG	ALA	VAL	GLU	VAL	LYS
23	ALA	SER	ASP	VAL	PRO	LEU	THR	VAL	PRO	ARG
24	SER	PRO	ASN	PHE	SER	ASP	ARG	PHE	LYS	CYS

Samples:

sample_1: TPX2a5-7, [U-13C; U-15N], 1.5 ± 0.2 mM; Microtubules 100 ± 10 uM; phosphate 100 mM; MgCl2 100 mM; DTT 100 mM; EGTA 100 mM

sample_2: TPX2a5-7, [U-13C; U-15N, D; 100% back-exchanged], 1.5 ± 0.2 mM; Microtubules 100 ± 10 uM; phosphate 100 mM; MgCl2 100 mM; DTT 100 mM; EGTA 100 mM

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 276 K

sample_conditions_2: pH: 6.8; pressure: 1 atm; temperature: 283 K

sample_conditions_3: pH: 6.8; pressure: 1 atm; temperature: 285 K

sample_conditions_4: pH: 6.8; pressure: 1 atm; temperature: 288 K

sample_conditions_5: pH: 6.8; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NH HETCOR	sample_2	isotropic	sample_conditions_2
2D CH HETCOR	sample_2	isotropic	sample_conditions_2
3D (H)CANH	sample_2	isotropic	sample_conditions_2
3D (H)(CO)CA(CO)NH	sample_2	isotropic	sample_conditions_2
3D (H)CONH	sample_2	isotropic	sample_conditions_2
2D RFDR 2.4 ms	sample_2	isotropic	sample_conditions_2
2D CORD (200ms mixing)	sample_1	isotropic	sample_conditions_1
2D CORD (50ms mixing)	sample_1	isotropic	sample_conditions_1
2D CH HETCOR	sample_2	isotropic	sample_conditions_4
2D CH HETCOR	sample_2	isotropic	sample_conditions_2
2D CH HETCOR (2.8 ms/2.7 ms CP)	sample_2	isotropic	sample_conditions_3
2D CH HETCOR (2.1 ms/2.1 ms CP)	sample_2	isotropic	sample_conditions_3
2D CH HETCOR	sample_1	isotropic	sample_conditions_5
2D CH HETCOR	sample_1	isotropic	sample_conditions_5
2D HN HETCOR	sample_1	isotropic	sample_conditions_1
2D NCA	sample_1	isotropic	sample_conditions_1
2D RFDR	sample_1	isotropic	sample_conditions_1
2D NCACX	sample_1	isotropic	sample_conditions_5
2D CORD (200ms mixing)	sample_1	isotropic	sample_conditions_5
2D RFDR	sample_1	isotropic	sample_conditions_5
3D (H)CONH	sample_1	isotropic	sample_conditions_5
3D (H)CANH	sample_1	isotropic	sample_conditions_5
2D NH HETCOR	sample_1	isotropic	sample_conditions_5
2D NCOCX	sample_1	isotropic	sample_conditions_5

Software:

TopSpin, Bruker Biospin - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

MestreLab (Mnova / MestReNova / MestReC), MestreLab - data analysis

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

TALOS, Cornilescu, Delaglio and Bax - data analysis

Sparky, Goddard - data analysis

NMR spectrometers:

Agilent VARIAN 600 MHz
Bruker AVANCE III HD 850 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	VAL	PRO	VAL	ILE	LYS	ALA	THR	ARG	MET	PRO
2	HIS	TYR	GLY	VAL	PRO	PHE	LYS	PRO	LYS	LEU
3	VAL	GLU	GLN	ARG	GLN	VAL	ASP	VAL	CYS	PRO
4	PHE	SER	PHE	CYS	ASP	ARG	ASP	LYS	GLU	ARG
5	GLN	LEU	GLN	LYS	GLU	LYS	ARG	LEU	ASP	GLU
6	LEU	ARG	LYS	ASP	GLU	VAL	PRO	LYS	PHE	LYS
7	ALA	GLN	PRO	LEU	PRO	GLN	PHE	ASP	ASN	ILE
8	ARG	LEU	PRO	GLU	LYS	LYS	VAL	LYS	MET	PRO
9	THR	GLN	GLN	GLU	PRO	PHE	ASP	LEU	GLU	ILE
10	GLU	LYS	ARG	GLY	ALA	SER	LYS	LEU	GLN	ARG
11	TRP	GLN	GLN	GLN	ILE	GLN	GLU	GLU	LEU	LYS
12	GLN	GLN	LYS	GLU	MET	VAL	VAL	PHE	LYS	ALA
13	ARG	PRO	ASN	THR	VAL	VAL	HIS	GLN	GLU	PRO
14	PHE	VAL	PRO	LYS	LYS	GLU	ASN	ARG	SER	LEU
15	THR	GLU	SER	LEU	SER	GLY	SER	ILE	VAL	GLN
16	GLU	GLY	PHE	GLU	LEU	ALA	THR	ALA	LYS	ARG
17	ALA	LYS	GLU	ARG	GLN	GLU	PHE	ASP	LYS	CYS
18	LEU	ALA	GLU	THR	GLU	ALA	GLN	LYS	SER	LEU
19	LEU	GLU	GLU	GLU	ILE	ARG	LYS	ARG	ARG	GLU
20	GLU	GLU	GLU	LYS	GLU	GLU	ILE	SER	GLN	LEU
21	ARG	GLN	GLU	LEU	VAL	HIS	LYS	ALA	LYS	PRO
22	ILE	ARG	LYS	TYR	ARG	ALA	VAL	GLU	VAL	LYS
23	ALA	SER	ASP	VAL	PRO	LEU	THR	VAL	PRO	ARG
24	SER	PRO	ASN	PHE	SER	ASP	ARG	PHE	LYS	CYS

1	VAL	PRO	VAL	ILE	LYS	ALA	THR	ARG	MET	PRO
2	HIS	TYR	GLY	VAL	PRO	PHE	LYS	PRO	LYS	LEU
3	VAL	GLU	GLN	ARG	GLN	VAL	ASP	VAL	CYS	PRO
4	PHE	SER	PHE	CYS	ASP	ARG	ASP	LYS	GLU	ARG
5	GLN	LEU	GLN	LYS	GLU	LYS	ARG	LEU	ASP	GLU
6	LEU	ARG	LYS	ASP	GLU	VAL	PRO	LYS	PHE	LYS
7	ALA	GLN	PRO	LEU	PRO	GLN	PHE	ASP	ASN	ILE
8	ARG	LEU	PRO	GLU	LYS	LYS	VAL	LYS	MET	PRO
9	THR	GLN	GLN	GLU	PRO	PHE	ASP	LEU	GLU	ILE
10	GLU	LYS	ARG	GLY	ALA	SER	LYS	LEU	GLN	ARG
11	TRP	GLN	GLN	GLN	ILE	GLN	GLU	GLU	LEU	LYS
12	GLN	GLN	LYS	GLU	MET	VAL	VAL	PHE	LYS	ALA
13	ARG	PRO	ASN	THR	VAL	VAL	HIS	GLN	GLU	PRO
14	PHE	VAL	PRO	LYS	LYS	GLU	ASN	ARG	SER	LEU
15	THR	GLU	SER	LEU	SER	GLY	SER	ILE	VAL	GLN
16	GLU	GLY	PHE	GLU	LEU	ALA	THR	ALA	LYS	ARG
17	ALA	LYS	GLU	ARG	GLN	GLU	PHE	ASP	LYS	CYS
18	LEU	ALA	GLU	THR	GLU	ALA	GLN	LYS	SER	LEU
19	LEU	GLU	GLU	GLU	ILE	ARG	LYS	ARG	ARG	GLU
20	GLU	GLU	GLU	LYS	GLU	GLU	ILE	SER	GLN	LEU
21	ARG	GLN	GLU	LEU	VAL	HIS	LYS	ALA	LYS	PRO
22	ILE	ARG	LYS	TYR	ARG	ALA	VAL	GLU	VAL	LYS
23	ALA	SER	ASP	VAL	PRO	LEU	THR	VAL	PRO	ARG
24	SER	PRO	ASN	PHE	SER	ASP	ARG	PHE	LYS	CYS

1	VAL	PRO	VAL	ILE	LYS	ALA	THR	ARG	MET	PRO
2	HIS	TYR	GLY	VAL	PRO	PHE	LYS	PRO	LYS	LEU
3	VAL	GLU	GLN	ARG	GLN	VAL	ASP	VAL	CYS	PRO
4	PHE	SER	PHE	CYS	ASP	ARG	ASP	LYS	GLU	ARG
5	GLN	LEU	GLN	LYS	GLU	LYS	ARG	LEU	ASP	GLU
6	LEU	ARG	LYS	ASP	GLU	VAL	PRO	LYS	PHE	LYS
7	ALA	GLN	PRO	LEU	PRO	GLN	PHE	ASP	ASN	ILE
8	ARG	LEU	PRO	GLU	LYS	LYS	VAL	LYS	MET	PRO
9	THR	GLN	GLN	GLU	PRO	PHE	ASP	LEU	GLU	ILE
10	GLU	LYS	ARG	GLY	ALA	SER	LYS	LEU	GLN	ARG
11	TRP	GLN	GLN	GLN	ILE	GLN	GLU	GLU	LEU	LYS
12	GLN	GLN	LYS	GLU	MET	VAL	VAL	PHE	LYS	ALA
13	ARG	PRO	ASN	THR	VAL	VAL	HIS	GLN	GLU	PRO
14	PHE	VAL	PRO	LYS	LYS	GLU	ASN	ARG	SER	LEU
15	THR	GLU	SER	LEU	SER	GLY	SER	ILE	VAL	GLN
16	GLU	GLY	PHE	GLU	LEU	ALA	THR	ALA	LYS	ARG
17	ALA	LYS	GLU	ARG	GLN	GLU	PHE	ASP	LYS	CYS
18	LEU	ALA	GLU	THR	GLU	ALA	GLN	LYS	SER	LEU
19	LEU	GLU	GLU	GLU	ILE	ARG	LYS	ARG	ARG	GLU
20	GLU	GLU	GLU	LYS	GLU	GLU	ILE	SER	GLN	LEU
21	ARG	GLN	GLU	LEU	VAL	HIS	LYS	ALA	LYS	PRO
22	ILE	ARG	LYS	TYR	ARG	ALA	VAL	GLU	VAL	LYS
23	ALA	SER	ASP	VAL	PRO	LEU	THR	VAL	PRO	ARG
24	SER	PRO	ASN	PHE	SER	ASP	ARG	PHE	LYS	CYS