BMRBj - BMREntryMaster

Found 1 Document (1.978 seconds)

BMRB: 6346

2JPH

1H, 15N and 13C Resonance Assignments and Secondary Structure Determination Reveal that the Minimal Rac1 GTPase Binding Domain of Plexin-B1 Has a Ubiquitin Fold

Authors

Tong, Y., Buck, M.

Assembly

h. plexin-B1 RBD-W1830F

Entity

1. h. plexin-B1 RBD-W1830F (polymer, Thiol state: all free), 122 monomers, 13441.26 Da Detail

KKDVEYRPLT LNALLAVGPG AGEAQGVPVK VLDCDTISQA KEKMLDQLYK GVPLTQRPDP RTLDVEWRSG VAGHLILSDE DVTSEVQGLF RRLNTLQHYK VPDGATVALV PCLTKHVLRE NQ

Formula weight

13441.26 Da

Source organism

Homo sapiens

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 92.3 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.3 % (1294 of 1402)	91.8 % (669 of 729)	92.0 % (504 of 548)	96.8 % (121 of 125)
Backbone	97.1 % (695 of 716)	97.1 % (238 of 245)	97.2 % (347 of 357)	96.5 % (110 of 114)
Sidechain	88.7 % (709 of 799)	89.0 % (431 of 484)	87.8 % (267 of 304)	100.0 % (11 of 11)
Aromatic	8.6 % (5 of 58)	13.8 % (4 of 29)	0.0 % (0 of 28)	100.0 % (1 of 1)
Methyl	100.0 % (164 of 164)	100.0 % (82 of 82)	100.0 % (82 of 82)

1. plexin-B1 RBD

KKDVEYRPLT LNALLAVGPG AGEAQGVPVK VLDCDTISQA KEKMLDQLYK GVPLTQRPDP RTLDVEWRSG VAGHLILSDE DVTSEVQGLF RRLNTLQHYK VPDGATVALV PCLTKHVLRE NQ

Show sample condition

Sample

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

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: 0.59 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: 0.59 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: -0.11 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	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.37 ppm, Outliers: 1 Detail

Release date

2005-07-24

Citation 1

1H, 15N and 13C Resonance assignments and secondary structure determination reveal that the minimal Rac1 GTPase binding domain of plexin-B1 has a ubiquitin fold
Tong, Y., Buck, M.
J. Biomol. NMR (2005), 31, 369-370, PubMed 15929008 , DOI 10.1007/s10858-005-0943-9 , Abstract

Show more 1 citaion

Citation 2

The semaphorin receptor plexin-B1 specifically interacts with active Rac in a ligand-dependent manner
Vikis, H.G., Li, W., He, Z., Guan, K.L.
Proc. Natl. Acad. Sci. U. S. A. (2000), 97, 12457-12462, PubMed 11035813 , DOI 10.1073/pnas.220421797 , Abstract

Hide non-primary 1 citaion

Entries sharing articles Swiss-Prot: 2 entries Detail

  Swiss-Prot: O43157 released on 2004-08-31
    Title PLXB1_HUMAN Entity Plexin-B1
  Swiss-Prot: P63000 released on 2004-08-31
    Title RAC1_HUMAN Entity Ras-related C3 botulinum toxin substrate 1

Related entities 1. h. plexin-B1 RBD-W1830F, : 1 : 5 : 76 entities Detail

Interaction partners 1. h. plexin-B1 RBD-W1830F, : 19 interactors Detail

More details for 19 interactors identified by 7 citations

Experiments performed 14 experiments Detail

1 1H-15N HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

2 1H-13C CT-HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

3 HNCA

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

4 HNCO

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

5 HNCACB

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

6 CBCA(CO)NH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

7 HNHA

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

8 H(CCCO)NH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

9 CC(CO)NH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

10 HCCH-TOSY

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

11 RD-HBCB(CGCD)HD

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

12 1H-TOCSY-relayed RD-HCH-COSY

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

13 NOESY-15N-HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

14 NOESY-13C-HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Bruker ICE (600 MHz)

Sample #1

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	plexin-B1 RBD	[U-13C; U-15N]		1.2 mM

Sample #2

Temperature 298 (±0.1) K, pH 6.8 (±0.2)

#	Name	Isotope labeling	Type	Concentration
2	plexin-B1 RBD	[U-13C]		2 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr6346_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: bmr6346_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_1	Warning	1480		98.4 (chain: 1, length: 122)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 122, Sequence coverage: 98.4%
- Total number of assignments
  - ¹⁵N chemical shifts: 123
  - ¹H chemical shifts: 840
  - ¹³C chemical shifts: 517
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
12	ASN	CG	176.74
25	GLN	CD	180.713
39	GLN	CD	179.96
47	GLN	CD	179.605
56	GLN	CD	180.09
87	GLN	CD	180.384
94	ASN	CG	175.502
97	GLN	CD	179.944
121	ASN	CG	177.407
122	GLN	CD	181.164

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	114	112	98.2
¹H chemical shifts	245	241	98.4
¹³C chemical shifts	244	239	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	132	123	93.2
¹H chemical shifts	729	674	92.5
¹³C chemical shifts	548	507	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	18	11	61.1
¹H chemical shifts	484	433	89.5
¹³C chemical shifts	304	268	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	1	1	100.0
¹H chemical shifts	29	4	13.8
¹³C chemical shifts	28	0	0.0

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Found 1 Document (1.978 seconds)

BMRB: 6346

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 2 entries Detail

Related entities 1. h. plexin-B1 RBD-W1830F, : 1 : 5 : 76 entities Detail

Interaction partners 1. h. plexin-B1 RBD-W1830F, : 19 interactors Detail

Experiments performed 14 experiments Detail

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Chemical shift validation 3 contents Detail