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Found 1 Document (4.671 seconds)

BMRB: 17772

3ZTG

Solution structure of the RING finger-like domain of Retinoblastoma Binding Protein-6 (RBBP6)

Authors

Kappo, M.A., Ab, E., Atkinson, R.A., Faro, A., Muleya, V., Mulaudzi, T., Poole, J.O., Mckenzie, J.M., PUGH, D.JOHN.RHYDWYN.

Assembly

Solution structure of the RING finger-like domain of Retinoblastoma Binding Protein-6 (RBBP6)

Entity

1. E3 UBIQUITIN-PROTEIN LIGASE RBBP6 (polymer, Thiol state: all disulfide bound), 92 monomers, 10229.51 × 2 Da Detail

GPLGSEDDPI PDELLCLICK DIMTDAVVIP CCGNSYCDEC IRTALLESDE HTCPTCHQND VSPDALIANK FLRQAVNNFK NETGYTKRLR KQ

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

20589.838 Da

Max. entity weight

10229.51 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

CYANA FOLLOWED BY HADDOCK

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.8 %, Completeness (bb): 84.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.8 % (926 of 1031)	97.2 % (522 of 537)	77.9 % (311 of 399)	97.9 % (93 of 95)
Backbone	84.1 % (454 of 540)	97.8 % (178 of 182)	70.6 % (192 of 272)	97.7 % (84 of 86)
Sidechain	95.0 % (550 of 579)	95.2 % (338 of 355)	94.4 % (203 of 215)	100.0 % (9 of 9)
Aromatic	81.8 % (36 of 44)	100.0 % (22 of 22)	63.6 % (14 of 22)
Methyl	98.0 % (96 of 98)	95.9 % (47 of 49)	100.0 % (49 of 49)

1. E3 UBIQUITIN-PROTEIN LIGASE RBBP6

GPLGSEDDPI PDELLCLICK DIMTDAVVIP CCGNSYCDEC IRTALLESDE HTCPTCHQND VSPDALIANK FLRQAVNNFK NETGYTKRLR KQ

Show sample condition

Sample

Solvent system 95% H2O, 5% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.000, Details 0.7 mM

#	Name	Isotope labeling	Type	Concentration
1	E3 UBIQUITIN-PROTEIN LIGASE RBBP6	[U-13C; U-15N]		0.7 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbon	0.0 ppm	external	direct	1.0
¹H	HDO	H	4.812 ppm	internal	direct	1.0
¹⁵N	Liquid NH3	N	0.0 ppm	external	direct	1.0

Referencing offset: -0.19 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbon	0.0 ppm	external	direct	1.0
¹H	HDO	H	4.812 ppm	internal	direct	1.0
¹⁵N	Liquid NH3	N	0.0 ppm	external	direct	1.0

Referencing offset: -0.19 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbon	0.0 ppm	external	direct	1.0
¹H	HDO	H	4.812 ppm	internal	direct	1.0
¹⁵N	Liquid NH3	N	0.0 ppm	external	direct	1.0

Referencing offset: 0.07 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 32 models in PDB: 3ZTG, Strand ID: A, B Detail

Release date

2011-12-05

Citation

Solution structure of RING finger-like domain of retinoblastoma-binding protein-6 (RBBP6) suggests it functions as a U-box
Kappo, M.A., Ab, E., Hassem, F., Atkinson, R., Faro, A., Muleya, V., Mulaudzi, T., Poole, J.O., McKenzie, J.M., Chibi, M., Moolman-Smook, J.C., Rees, D., Pugh, D.J.R.
J. Biol. Chem. (2012), 287, 7146-7158, PubMed 22130672 , DOI 10.1074/jbc.M110.217059 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 17466 released on 2011-12-11
    Title Solution structure of the RING finger-like domain of Retinoblastoma Binding Protein-6 (RBBP6)
  BMRB: 11159 released on 2011-05-04
    Title Solution structure of the Ring finger of human Retinoblastoma-binding protein 6

Related entities 1. E3 UBIQUITIN-PROTEIN LIGASE RBBP6, : 1 : 5 : 50 entities Detail

Interaction partners 1. E3 UBIQUITIN-PROTEIN LIGASE RBBP6, : 7 interactors Detail

More details for 7 interactors identified by 1 citations

Experiments performed 1 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17772_3ztg.nef
Input source #2: Coordindates	3ztg.cif
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)
3:1:ZN:ZN	1:19:CYS:SG	unknown	unknown	n/a
3:1:ZN:ZN	1:40:CYS:SG	unknown	unknown	n/a
3:1:ZN:ZN	1:16:CYS:SG	unknown	unknown	n/a
3:1:ZN:ZN	1:37:CYS:SG	unknown	unknown	n/a
3:2:ZN:ZN	1:53:CYS:SG	unknown	unknown	n/a
3:2:ZN:ZN	1:31:CYS:SG	unknown	unknown	n/a
3:2:ZN:ZN	1:32:CYS:SG	unknown	unknown	n/a
3:2:ZN:ZN	1:56:CYS:SG	unknown	unknown	n/a
3:3:ZN:ZN	2:16:CYS:SG	unknown	unknown	n/a
3:3:ZN:ZN	2:40:CYS:SG	unknown	unknown	n/a
3:3:ZN:ZN	2:19:CYS:SG	unknown	unknown	n/a
3:3:ZN:ZN	2:37:CYS:SG	unknown	unknown	n/a
3:4:ZN:ZN	2:53:CYS:SG	unknown	unknown	n/a
3:4:ZN:ZN	2:56:CYS:SG	unknown	unknown	n/a
3:4:ZN:ZN	2:32:CYS:SG	unknown	unknown	n/a
3:4:ZN:ZN	2:31:CYS:SG	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	ZN	ZINC ION	None
C	2	ZN	ZINC ION	None
C	3	ZN	ZINC ION	None
C	4	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

----250-------260-------270-------280-------290-------300-------310-------320-------330-----
GPLGSEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLRQAVNNFKNETGYTKRLRKQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLRQAVNNFKNETGYTKRLRKQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90--

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

----250-------260-------270-------280-------290-------300-------310-------320-------330-----
GPLGSEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLRQAVNNFKNETGYTKRLRKQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLRQAVNNFKNETGYTKRLRKQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	92	0	0	100.0
B	B	92	0	0	100.0

Content subtype: combined_17772_3ztg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	16		No information
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	927		100.0 (chain: A, length: 92)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	6593 (1)	noe	100.0 (chain: A, length: 92), 100.0 (chain: B, length: 92)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 92, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 531
  - ¹³C chemical shifts: 300
  - ¹⁵N chemical shifts: 96
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
279	TYR	HH	5.979
285	ARG	HH11	7.006
285	ARG	HH21	6.665
335	GLN	CD	21.343

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	537	528	98.3
¹³C chemical shifts	399	299	74.9
¹⁵N chemical shifts	99	96	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	182	179	98.4
¹³C chemical shifts	184	92	50.0
¹⁵N chemical shifts	86	83	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	355	349	98.3
¹³C chemical shifts	215	207	96.3
¹⁵N chemical shifts	13	13	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	50	100.0
¹³C chemical shifts	50	50	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	22	100.0
¹³C chemical shifts	22	14	63.6

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 92, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 92, Sequence coverage: 100.0%
- Total number of restraints: 6565
- Weight of restraints: 1.0 (6565)
- Potential type of restraints: square-well-parabolic (6565)
- Range of distance target values: 1.16, 2.85 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map

Keywords E3 ligase, LIGASE, mRNA processing, mRNA splicing, PACT, RBBP6, Retinoblastoma Binding Protein-6, RING finger, U-Box

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Found 1 Document (4.671 seconds)

BMRB: 17772

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 2 entries Detail

Related entities 1. E3 UBIQUITIN-PROTEIN LIGASE RBBP6, : 1 : 5 : 50 entities Detail

Interaction partners 1. E3 UBIQUITIN-PROTEIN LIGASE RBBP6, : 7 interactors Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 3 contents Detail