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Found 1 Document (6.241 seconds)

BMRB: 25545

2N13

Complex structure of MyUb (1080-1122) of human Myosin VI with K63-diUb

Authors

He, F., Walters, K.

Assembly

MyUb (1080-1122) of human Myosin VI with K63-diUb

Entity

1. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 1 (polymer), 43 monomers, 5201.892 × 2 Da Detail

GTKKYDLSKW KYAELRDTIN TSCDIELLAA CREEFHRRLK VYH

2. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 2 (polymer), 76 monomers, 8592.745 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQRESTLHLV LRLRGG

3. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 3 (polymer), 76 monomers, 8610.822 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC

Total weight

27607.352 Da

Max. entity weight

8610.822 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 77.9 %, Completeness: 75.9 %, Completeness (bb): 76.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.9 % (1782 of 2347)	75.3 % (928 of 1233)	77.0 % (698 of 907)	75.4 % (156 of 207)
Backbone	76.3 % (884 of 1158)	76.0 % (301 of 396)	77.3 % (443 of 573)	74.1 % (140 of 189)
Sidechain	75.7 % (1039 of 1372)	74.9 % (627 of 837)	76.6 % (396 of 517)	88.9 % (16 of 18)
Aromatic	54.2 % (64 of 118)	54.2 % (32 of 59)	55.2 % (32 of 58)	0.0 % (0 of 1)
Methyl	81.7 % (196 of 240)	81.7 % (98 of 120)	81.7 % (98 of 120)

1. entity 1

GTKKYDLSKW KYAELRDTIN TSCDIELLAA CREEFHRRLK VYH

2. entity 2

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQRESTLHLV LRLRGG

3. entity 3

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-13C; U-15N]	0.5 mM
2	entity_2	[U-13C; U-15N]	0.5 mM
3	entity_3	[U-13C; U-15N]	0.5 mM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	2 mM
7	NaN3	natural abundance	0.1 %

LACS Plot; CA

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

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.13 ppm, Outliers: 5 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N13, Strand ID: A, B, C, D Detail

Release date

2016-03-06

Citation

Myosin VI Contains a Compact Structural Motif that Binds to Ubiquitin Chains
He, F., Wollscheid, H., Nowicka, U., Biancospino, M., Valentini, E., Ehlinger, A., Acconcia, F., Magistrati, E., Polo, S., Walters, K.J.
Cell Rep. (2016), 14, 2683-2694, PubMed 26971995 , DOI 10.1016/j.celrep.2016.01.079 , Abstract

Entries sharing articles BMRB: 4 entries Detail

  BMRB: 25541 released on 2016-03-06
    Title Solution structure of MyUb (1080-1122) of human Myosin VI
  BMRB: 25542 released on 2016-03-06
    Title Solution structure of MyUb (1080-1131) of human Myosin VI
  BMRB: 25543 released on 2016-03-06
    Title Solution structure of human Myosin VI isoform3 (998-1071)
  BMRB: 25544 released on 2016-02-28
    Title Solution structure of human Myosin VI isoform3 (1050-1131)

Related entities 1. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 1, : 1 : 6 : 3 : 1 : 9 entities Detail

Related entities 2. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 2, : 98 : 229 entities Detail

Related entities 3. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 3, : 139 : 188 entities Detail

Interaction partners 1. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 1, : 74 interactors Detail

More details for 74 interactors identified by 22 citations

Experiments performed 3 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25545_2n13.nef
Input source #2: Coordindates	2n13.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)
3:76:GLY:C	4:63:LYS:NZ	unknown	unknown	n/a

Non-standard residues

None

Sequence alignments

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

-10-------20--------30--------40--------50-
GTKKYDLSKWKYAELRDTINTSCDIELLAACREEFHRRLKVYH
|||||||||||||||||||||||||||||||||||||||||||
GTKKYDLSKWKYAELRDTINTSCDIELLAACREEFHRRLKVYH
--------10--------20--------30--------40---

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

-------110-------120-------130-------140-------150-------160-------170------
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG
--------10--------20--------30--------40--------50--------60--------70------

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

-------210-------220-------230-------240-------250-------260-------270------
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC
--------10--------20--------30--------40--------50--------60--------70------

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

-310-----320-------330-------340-------350-
GTKKYDLSKWKYAELRDTINTSCDIELLAACREEFHRRLKVYH
|||||||||||||||||||||||||||||||||||||||||||
GTKKYDLSKWKYAELRDTINTSCDIELLAACREEFHRRLKVYH
--------10--------20--------30--------40---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	43	100.0
B	B	76	100.0
C	C	76	100.0
D	D	43	100.0

Content subtype: combined_25545_2n13.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1799		100.0 (chain: B, length: 76), 100.0 (chain: C, length: 76)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	40 (1)	noe	6.6 (chain: C, length: 76), 23.3 (chain: A, length: 43), 3.9 (chain: B, length: 76)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 76, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 76, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 945
  - ¹³C chemical shifts: 698
  - ¹⁵N chemical shifts: 156
- Completeness of assignments
  - Entity_assemble_ID: B
  - Entity_assemble_ID: C
- 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: B
  - Chain_ID: C

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	477	471	98.7
¹³C chemical shifts	349	348	99.7
¹⁵N chemical shifts	86	78	90.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	154	99.4
¹³C chemical shifts	152	151	99.3
¹⁵N chemical shifts	73	70	95.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	322	317	98.4
¹³C chemical shifts	197	197	100.0
¹⁵N chemical shifts	13	8	61.5

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	16	16	100.0
¹³C chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	479	474	99.0
¹³C chemical shifts	351	350	99.7
¹⁵N chemical shifts	85	78	91.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	154	153	99.4
¹³C chemical shifts	152	151	99.3
¹⁵N chemical shifts	73	70	95.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	325	321	98.8
¹³C chemical shifts	199	199	100.0
¹⁵N chemical shifts	12	8	66.7

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	16	16	100.0
¹³C chemical shifts	16	16	100.0

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: C, Chain length: 76, Sequence coverage: 6.6%
  - Entity_assembly_ID: A, Chain length: 43, Sequence coverage: 23.3%
  - Entity_assembly_ID: B, Chain length: 76, Sequence coverage: 3.9%
- Total number of restraints: 40
- Weight of restraints: 1.0 (40)
- Potential type of restraints: square-well-parabolic (40)
- Range of distance target values: 2.5, 2.5 (Å)
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
  - Chain_ID: D
    None
- Distance restraints on contact map

Keywords K63-diUb, MyUb, Myosin VI

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Found 1 Document (6.241 seconds)

BMRB: 25545

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 4 entries Detail

Related entities 1. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 1, : 1 : 6 : 3 : 1 : 9 entities Detail

Related entities 2. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 2, : 98 : 229 entities Detail

Related entities 3. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 3, : 139 : 188 entities Detail

Interaction partners 1. MyUb (1080-1122) of human Myosin VI with K63-diUb, entity 1, : 74 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail