BMRBj - BMREntryMaster

Found 1 Document (0.646 seconds)

BMRB: 30410

6CGH

Solution structure of the four-helix bundle region of human J-protein Zuotin, a component of ribosome-associated complex (RAC)

Authors

Shrestha, O.K., Lee, W., Tonelli, M., Cornilescu, G., Markley, J.L., Ciesielski, S.J., Craig, E.A.

Assembly

DnaJ homolog subfamily C member 2

Entity

1. DnaJ homolog subfamily C member 2 (polymer), 89 monomers, 10381.72 Da Detail

GSKKAIKKER QKLRNSCKTW NHFSDNEAER VKMMEEVEKL CDRLELASLQ CLNETLTSCT KEVGKAALEK QIEEINEQIR KEKEEAEAR

Formula weight

10381.72 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamicsmolecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.6 %, Completeness: 76.0 %, Completeness (bb): 77.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.0 % (814 of 1071)	78.5 % (450 of 573)	69.4 % (277 of 399)	87.9 % (87 of 99)
Backbone	77.2 % (412 of 534)	88.3 % (159 of 180)	63.4 % (168 of 265)	95.5 % (85 of 89)
Sidechain	77.4 % (483 of 624)	74.0 % (291 of 393)	86.0 % (190 of 221)	20.0 % (2 of 10)
Aromatic	76.9 % (20 of 26)	84.6 % (11 of 13)	75.0 % (9 of 12)	0.0 % (0 of 1)
Methyl	97.6 % (80 of 82)	97.6 % (40 of 41)	97.6 % (40 of 41)

1. entity 1

GSKKAIKKER QKLRNSCKTW NHFSDNEAER VKMMEEVEKL CDRLELASLQ CLNETLTSCT KEVGKAALEK QIEEINEQIR KEKEEAEAR

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
4	Mpp11 (346-432)	[U-100% 15N]	300 uM
5	NaCl	natural abundance	250 mM
6	sodium phosphate	natural abundance	20 mM

Sample #3

Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 200 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
7	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	200 uM
8	NaCl	natural abundance	250 mM
9	sodium phosphate	natural abundance	20 mM

Sample #4

Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 150 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
10	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	150 uM
11	NaCl	natural abundance	250 mM
12	sodium phosphate	natural abundance	20 mM

LACS Plot; CA

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

Referencing offset: -0.31 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.31 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6CGH, Strand ID: A Detail

Release date

2018-04-04

Citation

Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70
Shrestha, O.K., Sharma, R., Tomiczek, B., Lee, W., Tonelli, M., Cornilescu, G., Stolarska, M., Nierzwicki, L., Czub, J., Markley, J.L., Marszalek, J., Ciesielski, S.J., Craig, E.A.
PLoS One (2019), 14, e0217098-e0217098, PubMed 31091298 , DOI 10.1371/journal.pone.0217098 , Abstract

Related entities 1. DnaJ homolog subfamily C member 2, : 1 : 3 : 16 entities Detail

Interaction partners 1. DnaJ homolog subfamily C member 2, : 5 interactors Detail

More details for 5 interactors identified by 2 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

2 3D HNCACB

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

3 3D CBCA(CO)NH

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

4 3D HBHA(CO)NH

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

5 2D 1H-13C HSQC aliphatic

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

6 3D 1H-15N NOESY

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

7 3D 1H-13C NOESY

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

8 3D H(CCO)NH

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

9 3D C(CO)NH

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

10 1H-15N IPAP HSQC

Instrument

Bruker Avance - 750 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

11 1H-15N IPAP HSQC

Instrument

Bruker Avance - 750 MHz

Sample

State anisotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 200 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
7	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	200 uM
8	NaCl	natural abundance	250 mM
9	sodium phosphate	natural abundance	20 mM

12 1H-15N IPAP HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 150 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
10	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	150 uM
11	NaCl	natural abundance	250 mM
12	sodium phosphate	natural abundance	20 mM

13 2D 1H-15N HSQC

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
4	Mpp11 (346-432)	[U-100% 15N]	300 uM
5	NaCl	natural abundance	250 mM
6	sodium phosphate	natural abundance	20 mM

14 3D 1H-13C NOESY aromatic

Instrument

Varian VNS - 900 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 Pa, Temperature 278 K, pH 7.5, Details 300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O

#	Name	Isotope labeling	Concentration
1	Mpp11 (346-432)	[U-100% 13C; U-100% 15N]	300 uM
2	NaCl	natural abundance	250 mM
3	sodium phosphate	natural abundance	20 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30410_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30410_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	874		96.6 (chain: 1, length: 89)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 89, Sequence coverage: 96.6%
- Total number of assignments
  - ¹H chemical shifts: 521
  - ¹⁵N chemical shifts: 85
  - ¹³C chemical shifts: 268
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	573	441	77.0
¹⁵N chemical shifts	105	85	81.0
¹³C chemical shifts	399	268	67.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	180	160	88.9
¹⁵N chemical shifts	89	85	95.5
¹³C chemical shifts	178	81	45.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	393	281	71.5
¹⁵N chemical shifts	16	0	0.0
¹³C chemical shifts	221	187	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	40	93.0
¹³C chemical shifts	43	40	93.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	11	84.6
¹⁵N chemical shifts	1	0	0.0
¹³C chemical shifts	12	9	75.0

Keywords CHAPERONE, DNAJC2, Hsp40, Hsp70, J-protein, Mpp11, Ribosome-Associated Complex (RAC), Zuotin, molecular chaperone

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.646 seconds)

BMRB: 30410

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DnaJ homolog subfamily C member 2, : 1 : 3 : 16 entities Detail

Interaction partners 1. DnaJ homolog subfamily C member 2, : 5 interactors Detail

Experiments performed 14 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail