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Found 1 Document (0.722 seconds)

BMRB: 30137

5KTF

Structure of the C-terminal transmembrane domain of scavenger receptor BI (SR-BI)

Authors

Chadwick, A.C., Peterson, F.C., Volkman, B.F., Sahoo, D.

Assembly

Scavenger receptor class B member 1

Entity

1. Scavenger receptor class B member 1 (polymer), 73 monomers, 8180.749 Da Detail

GSKIEPVVLP LLWFEQSGAM GGKPLSTFYT QLVLMPQVLH YAQYVLLGLG GLLLLVPIIC QLRSQEKCFL FWS

Formula weight

8180.749 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 84.6 %, Completeness (bb): 92.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.6 % (764 of 903)	87.6 % (408 of 466)	79.8 % (288 of 361)	89.5 % (68 of 76)
Backbone	92.8 % (397 of 428)	93.2 % (138 of 148)	91.0 % (193 of 212)	97.1 % (66 of 68)
Sidechain	79.1 % (428 of 541)	84.9 % (270 of 318)	72.6 % (156 of 215)	25.0 % (2 of 8)
Aromatic	76.1 % (70 of 92)	89.1 % (41 of 46)	61.4 % (27 of 44)	100.0 % (2 of 2)
Methyl	63.9 % (69 of 108)	74.1 % (40 of 54)	53.7 % (29 of 54)

1. entity 1

GSKIEPVVLP LLWFEQSGAM GGKPLSTFYT QLVLMPQVLH YAQYVLLGLG GLLLLVPIIC QLRSQEKCFL FWS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.8, Details 1 mM [U-99% 13C; U-99% 15N] scavenger receptor BI (SR-BI), 5.0 w/v [U-2H] LPPG, 0.02 w/v sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	LPPG	[U-2H]	5.0 w/v
2	scavenger receptor BI (SR-BI)	[U-99% 13C; U-99% 15N]	1 mM
3	sodium azide	natural abundance	0.02 w/v

Protein Blocks Logo

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

Release date

2016-11-10

Citation

NMR Structure of the C-Terminal Transmembrane Domain of the HDL Receptor, SR-BI, and a Functionally Relevant Leucine Zipper Motif
Chadwick, A.C., Jensen, D.R., Hanson, P.J., Lange, P.T., Proudfoot, S.C., Peterson, F.C., Volkman, B.F., Sahoo, D.
Structure (2017), 25, 446-457, PubMed 28162952 , DOI 10.1016/j.str.2017.01.001 , Abstract

Related entities 1. Scavenger receptor class B member 1, : 2 : 16 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30137_5ktf.nef
Input source #2: Coordindates	5ktf.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

-----410-------420-------430-------440-------450-------460-------470-----
GSKIEPVVLPLLWFEQSGAMGGKPLSTFYTQLVLMPQVLHYAQYVLLGLGGLLLLVPIICQLRSQEKCFLFWS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSKIEPVVLPLLWFEQSGAMGGKPLSTFYTQLVLMPQVLHYAQYVLLGLGGLLLLVPIICQLRSQEKCFLFWS
--------10--------20--------30--------40--------50--------60--------70---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	0	0	100.0

Content subtype: combined_30137_5ktf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	766		98.6 (chain: A, length: 73)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	819 (1)	noe	98.6 (chain: A, length: 73)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	119 (119)	.	93.2 (chain: A, length: 73)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 414
  - ¹³C chemical shifts: 284
  - ¹⁵N chemical shifts: 68
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	466	414	88.8
¹³C chemical shifts	361	284	78.7
¹⁵N chemical shifts	77	68	88.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	148	144	97.3
¹³C chemical shifts	146	134	91.8
¹⁵N chemical shifts	68	66	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	318	270	84.9
¹³C chemical shifts	215	150	69.8
¹⁵N chemical shifts	9	2	22.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	41	73.2
¹³C chemical shifts	56	28	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	41	89.1
¹³C chemical shifts	44	27	61.4
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 98.6%
- Total number of restraints: 819
- Weight of restraints: 1.0 (819)
- Potential type of restraints: upper-bound-parabolic (819)
- Range of distance target values: 2.28, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 93.2%
- Total number of restraints: 119
- Total number of restraints per polymer type: 119
- Weight of restraints: 1.0 (119)
- Potential type of restraints: square-well-parabolic (119)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SIGNALING PROTEIN, SR-BI, cholesterol, transmembrane domain

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Found 1 Document (0.722 seconds)

BMRB: 30137

Sample

Related entities 1. Scavenger receptor class B member 1, : 2 : 16 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail