BMRB Entry 18713

Name: The budding yeast chaperone Scm3 recognizes the partially unfolded dimer of the centromere-specific Cse4/H4 histone variant
Published: 2012-12-10

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PDB ID: 2ly8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18713
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:

The budding yeast chaperone Scm3 recognizes the partially unfolded dimer of the centromere-specific Cse4/H4 histone variant

Deposition date:

2012-09-13

Original release date:

2012-12-10

Authors:

Hong, Jingjun; Feng, Hanqiao; Zhou, Zheng; Ghirlando, Rodolfo; Bai, Yawen

Citation:

Citation: Hong, Jingjun; Feng, Hanqiao; Zhou, Zheng; Ghirlando, Rodolfo; Bai, Yawen. "The budding yeast chaperone Scm3 recognizes the partially unfolded dimer of the" J. Mol. Biol. ., .-..

Assembly members:

Assembly members:
sC4, polymer, 121 residues, 13718.007 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-28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
sC4: LISKIPFARLVKEVTDEFTT KDQDLRWQSMAIMALQEASE AYLVGLLEHTNLLALHLVPR GSKRISGLIYEEVRAVLKSF LESVIRDSVTYTEHAKRKTV TSLDVVYALKRQGRTLYGFG G

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	487
15N chemical shifts	116
1H chemical shifts	843

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	sC4	1

Entities:

Entity 1, sC4 121 residues - 13718.007 Da.

The segment LVPRGS (L57-S62 in the sequence) is a thrombin cutting site.

1

LEU

ILE

SER

LYS

ILE

PRO

PHE

ALA

ARG

LEU

2

VAL

LYS

GLU

VAL

THR

ASP

GLU

PHE

THR

3

LYS

ASP

GLN

ASP

LEU

ARG

TRP

GLN

SER

MET

4

ALA

ILE

MET

ALA

LEU

GLN

GLU

ALA

SER

GLU

5

ALA

TYR

LEU

VAL

GLY

LEU

GLU

HIS

THR

6

ASN

LEU

ALA

LEU

HIS

LEU

VAL

PRO

ARG

7

GLY

SER

LYS

ARG

ILE

SER

GLY

LEU

ILE

TYR

8

GLU

VAL

ARG

ALA

VAL

LEU

LYS

SER

PHE

9

LEU

GLU

SER

VAL

ILE

ARG

ASP

SER

VAL

THR

10

TYR

THR

GLU

HIS

ALA

LYS

ARG

LYS

THR

VAL

11

THR

SER

LEU

ASP

VAL

TYR

ALA

LEU

LYS

12

ARG

GLN

GLY

ARG

THR

LEU

TYR

GLY

PHE

GLY

13

GLY

Samples:

sample_1: sC4, [U-100% 15N], 0.8 ± 0.05 mM; sC4, [U-100% 13C; U-100% 15N], 0.8 ± 0.05 mM; sC4, [U-13C; U-15N; U-2H], 0.8 ± 0.05 mM; sC4, [U-13C; U-15N; U-2H], 0.8 ± 0.05 mM; H2O 90 ± 0.05 %; D2O 10 ± 0.05 %

sample_2: sC4, [U-100% 13C; U-100% 15N], 0.8 ± 0.05 mM; D2O 100 ± 0.05 %

sample_3: sC4 0.8 ± 0.05 mM; D2O 100 ± 0.05 %

sample_conditions_1: pH: 5.4; pressure: 1 atm; temperature: 308.1 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1

Software:

NMRPipe vupdated, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView vupdated, Johnson, One Moon Scientific - chemical shift assignment

X-PLOR NIH vupdated, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMRDraw, Cornilescu, Delaglio and Bax - data analysis

ProcheckNMR vupdated, Laskowski and MacArthur - structure solution

Molmol, Koradi, Billeter and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 700 MHz
Bruker Avance 900 MHz

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