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BMRB: 6845

2AQC

NMR Structural analysis of archaeal Nop10

Authors

Hamma, T., Reichow, S., Varani, G., Ferre-D'Amare, A.

Assembly

Ribosome biogenesis protein Nop10

Entity

1. Ribosome biogenesis protein Nop10 (polymer, Thiol state: all other bound), 63 monomers, 7410.927 Da Detail

GSHMVEMRMK KCPKCGLYTL KEICPKCGEK TVIPKPPKFS LEDRWGKYRR MLKRALKNKN KAE

2. ZN (non-polymer), 65.409 Da

Total weight

7476.336 Da

Max. entity weight

7410.927 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS12:SG	2:ZN1:ZN
2	na	sing	1:CYS15:SG	2:ZN1:ZN
3	na	sing	1:CYS24:SG	2:ZN1:ZN
4	na	sing	1:CYS27:SG	2:ZN1:ZN

Source organism

Methanocaldococcus jannaschii

Exptl. method

NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 95.4 %, Completeness (bb): 96.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.4 % (762 of 799)	98.4 % (427 of 434)	90.5 % (275 of 304)	98.4 % (60 of 61)
Backbone	96.5 % (355 of 368)	97.6 % (122 of 125)	95.1 % (176 of 185)	98.3 % (57 of 58)
Sidechain	95.1 % (466 of 490)	98.7 % (305 of 309)	88.8 % (158 of 178)	100.0 % (3 of 3)
Aromatic	45.2 % (19 of 42)	85.7 % (18 of 21)	0.0 % (0 of 20)	100.0 % (1 of 1)
Methyl	100.0 % (44 of 44)	100.0 % (22 of 22)	100.0 % (22 of 22)

1. Ribosome biogenesis protein Nop10

GSHMVEMRMK KCPKCGLYTL KEICPKCGEK TVIPKPPKFS LEDRWGKYRR MLKRALKNKN KAE

Show sample condition

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Concentration
1	Ribosome biogenesis protein Nop10	1 mM
2	Sodium Acetate	50 mM
3	KCl	100 mM
4	DTT	2 mM
5	ZnCl2	100 uM
6	H2O	90 %
7	D2O	10 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Concentration
8	Ribosome biogenesis protein Nop10	1 mM
9	Sodium Acetate	50 mM
10	KCl	100 mM
11	DTT	2 mM
12	ZnCl2	100 uM
13	D2O	100 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Concentration
14	Ribosome biogenesis protein Nop10	[U-15N]	1 mM
15	Sodium Acetate		50 mM
16	KCl		100 mM
17	DTT		2 mM
18	ZnCl2		100 uM
19	H2O		90 %
20	D2O		10 %

Sample #4

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Concentration
21	Ribosome biogenesis protein Nop10	[U-13C; U-15N]	1 mM
22	Sodium Acetate		50 mM
23	KCl		100 mM
24	DTT		2 mM
25	ZnCl2		100 uM
26	H2O		90 %
27	D2O		10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2AQC, Strand ID: A Detail

Release date

2005-12-27

Citation

The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs
Hamma, T., Reichow, S.L., Varani, G., Ferre-D'Amare, A.R.
Nat. Struct. Mol. Biol. (2005), 12, 1101-1107, PubMed 16286935 , DOI 10.1038/nsmb1036 , Abstract

Related entities 1. Ribosome biogenesis protein Nop10, : 1 : 3 : 23 entities Detail

Interaction partners 1. Ribosome biogenesis protein Nop10, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 3 experiments Detail

1 2D NOESY

Instrument

Model Varian INOVA (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Concentration
1	Ribosome biogenesis protein Nop10	1 mM
2	Sodium Acetate	50 mM
3	KCl	100 mM
4	DTT	2 mM
5	ZnCl2	100 uM
6	H2O	90 %
7	D2O	10 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Concentration
8	Ribosome biogenesis protein Nop10	1 mM
9	Sodium Acetate	50 mM
10	KCl	100 mM
11	DTT	2 mM
12	ZnCl2	100 uM
13	D2O	100 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Concentration
14	Ribosome biogenesis protein Nop10	[U-15N]	1 mM
15	Sodium Acetate		50 mM
16	KCl		100 mM
17	DTT		2 mM
18	ZnCl2		100 uM
19	H2O		90 %
20	D2O		10 %

Sample #4

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Concentration
21	Ribosome biogenesis protein Nop10	[U-13C; U-15N]	1 mM
22	Sodium Acetate		50 mM
23	KCl		100 mM
24	DTT		2 mM
25	ZnCl2		100 uM
26	H2O		90 %
27	D2O		10 %

2 3D 15N-separated NOESY

Instrument

Model Varian INOVA (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Concentration
1	Ribosome biogenesis protein Nop10	1 mM
2	Sodium Acetate	50 mM
3	KCl	100 mM
4	DTT	2 mM
5	ZnCl2	100 uM
6	H2O	90 %
7	D2O	10 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Concentration
8	Ribosome biogenesis protein Nop10	1 mM
9	Sodium Acetate	50 mM
10	KCl	100 mM
11	DTT	2 mM
12	ZnCl2	100 uM
13	D2O	100 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Concentration
14	Ribosome biogenesis protein Nop10	[U-15N]	1 mM
15	Sodium Acetate		50 mM
16	KCl		100 mM
17	DTT		2 mM
18	ZnCl2		100 uM
19	H2O		90 %
20	D2O		10 %

Sample #4

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Concentration
21	Ribosome biogenesis protein Nop10	[U-13C; U-15N]	1 mM
22	Sodium Acetate		50 mM
23	KCl		100 mM
24	DTT		2 mM
25	ZnCl2		100 uM
26	H2O		90 %
27	D2O		10 %

3 3D 13C-separated NOESY

Instrument

Model Varian INOVA (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Concentration
1	Ribosome biogenesis protein Nop10	1 mM
2	Sodium Acetate	50 mM
3	KCl	100 mM
4	DTT	2 mM
5	ZnCl2	100 uM
6	H2O	90 %
7	D2O	10 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Concentration
8	Ribosome biogenesis protein Nop10	1 mM
9	Sodium Acetate	50 mM
10	KCl	100 mM
11	DTT	2 mM
12	ZnCl2	100 uM
13	D2O	100 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Concentration
14	Ribosome biogenesis protein Nop10	[U-15N]	1 mM
15	Sodium Acetate		50 mM
16	KCl		100 mM
17	DTT		2 mM
18	ZnCl2		100 uM
19	H2O		90 %
20	D2O		10 %

Sample #4

Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Concentration
21	Ribosome biogenesis protein Nop10	[U-13C; U-15N]	1 mM
22	Sodium Acetate		50 mM
23	KCl		100 mM
24	DTT		2 mM
25	ZnCl2		100 uM
26	H2O		90 %
27	D2O		10 %

nullKeywords aNop10, Zinc-Ribbon

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Found 1 Document (1.048 seconds)

BMRB: 6845

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Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Ribosome biogenesis protein Nop10, : 1 : 3 : 23 entities Detail

Interaction partners 1. Ribosome biogenesis protein Nop10, : 1 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample #1

Sample #2

Sample #3

Sample #4

Instrument

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Sample #2

Sample #3

Sample #4

Instrument

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Sample #2

Sample #3

Sample #4