BMRBj - BMREntryMaster

Found 1 Document (0.356 seconds)

BMRB: 30880

7M1W

NMR structure of the Human T-cell leukemia virus 1 matrix protein

Authors

Herrmann, D., Saad, J.S.

Assembly

Matrix protein p19

Entity

1. Matrix protein p19 (polymer), 105 monomers, 12005.81 Da Detail

MGRIFSRSAS PIPRPPRGLA AHHWLNFLQA AYRLEPGPSS YDFHQLKKFL KIALETPVWI CPINYSLLAS LLPKGYPGRV NEILHILIQT QAQIPSRPAH HHHHH

Formula weight

12005.81 Da

Source organism

Human T-cell leukemia virus type I

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.4 %, Completeness: 86.0 %, Completeness (bb): 88.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.0 % (1110 of 1290)	85.9 % (577 of 672)	86.4 % (439 of 508)	85.5 % (94 of 110)
Backbone	88.8 % (538 of 606)	89.2 % (181 of 203)	87.7 % (272 of 310)	91.4 % (85 of 93)
Sidechain	84.7 % (664 of 784)	84.4 % (396 of 469)	86.9 % (259 of 298)	52.9 % (9 of 17)
Aromatic	77.9 % (106 of 136)	79.4 % (54 of 68)	75.8 % (50 of 66)	100.0 % (2 of 2)
Methyl	97.5 % (115 of 118)	98.3 % (58 of 59)	96.6 % (57 of 59)

1. entity 1

MGRIFSRSAS PIPRPPRGLA AHHWLNFLQA AYRLEPGPSS YDFHQLKKFL KIALETPVWI CPINYSLLAS LLPKGYPGRV NEILHILIQT QAQIPSRPAH HHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 100 mM sodium chloride, 50 mM sodium phosphate, 2 mM TCEP, 400 uM [U-99% 13C; U-99% 15N] HTLV-1 Matrix, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	50 mM
3	TCEP	natural abundance	2 mM
4	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	400 uM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 100 mM sodium chloride, 50 mM sodium phosphate, 2 mM TCEP, 320 uM [U-99% 13C; U-99% 15N] HTLV-1 Matrix, 100% D2O

#	Name	Isotope labeling	Concentration
5	sodium chloride	natural abundance	100 mM
6	sodium phosphate	natural abundance	50 mM
7	TCEP	natural abundance	2 mM
8	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	320 uM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 100 mM sodium chloride, 50 mM sodium phosphate, 2 mM TCEP, 500 uM [U-99% 15N] HTLV-1 Matrix, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	50 mM
11	TCEP	natural abundance	2 mM
12	HTLV-1 Matrix	[U-99% 15N]	500 uM

Release date

2021-03-17

Citation

Structural Insights into the Mechanism of Human T-cell Leukemia Virus Type 1 Gag Targeting to the Plasma Membrane for Assembly
Herrmann, D., Zhou, L.W., Hanson, H.M., Willkomm, N.A., Mansky, L.M., Saad, J.S.
J. Mol. Biol. (2021), 433, 167161-167161, PubMed 34298060 , DOI 10.1016/j.jmb.2021.167161 , Abstract

Related entities 1. Matrix protein p19, : 1 : 20 entities Detail

Experiments performed 11 experiments Detail

1 3D HNCA

Instrument

Bruker AVANCE II - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 100 mM sodium chloride, 50 mM sodium phosphate, 2 mM TCEP, 400 uM [U-99% 13C; U-99% 15N] HTLV-1 Matrix, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	50 mM
3	TCEP	natural abundance	2 mM
4	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	400 uM

2 3D HNCO

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	50 mM
3	TCEP	natural abundance	2 mM
4	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	400 uM

3 3D HNCACB

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	50 mM
3	TCEP	natural abundance	2 mM
4	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	400 uM

4 HN(CO)CACB

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	50 mM
3	TCEP	natural abundance	2 mM
4	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	400 uM

5 3D HN(CO)CA

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	50 mM
3	TCEP	natural abundance	2 mM
4	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	400 uM

6 3D 15N-separated NOESY

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	50 mM
11	TCEP	natural abundance	2 mM
12	HTLV-1 Matrix	[U-99% 15N]	500 uM

7 3D 13C-separated NOESY

Instrument

Bruker AVANCE II - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 100 mM sodium chloride, 50 mM sodium phosphate, 2 mM TCEP, 320 uM [U-99% 13C; U-99% 15N] HTLV-1 Matrix, 100% D2O

#	Name	Isotope labeling	Concentration
5	sodium chloride	natural abundance	100 mM
6	sodium phosphate	natural abundance	50 mM
7	TCEP	natural abundance	2 mM
8	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	320 uM

8 3D HCCH-TOCSY arom.

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	sodium chloride	natural abundance	100 mM
6	sodium phosphate	natural abundance	50 mM
7	TCEP	natural abundance	2 mM
8	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	320 uM

9 3D HCCH-TOCSY ali.

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	sodium chloride	natural abundance	100 mM
6	sodium phosphate	natural abundance	50 mM
7	TCEP	natural abundance	2 mM
8	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	320 uM

10 2D 1H-15N HSQC

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	50 mM
3	TCEP	natural abundance	2 mM
4	HTLV-1 Matrix	[U-99% 13C; U-99% 15N]	400 uM

11 3D 15N-separated TOCSY

Instrument

Bruker AVANCE II - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
9	sodium chloride	natural abundance	100 mM
10	sodium phosphate	natural abundance	50 mM
11	TCEP	natural abundance	2 mM
12	HTLV-1 Matrix	[U-99% 15N]	500 uM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30880_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: bmr30880_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1232		92.4 (chain: 1, length: 105)
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: 105, Sequence coverage: 92.4%
- Total number of assignments
  - ¹H chemical shifts: 698
  - ¹³C chemical shifts: 439
  - ¹⁵N chemical shifts: 95
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
85	HIS	HD1	8.226
85	HIS	ND1	197.915

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	672	581	86.5
¹³C chemical shifts	508	439	86.4
¹⁵N chemical shifts	110	94	85.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	203	185	91.1
¹³C chemical shifts	210	180	85.7
¹⁵N chemical shifts	93	85	91.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	469	396	84.4
¹³C chemical shifts	298	259	86.9
¹⁵N chemical shifts	17	9	52.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	58	96.7
¹³C chemical shifts	60	57	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	54	79.4
¹³C chemical shifts	66	50	75.8
¹⁵N chemical shifts	2	2	100.0

Keywords Gag, HTLV-1, Human T-cell leukemia virus 1, Matrix, VIRAL PROTEIN, membrane-binding protein

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.356 seconds)

BMRB: 30880

Sample #1

Sample #2

Sample #3

Related entities 1. Matrix protein p19, : 1 : 20 entities Detail

Experiments performed 11 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail