BMRBj - BMREntryMaster

Found 1 Document (1.979 seconds)

BMRB: 15014

2JMD

Solution structure of the RING domain from human TRAF6.

Authors

Mercier, P., Lewis, M.J., Hau, D.D., Saltibus, L.F., Xiao, W., Spyracopoulos, L.

Assembly

hTraf6 2Zn

Entity

1. hTRAF6 (polymer, Thiol state: all other bound), 63 monomers, 7004.164 Da Detail

GPLGSKYECP ICLMALREAV QTPCGHRFCK ACIIKSIRDA GHKCPVDNEI LLENQLFPDN FAK

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

7134.982 Da

Max. entity weight

7004.164 Da

Entity Connection

na 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS9:SG	2:ZN1:ZN
2	na	sing	1:CYS12:SG	2:ZN1:ZN
3	na	sing	1:CYS29:SG	2:ZN1:ZN
4	na	sing	1:CYS32:SG	2:ZN1:ZN
5	na	sing	1:CYS24:SG	2:ZN1:ZN
6	na	sing	1:HIS26:NE2	2:ZN1:ZN
7	na	sing	1:CYS44:SG	2:ZN1:ZN
8	na	sing	1:ASP47:OD2	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 90.1 %, Completeness (bb): 95.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.1 % (661 of 734)	89.4 % (345 of 386)	89.5 % (255 of 285)	96.8 % (61 of 63)
Backbone	95.7 % (352 of 368)	94.4 % (118 of 125)	96.2 % (178 of 185)	96.6 % (56 of 58)
Sidechain	86.6 % (368 of 425)	87.0 % (227 of 261)	85.5 % (136 of 159)	100.0 % (5 of 5)
Aromatic	34.8 % (16 of 46)	60.9 % (14 of 23)	8.7 % (2 of 23)
Methyl	100.0 % (64 of 64)	100.0 % (32 of 32)	100.0 % (32 of 32)

1. hTRAF6

GPLGSKYECP ICLMALREAV QTPCGHRFCK ACIIKSIRDA GHKCPVDNEI LLENQLFPDN FAK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5 (±0.5), Details 9:1 H2O/D2O with 50 mM phosphate (pH 7.5) 150 mM NaCl, 1 mM DTT, 1 mM DSS, 3 mL of 100x stock protease inhibitor cocktail I (Calbiochem catalog no. 539131)

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

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	internal	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	internal	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	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 3 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.28 ppm, Outliers: 1 Detail

Heteronucl. T₁

55 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 303 K, pH 7.5 (±0.5) Detail

Heteronucl. T₂

55 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 303 K, pH 7.5 (±0.5) Detail

Heteronucl. NOE

54 NOE values in 1 lists
Value type peak height, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 303 K, pH 7.5 (±0.5) Detail

Heteronucl. T₁/T₂

55 T₁/T₂ values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 303 K, pH 7.5 (±0.5) Detail

Release date

2007-04-23

Citation

Structure, interactions, and dynamics of the RING domain from human TRAF6
Mercier, P., Lewis, M.J., Hau, D.D., Saltibus, L.F., Xiao, W., Spyracopoulos, L.
Protein Sci. (2007), 16, 602-614, PubMed 17327397 , DOI 10.1110/ps.062358007 , Abstract

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

  BMRB: 15092 released on 2007-04-23
    Title 1H, 13C, 15N chemical shift assignments for the human E2 ubiquitin conjugating enzyme Ubc13
  Swiss-Prot: Q9Y4K3 released on 2003-05-09
    Title TRAF6_HUMAN Entity TNF receptor-associated factor 6

Related entities 1. hTRAF6, : 1 : 16 : 137 entities Detail

Interaction partners 1. hTRAF6, : 383 interactors Detail

More details for 383 interactors identified by 49 citations

Experiments performed 16 experiments Detail

1 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5 (±0.5), Details 9:1 H2O/D2O with 50 mM phosphate (pH 7.5) 150 mM NaCl, 1 mM DTT, 1 mM DSS, 3 mL of 100x stock protease inhibitor cocktail I (Calbiochem catalog no. 539131)

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

2 3D HNCA

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

3 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

4 3D HNHA

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

5 3D HNHB

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

9 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

10 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

11 3D HACA(CO)CANHh

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

12 3D H(CC)-TOCSY-(CO)NNH

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

13 3D (H)CCTOCSY(CO)NNH

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

14 2D (HB)CB(CGCD)HD

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

15 2D (HB)CB(CGCDCE)HE

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

16 3D HNN(CO,CA)

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	hTRAF6	[U-99% 13C; U-99% 15N]	protein	0.5 (±0.1) mM
2	phosphate		buffer	50.0 ~ 0.0 mM
3	NaCl		salt	150.0 ~ 0.0 mM
4	DTT		reducing agent	1.0 ~ 0.0 mM
5	DSS		internal reference	1.0 ~ 0.0 mM
6	H2O		solvent	90.0 ~ 0.0 %
7	D2O		solvent	10.0 ~ 0.0 %

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts, Heteronucl NOE exptl data, Heteronucl T1 relaxation data, Heteronucl T2 relaxation data	bmr15014_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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:9:CYS:SG	2:1:ZN:ZN	oxidized 83.4%, reduced 16.6%, CA 56.93, CB 34.0 ppm	unknown	n/a
1:12:CYS:SG	2:1:ZN:ZN	reduced, CA 59.17, CB 31.79 ppm	unknown	n/a
1:29:CYS:SG	2:1:ZN:ZN	reduced, CA 60.3, CB 31.4 ppm	unknown	n/a
1:32:CYS:SG	2:1:ZN:ZN	reduced, CA 63.73, CB 29.91 ppm	unknown	n/a
1:24:CYS:SG	3:1:ZN:ZN	reduced, CA 56.9, CB 28.52 ppm	unknown	n/a
1:26:HIS:NE2	3:1:ZN:ZN	unknown	unknown	n/a
1:44:CYS:SG	3:1:ZN:ZN	reduced, CA 56.46, CB 30.94 ppm	unknown	n/a
1:47:ASP:OD2	3:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr15014_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	730		98.4 (chain: 1, length: 63)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 63, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 413
  - ¹³C chemical shifts: 256
  - ¹⁵N chemical shifts: 61
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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	386	347	89.9
¹³C chemical shifts	285	256	89.8
¹⁵N chemical shifts	66	61	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	125	121	96.8
¹³C chemical shifts	126	120	95.2
¹⁵N chemical shifts	58	56	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	261	226	86.6
¹³C chemical shifts	159	136	85.5
¹⁵N chemical shifts	8	5	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	33	33	100.0
¹³C chemical shifts	33	33	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	14	60.9
¹³C chemical shifts	23	2	8.7

Keywords human TNF RECEPTOR-ASSOCIATED FACTOR 6, Protein, Zinc-binding, Zn2+ coordination

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Found 1 Document (1.979 seconds)

BMRB: 15014

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

Related entities 1. hTRAF6, : 1 : 16 : 137 entities Detail

Interaction partners 1. hTRAF6, : 383 interactors Detail

Experiments performed 16 experiments Detail

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Chemical shift validation 4 contents Detail