BMRBj - BMREntryMaster

Found 1 Document (1.237 seconds)

BMRB: 16824

2K42

Solution Structure of the GTPase Binding Domain of WASP in Complex with EspFU, an EHEC Effector

Authors

Cheng, H., Skehan, B.M., Campellone, K.G., Leong, J.M., Rosen, M.K.

Assembly

WASP/EspFU complex

Entity

1. GBD (polymer, Thiol state: not present), 72 monomers, 8118.827 Da Detail

GHMSGFKHVS HVGWDPQNGF DVNNLDPDLR SLFSRAGISE AQLTDAETSK LIYDFIEDQG GLEAVRQEMR RQ

2. R33 (polymer, Thiol state: not present), 36 monomers, 4064.631 Da Detail

GHMLPDVAQR LMQHLAEHGI QPARNMAEHI PPAPNW

Total weight

12183.458 Da

Max. entity weight

8118.827 Da

Source organism

Homo sapiens , Escherichia coli O157:H7

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.1 %, Completeness: 94.7 %, Completeness (bb): 95.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.7 % (1176 of 1242)	94.9 % (617 of 650)	94.1 % (448 of 476)	95.7 % (111 of 116)
Backbone	95.1 % (603 of 634)	94.5 % (206 of 218)	95.6 % (301 of 315)	95.0 % (96 of 101)
Sidechain	94.9 % (671 of 707)	95.1 % (411 of 432)	94.2 % (245 of 260)	100.0 % (15 of 15)
Aromatic	83.0 % (83 of 100)	94.0 % (47 of 50)	70.8 % (34 of 48)	100.0 % (2 of 2)
Methyl	100.0 % (98 of 98)	100.0 % (49 of 49)	100.0 % (49 of 49)

1. GBD

GHMSGFKHVS HVGWDPQNGF DVNNLDPDLR SLFSRAGISE AQLTDAETSK LIYDFIEDQG GLEAVRQEMR RQ

2. R33

GHMLPDVAQR LMQHLAEHGI QPARNMAEHI PPAPNW

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	GBD/R33 complex	[U-100% 13C; U-100% 15N]	1.0 ~ 1.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
8	GBD/R33 complex	[U-100% 13C; U-100% 15N]	1.0 ~ 1.5 mM
9	sodium phosphate	natural abundance	50 mM
10	NaCl	natural abundance	100 mM
11	DTT	natural abundance	1 mM
12	EDTA	natural abundance	1 mM
13	D2O	natural abundance	100 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
14	R33	natural abundance	1 mM
15	GBD	[U-100% 13C; U-100% 15N]	1 mM
16	sodium phosphate	natural abundance	50 mM
17	NaCl	natural abundance	100 mM
18	DTT	natural abundance	1 mM
19	EDTA	natural abundance	1 mM
20	D2O	natural abundance	100 %

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: -0.15 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: -0.15 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: 0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K42, Strand ID: A, B Detail

Release date

2010-05-04

Citation

Structural mechanism of WASP activation by the enterohaemorrhagic E. coli effector EspF(U)
Cheng, H., Skehan, B.M., Campellone, K.G., Leong, J.M., Rosen, M.K.
Nature (2008), 454, 1009-1013, PubMed 18650809 , DOI 10.1038/nature07160 , Abstract

Related entities 1. GBD, : 4 : 14 entities Detail

Related entities 2. R33, : 1 : 6 : 3 entities Detail

Interaction partners 1. GBD, : 46 interactors Detail

More details for 46 interactors identified by 20 citations

Experiments performed 8 experiments Detail

1 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	GBD/R33 complex	[U-100% 13C; U-100% 15N]	1.0 ~ 1.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	GBD/R33 complex	[U-100% 13C; U-100% 15N]	1.0 ~ 1.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
8	GBD/R33 complex	[U-100% 13C; U-100% 15N]	1.0 ~ 1.5 mM
9	sodium phosphate	natural abundance	50 mM
10	NaCl	natural abundance	100 mM
11	DTT	natural abundance	1 mM
12	EDTA	natural abundance	1 mM
13	D2O	natural abundance	100 %

4 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	GBD/R33 complex	[U-100% 13C; U-100% 15N]	1.0 ~ 1.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	GBD/R33 complex	[U-100% 13C; U-100% 15N]	1.0 ~ 1.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	GBD/R33 complex	[U-100% 13C; U-100% 15N]	1.0 ~ 1.5 mM
2	sodium phosphate	natural abundance	50 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

7 4D 13C-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
8	GBD/R33 complex	[U-100% 13C; U-100% 15N]	1.0 ~ 1.5 mM
9	sodium phosphate	natural abundance	50 mM
10	NaCl	natural abundance	100 mM
11	DTT	natural abundance	1 mM
12	EDTA	natural abundance	1 mM
13	D2O	natural abundance	100 %

8 3D 13C-filtered NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 6.8, Details 50 mM sodium phosphate pH 6.8, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA

#	Name	Isotope labeling	Concentration
14	R33	natural abundance	1 mM
15	GBD	[U-100% 13C; U-100% 15N]	1 mM
16	sodium phosphate	natural abundance	50 mM
17	NaCl	natural abundance	100 mM
18	DTT	natural abundance	1 mM
19	EDTA	natural abundance	1 mM
20	D2O	natural abundance	100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16824_2k42.nef
Input source #2: Coordindates	2k42.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	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

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--
GHMSGFKHVSHVGWDPQNGFDVNNLDPDLRSLFSRAGISEAQLTDAETSKLIYDFIEDQGGLEAVRQEMRRQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMSGFKHVSHVGWDPQNGFDVNNLDPDLRSLFSRAGISEAQLTDAETSKLIYDFIEDQGGLEAVRQEMRRQ

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

------80--------90-------100--------
GHMLPDVAQRLMQHLAEHGIQPARNMAEHIPPAPNW
||||||||||||||||||||||||||||||||||||
GHMLPDVAQRLMQHLAEHGIQPARNMAEHIPPAPNW
--------10--------20--------30------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	72	0	0	100.0
B	B	36	0	0	100.0

Content subtype: combined_16824_2k42.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1203		97.2 (chain: A, length: 72), 97.2 (chain: B, length: 36)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2318 (1)	noe	95.8 (chain: A, length: 72), 97.2 (chain: B, length: 36)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 72, Sequence coverage: 97.2%
  - Entity_assembly_ID: B, Chain length: 36, Sequence coverage: 97.2%
- Total number of assignments
  - ¹H chemical shifts: 648
  - ¹³C chemical shifts: 444
  - ¹⁵N chemical shifts: 111
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	429	405	94.4
¹³C chemical shifts	315	296	94.0
¹⁵N chemical shifts	84	75	89.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	149	141	94.6
¹³C chemical shifts	144	136	94.4
¹⁵N chemical shifts	70	66	94.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	280	264	94.3
¹³C chemical shifts	171	160	93.6
¹⁵N chemical shifts	14	9	64.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	34	100.0
¹³C chemical shifts	34	34	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	33	91.7
¹³C chemical shifts	35	25	71.4
¹⁵N chemical shifts	1	1	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
90	HIS	ND1	137.021

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	221	215	97.3
¹³C chemical shifts	161	148	91.9
¹⁵N chemical shifts	39	35	89.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	65	94.2
¹³C chemical shifts	72	64	88.9
¹⁵N chemical shifts	31	29	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	152	150	98.7
¹³C chemical shifts	89	84	94.4
¹⁵N chemical shifts	8	6	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0
¹³C chemical shifts	20	20	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0
¹³C chemical shifts	13	8	61.5
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 72, Sequence coverage: 95.8%
  - Entity_assembly_ID: B, Chain length: 36, Sequence coverage: 97.2%
- Total number of restraints: 2316
- Weight of restraints: 1.0 (2316)
- Potential type of restraints: square-well-parabolic (2316)
- Range of distance target values: 1.66, 7.74 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords autoinhibition, EspFU, GBD, WASP

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Found 1 Document (1.237 seconds)

BMRB: 16824

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. GBD, : 4 : 14 entities Detail

Related entities 2. R33, : 1 : 6 : 3 entities Detail

Interaction partners 1. GBD, : 46 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 3 contents Detail