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Found 1 Document (2.518 seconds)

BMRB: 30285

5VKG

Solution-state NMR structural ensemble of human Tsg101 UEV in complex with tenatoprazole

Authors

Strickland, M., Ehrlich, L.S., Watanabe, S., Khan, M., Strub, M., Luan, C., Powell, M.D., Leis, J., Tjandra, N., Carter, C.

Assembly

human Tsg101 UEV in complex with tenatoprazole

Entity

1. human Tsg101 UEV in complex with tenatoprazole, entity 1 (polymer, Thiol state: free and disulfide bound), 145 monomers, 16540.04 Da Detail

GAVSESQLKK MVSKYKYRDL TVRETVNVIT LYKDLKPVLD SYVFNDGSSR ELMNLTGTIP VPYRGNTYNI PICLWLLDTY PYNPPICFVK PTSSMTIKTG KHVDANGKIY LPYLHEWKHP QSDLLGLIQV MIVVFGDEPP VFSRP

2. human Tsg101 UEV in complex with tenatoprazole, entity 4N1 (non-polymer), 331.413 Da

Total weight

16871.451 Da

Max. entity weight

16540.04 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS73:SG	2:4N11:S20

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.7 %, Completeness (bb): 83.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.7 % (1573 of 1754)	97.3 % (887 of 912)	77.8 % (543 of 698)	99.3 % (143 of 144)
Backbone	83.9 % (708 of 844)	97.9 % (279 of 285)	69.8 % (298 of 427)	99.2 % (131 of 132)
Sidechain	95.6 % (1001 of 1047)	97.0 % (608 of 627)	93.4 % (381 of 408)	100.0 % (12 of 12)
Aromatic	88.5 % (138 of 156)	96.2 % (75 of 78)	80.3 % (61 of 76)	100.0 % (2 of 2)
Methyl	97.7 % (172 of 176)	100.0 % (88 of 88)	95.5 % (84 of 88)

1. entity 1

GAVSESQLKK MVSKYKYRDL TVRETVNVIT LYKDLKPVLD SYVFNDGSSR ELMNLTGTIP VPYRGNTYNI PICLWLLDTY PYNPPICFVK PTSSMTIKTG KHVDANGKIY LPYLHEWKHP QSDLLGLIQV MIVVFGDEPP VFSRP

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	Tenatoprazole	natural abundance	0.6 mM
2	Tsg101	[U-98% 13C; U-98% 15N]	0.6 mM
3	potassium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
5	Tenatoprazole	natural abundance	0.6 mM
6	Tsg101	[U-13C; U-15N]	0.6 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM

LACS Plot; CA

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

Referencing offset: 0.18 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: 0.18 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: -0.06 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5VKG, Strand ID: A Detail

Release date

2017-05-15

Citation

Tsg101 chaperone function revealed by HIV-1 assembly inhibitors
Strickland, M., Ehrlich, L.S., Watanabe, S., Khan, M., Strub, M., Luan, C., Powell, M.D., Leis, J., Tjandra, N., Carter, C.
Nat. Commun. (2017), 8, 1391-1391, PubMed 29123089 , DOI 10.1038/s41467-017-01426-2 , Abstract

Related entities 1. human Tsg101 UEV in complex with tenatoprazole, entity 1, : 1 : 14 : 40 entities Detail

Interaction partners 1. human Tsg101 UEV in complex with tenatoprazole, entity 1, : 109 interactors Detail

More details for 109 interactors identified by 28 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	Tenatoprazole	natural abundance	0.6 mM
2	Tsg101	[U-98% 13C; U-98% 15N]	0.6 mM
3	potassium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz Cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
5	Tenatoprazole	natural abundance	0.6 mM
6	Tsg101	[U-13C; U-15N]	0.6 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	Tenatoprazole	natural abundance	0.6 mM
2	Tsg101	[U-98% 13C; U-98% 15N]	0.6 mM
3	potassium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

4 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	Tenatoprazole	natural abundance	0.6 mM
2	Tsg101	[U-98% 13C; U-98% 15N]	0.6 mM
3	potassium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	Tenatoprazole	natural abundance	0.6 mM
2	Tsg101	[U-98% 13C; U-98% 15N]	0.6 mM
3	potassium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
5	Tenatoprazole	natural abundance	0.6 mM
6	Tsg101	[U-13C; U-15N]	0.6 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM

7 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz Cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
5	Tenatoprazole	natural abundance	0.6 mM
6	Tsg101	[U-13C; U-15N]	0.6 mM
7	potassium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM

8 3D 1H-13C-12C filtered NOESY aliphatic

Instrument

Bruker Avance - 800 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	Tenatoprazole	natural abundance	0.6 mM
2	Tsg101	[U-98% 13C; U-98% 15N]	0.6 mM
3	potassium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

9 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	Tenatoprazole	natural abundance	0.6 mM
2	Tsg101	[U-98% 13C; U-98% 15N]	0.6 mM
3	potassium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

10 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz Cryoprobe

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 300 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	Tenatoprazole	natural abundance	0.6 mM
2	Tsg101	[U-98% 13C; U-98% 15N]	0.6 mM
3	potassium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30285_5vkg.nef
Input source #2: Coordindates	5vkg.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:73:CYS:SG	2:1:4N1:S20	unknown	unknown	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	4N1	4-methoxy-1-(5-methoxy-3H-imidazo[4,5-b]pyridin-2-yl)-3,5-dimethyl-2-(sulfanylmethyl)pyridin-1-ium	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTG

-------110-------120-------130-------140-----
KHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRP
|||||||||||||||||||||||||||||||||||||||||||||
KHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	145	0	0	100.0

Content subtype: combined_30285_5vkg.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_chemical_shifts_1	Warning	1558		100.0 (chain: A, length: 145)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	8574 (1)	noe	99.3 (chain: A, length: 145)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	920 (1)	noe	82.8 (chain: A, length: 145)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	92 (1)	hbond	42.1 (chain: A, length: 145)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	276 (276)	.	100.0 (chain: A, length: 145)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 894
  - ¹³C chemical shifts: 521
  - ¹⁵N chemical shifts: 143
- 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)
15	TYR	HH	9.445
21	THR	HG1	3.851
25	THR	HG1	3.915

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	912	891	97.7
¹³C chemical shifts	698	521	74.6
¹⁵N chemical shifts	149	143	96.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	285	281	98.6
¹³C chemical shifts	290	143	49.3
¹⁵N chemical shifts	132	131	99.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	627	610	97.3
¹³C chemical shifts	408	378	92.6
¹⁵N chemical shifts	17	12	70.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	92	92	100.0
¹³C chemical shifts	92	87	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	75	96.2
¹³C chemical shifts	76	61	80.3
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 99.3%
- Total number of restraints: 7607
- Weight of restraints: 1.0 (7607)
- Potential type of restraints: square-well-parabolic (7607)
- Range of distance target values: 1.9, 9.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 82.8%
  - Total number of restraints: 883
  - Weight of restraints: 1.0 (883)
  - Potential type of restraints: square-well-parabolic (883)
  - Range of distance target values: 2.05, 5.1 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 42.1%
    - Total number of restraints: 92
    - Weight of restraints: 1.0 (92)
    - Potential type of restraints: square-well-parabolic (92)
    - Range of distance target values: 2.0, 3.25 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 100.0%
- Total number of restraints: 276
- Total number of restraints per polymer type: 276
- Weight of restraints: 1.0 (276)
- Potential type of restraints: square-well-parabolic (276)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ESCRT-I, cell cycle, inhibitor

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Found 1 Document (2.518 seconds)

BMRB: 30285

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. human Tsg101 UEV in complex with tenatoprazole, entity 1, : 1 : 14 : 40 entities Detail

Interaction partners 1. human Tsg101 UEV in complex with tenatoprazole, entity 1, : 109 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail