BMRB Entry 15393

Name: Structure of Chz1 Complexed with H2A.Z-H2B and Eviction of Nucleosomal H2A-H2B
Published: 2008-07-29

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PDB ID: 2jss
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15393
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of Chz1 Complexed with H2A.Z-H2B and Eviction of Nucleosomal H2A-H2B

Deposition date:

2007-07-19

Original release date:

2008-07-29

Authors:

Zhou, Zheng; Feng, Hanqiao; Hansen, Flemming; Luk, Ed; Kato, Hidenori; Freedberg, Daron; Key, Lewis; Wu, Carl; Bai, Yawen

Citation:

Citation: Zhou, Zheng; Feng, Hanqiao; Hansen, Flemming; Kato, Hidenori; Luk, Ed; Freedberg, Daron; Key, Lewis; Wu, Carl; Bai, Yawen. "NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B" Nat. Struct. Mol. Biol. 15, 868-869 (2008).
PubMed: 18641662

Assembly members:

Assembly members:
H2A.Z-H2B, polymer, 200 residues, 27270.035 Da.
Chz1, polymer, 62 residues, 161.126 Da.

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PET-17b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
H2A.Z-H2B: RKETYSSYIYKVLKQTHPDT GISQKSMSILNSFVNDIFER IATEASKLAAYNKKSTISAR EIQTAVRLILPGELAKHAVS EGTRAVTKYSSSTQAQSSSA RAGLQFPVGRIKRYLKRHAT GRTRVGSKAAIYLTAVLEYL TAEVLELAGNAAKDLKVKRI TPRHLQLAIRGDDELDSLIR ATIASGGVLPHIAEELDKKE
Chz1: TVEDSESDMDDAKLDALMGN EGEEEEDDLAEIDTSNIITS GRRTRGKVIDYKKTAEELDK KE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	979
15N chemical shifts	251
1H chemical shifts	1439

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	H2A.Z-H2B	1
2	Chz1	2

Entities:

Entity 1, H2A.Z-H2B 200 residues - 27270.035 Da.

as polymer sequence

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

Entity 2, Chz1 62 residues - 161.126 Da.

as polymer sequence

1

THR

VAL

GLU

ASP

SER

GLU

SER

ASP

MET

ASP

2

ASP

ALA

LYS

LEU

ASP

ALA

LEU

MET

GLY

ASN

3

GLU

GLY

GLU

ASP

LEU

ALA

4

GLU

ILE

ASP

THR

SER

ASN

ILE

THR

SER

5

GLY

ARG

THR

ARG

GLY

LYS

VAL

ILE

ASP

6

TYR

LYS

THR

ALA

GLU

LEU

ASP

LYS

7

LYS

GLU

Samples:

sample_1: H2A.Z-H2B, [U-35% 2H], 1.0 – 1.2 mM; Chz1, [U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_2: H2A.Z-H2B, [U-100% 15N; U-100% 2H], 1.0 – 1.2 mM; Chz1, [U-30%2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_3: H2A.Z-H2B, [U-100% 13C; U-30% 2H], 1.0 – 1.2 mM; Chz1, [U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_4: H2A.Z-H2B, [U-13C; U-15N; U-2H], 1.0 – 1.2 mM; Chz1, [U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_5: H2A.Z-H2B, [U-100% 15N; U-30%2H], 1.0 – 1.2 mM; Chz1, [U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_6: H2A.Z-H2B, [U-100% 13C;U-35%2H]/[U-100% 2H], 1.0 – 1.2 mM; Chz1, [U-100% 13C;U-35%2H]/[U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_7: H2A.Z-H2B, [U-100% 15N; U-100%2H], 1.0 – 1.2 mM; Chz1, [U-30% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_8: Chz1, [U-100% 13C; U-35%2H], 1.0 – 1.2 mM; H2A.Z-H2B, [U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_9: Chz1, [U-100% 15N; U-30%2H], 1.0 – 1.2 mM; H2A.Z-H2B, [U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_10: Chz1, [U-100% 13C; U-35%2H], 1.0 – 1.2 mM; H2A.Z-H2B, [U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_11: Chz1, [U-100%15N; U-100% 2H], 1.0 – 1.2 mM; H2A.Z-H2B, [U-100%15N; U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_12: H2A.Z-H2B, [U-100% 13C; U-100% 15N; U-100%2H], 1.0 – 1.2 mM; Chz1, [U-100% 13C; U-100% 15N; U-100%2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_13: Chz1, [U-10% 13C; U-100% 15N], 1.0 – 1.2 mM; H2A.Z-H2B, [U-100% 2H], 1.0 – 1.2 mM; MES 25 mM; KCl 200 mM; EDTA 1 mM

sample_conditions_1: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	not available	isotropic	sample_conditions_1
2D 1H-1H NOESY	not available	isotropic	sample_conditions_1
3D CBCA(CO)NH	not available	isotropic	sample_conditions_1
3D CBCA(CO)NH	not available	isotropic	sample_conditions_1
3D HNCACB	not available	isotropic	sample_conditions_1
3D HNCACB	not available	isotropic	sample_conditions_1
3D HNCO	not available	isotropic	sample_conditions_1
3D HNCO	not available	isotropic	sample_conditions_1
3D HNCA	not available	isotropic	sample_conditions_1
3D HN(CO)CA	not available	isotropic	sample_conditions_1
3D H(CCO)NH	not available	isotropic	sample_conditions_1
3D HCCH-TOCSY	not available	isotropic	sample_conditions_1
3D HBHA(CO)NH	not available	isotropic	sample_conditions_1
3D HNHA	not available	isotropic	sample_conditions_1
3D HNCANNH	not available	isotropic	sample_conditions_1
3D TOCSY-HSQC	not available	isotropic	sample_conditions_1
3D 1H-15N NOESY	not available	isotropic	sample_conditions_1
3D 1H-15N NOESY	not available	isotropic	sample_conditions_1
3D 1H-13C NOESY	not available	isotropic	sample_conditions_1
3D 1H-13C NOESY	not available	isotropic	sample_conditions_1

Software:

NMRView v5.0.4, Johnson, One Moon Scientific - chemical shift assignment, NMR data process and analysis, peak picking

X-PLOR NIH v2.16, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMRPipe v2004, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment, data analysis, processing

PIPP v4.3.3, Garrett - chemical shift assignment, peak picking

TALOS v2004, Cornilescu, Delaglio and Bax - data analysis

ProcheckNMR v3.5.4, Laskowski and MacArthur - structure analysis

NMR spectrometers:

Bruker Avance 500 MHz
Bruker DRX 700 MHz

BMRB	17114 17114
PDB	2JSS 4M6B 2JSS
DBJ	GAA22856
EMBL	CAY79198
GB	AAB64563 AHY75583 EDN62999 EDV08859 EDZ72631
REF	NP_010947
SP	A6ZQX9 P40019
TPG	DAA07683
AlphaFold	A6ZQX9 P40019

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

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