BMRBj - BMREntryMaster

Found 1 Document (1.48 seconds)

BMRB: 30736

6W9N

Solution structure of the FYVE domain of ALFY

Authors

Reinhart, E.F., Pellegrini, M., Ragusa, M.J.

Assembly

WD repeat and FYVE domain-containing protein 3

Entity

1. WD repeat and FYVE domain-containing protein 3, entity 1 (polymer, Thiol state: all other bound), 78 monomers, 8922.930 Da Detail

SNAGRSAADH WVKDEGGDSC SGCSVRFSLT ERRHHCRNCG QLFCQKCSRF QSEIKRLKIS SPVRVCQNCY YNLQHERG

2. WD repeat and FYVE domain-containing protein 3, entity ZN (non-polymer), 65.409 × 2 Da

Total weight

9053.748 Da

Max. entity weight

8922.93 Da

Entity Connection

na 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS20:SG	2:ZN1:ZN
2	na	sing	1:CYS23:SG	2:ZN1:ZN
3	na	sing	1:CYS44:SG	2:ZN1:ZN
4	na	sing	1:CYS47:SG	2:ZN1:ZN
5	na	sing	1:CYS36:SG	2:ZN1:ZN
6	na	sing	1:CYS39:SG	2:ZN1:ZN
7	na	sing	1:CYS66:SG	2:ZN1:ZN
8	na	sing	1:CYS69:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.1 %, Completeness (bb): 98.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.1 % (791 of 898)	90.0 % (423 of 470)	88.0 % (292 of 332)	79.2 % (76 of 96)
Backbone	98.1 % (457 of 466)	97.5 % (157 of 161)	98.2 % (224 of 228)	98.7 % (76 of 77)
Sidechain	80.6 % (406 of 504)	86.1 % (266 of 309)	79.5 % (140 of 176)	0.0 % (0 of 19)
Aromatic	32.4 % (24 of 74)	64.9 % (24 of 37)	0.0 % (0 of 36)	0.0 % (0 of 1)
Methyl	100.0 % (48 of 48)	100.0 % (24 of 24)	100.0 % (24 of 24)

1. entity 1

SNAGRSAADH WVKDEGGDSC SGCSVRFSLT ERRHHCRNCG QLFCQKCSRF QSEIKRLKIS SPVRVCQNCY YNLQHERG

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 768 uM [U-99% 13C; U-99% 15N] The FYVE domain of ALFY, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

Sample #2

Solvent system 99% H2O/1% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 583 uM [U-99% 15N] The FYVE domain of ALFY, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM TCEP, 99% H2O/1% D2O

#	Name	Isotope labeling	Concentration
5	The FYVE domain of ALFY	[U-99% 15N]	583 uM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	150 mM
8	TCEP	natural abundance	0.2 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 589 uM The FYVE domain of ALFY, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM TCEP, 100% D2O

#	Name	Isotope labeling	Concentration
9	The FYVE domain of ALFY	natural abundance	589 uM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	150 mM
12	TCEP	natural abundance	0.2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6W9N, Strand ID: A Detail

Release date

2020-04-07

Citation

A highly conserved glutamic acid in ALFY inhibits membrane binding to aid in aggregate clearance
Reinhart, E.F., Litt, N.A., Katzenell, S., Pellegrini, M., Yamamoto, A., Ragusa, M.J.
Traffic (2021), 22, 23-37, PubMed 33225481 , DOI 10.1111/tra.12771 , Abstract

Related entities 1. WD repeat and FYVE domain-containing protein 3, entity 1, : 1 : 1 : 115 entities Detail

Interaction partners 1. WD repeat and FYVE domain-containing protein 3, entity 1, : 41 interactors Detail

More details for 41 interactors identified by 12 citations

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 700 MHz

Sample

State isotropic, Solvent system 99% H2O/1% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 583 uM [U-99% 15N] The FYVE domain of ALFY, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM TCEP, 99% H2O/1% D2O

#	Name	Isotope labeling	Concentration
5	The FYVE domain of ALFY	[U-99% 15N]	583 uM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	150 mM
8	TCEP	natural abundance	0.2 mM

2 3D 1H-15N NOESY

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	The FYVE domain of ALFY	[U-99% 15N]	583 uM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	150 mM
8	TCEP	natural abundance	0.2 mM

3 3D CBCA(CO)NH

Instrument

Bruker AVANCE - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 768 uM [U-99% 13C; U-99% 15N] The FYVE domain of ALFY, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

4 2D 1H-1H NOESY

Instrument

Bruker AVANCE - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 589 uM The FYVE domain of ALFY, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM TCEP, 100% D2O

#	Name	Isotope labeling	Concentration
9	The FYVE domain of ALFY	natural abundance	589 uM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	150 mM
12	TCEP	natural abundance	0.2 mM

5 2D 1H-1H COSY

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
9	The FYVE domain of ALFY	natural abundance	589 uM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	150 mM
12	TCEP	natural abundance	0.2 mM

6 2D 1H-1H TOCSY

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
9	The FYVE domain of ALFY	natural abundance	589 uM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	150 mM
12	TCEP	natural abundance	0.2 mM

7 3D HN(CO)CA

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

8 3D HNCA

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

9 3D HNCACB

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

10 3D HNCO

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

11 3D HCCH-TOCSY

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

12 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

13 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

14 3D HCCH-COSY

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

15 3D HN(CA)CO

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

16 3D (H)C(CCO)NH

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

17 3D HBHA(CBCACO)NH

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

18 3D H(CCCO)NH

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

19 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	The FYVE domain of ALFY	[U-99% 13C; U-99% 15N]	768 uM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	TCEP	natural abundance	0.2 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30736_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)
1:20:CYS:SG	2:1:ZN:ZN	reduced, CA 60.129, CB 31.08 ppm	unknown	n/a
1:23:CYS:SG	2:1:ZN:ZN	oxidized 18.6%, reduced 81.4%, CA 59.162, CB 32.775 ppm	unknown	n/a
1:44:CYS:SG	2:1:ZN:ZN	reduced, CA 57.674, CB 31.412 ppm	unknown	n/a
1:47:CYS:SG	2:1:ZN:ZN	reduced, CA 63.605, CB 30.79 ppm	unknown	n/a
1:36:CYS:SG	3:1:ZN:ZN	oxidized 12.6%, reduced 87.4%, CA 58.903, CB 32.352 ppm	unknown	n/a
1:39:CYS:SG	3:1:ZN:ZN	oxidized 16.8%, reduced 83.2%, CA 58.988, CB 32.623 ppm	unknown	n/a
1:66:CYS:SG	3:1:ZN:ZN	reduced, CA 56.524, CB 31.105 ppm	unknown	n/a
1:69:CYS:SG	3:1:ZN:ZN	reduced, CA 65.778, CB 29.081 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr30736_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	832		98.7 (chain: 1, length: 78)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 78, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 467
  - ¹³C chemical shifts: 290
  - ¹⁵N chemical shifts: 75
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	470	419	89.1
¹³C chemical shifts	332	290	87.3
¹⁵N chemical shifts	96	75	78.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	155	96.3
¹³C chemical shifts	156	151	96.8
¹⁵N chemical shifts	77	75	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	309	264	85.4
¹³C chemical shifts	176	139	79.0
¹⁵N chemical shifts	19	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	24	100.0
¹³C chemical shifts	24	24	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	37	24	64.9
¹³C chemical shifts	36	0	0.0
¹⁵N chemical shifts	1	0	0.0

Keywords FYVE domain, LIPID BINDING PROTEIN, phosphoinositide binding, zinc binding

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Found 1 Document (1.48 seconds)

BMRB: 30736

Sample #1

Sample #2

Sample #3

Related entities 1. WD repeat and FYVE domain-containing protein 3, entity 1, : 1 : 1 : 115 entities Detail

Interaction partners 1. WD repeat and FYVE domain-containing protein 3, entity 1, : 41 interactors Detail

Experiments performed 19 experiments Detail

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Chemical shift validation 4 contents Detail