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BMRB: 18097

2LM3

Backbone 1H, 13C, and 15N Chemical Shift Assignments for primate innate immunity protein

Authors

Biris, N., Yang, Y., Taylor, A.B., Tomashevski, A., Guo, M., Hart, P.JOHN., Diaz-Griffero, F., Ivanov, D.N.

Assembly

rhesus SPRY domain

Entity

1. rhesus SPRY domain (polymer, Thiol state: all free), 208 monomers, 23342.22 Da Detail

GTELTDARRY WVDVTLATNN ISHAVIAEDK RQVSSRNPQI MYQAPGTLFT FPSLTNFNYC TGVLGSQSIT SGKHYWEVDV SKKSAWILGV CAGFQSDAMY NIEQNENYQP KYGYWVIGLQ EGVKYSVFQD GSSHTPFAPF IVPLSVIICP DRVGVFVDYE ACTVSFFNIT NHGFLIYKFS QCSFSKPVFP YLNPRKCTVP MTLCSPSS

Formula weight

23342.22 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 73.6 %, Completeness: 38.0 %, Completeness (bb): 60.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	38.0 % (927 of 2441)	32.2 % (404 of 1255)	38.8 % (375 of 966)	67.3 % (148 of 220)
Backbone	60.8 % (743 of 1222)	63.5 % (264 of 416)	54.2 % (331 of 611)	75.9 % (148 of 195)
Sidechain	15.6 % (220 of 1414)	16.7 % (140 of 839)	14.5 % (80 of 550)	0.0 % (0 of 25)
Aromatic	6.0 % (18 of 300)	10.0 % (15 of 150)	2.1 % (3 of 146)	0.0 % (0 of 4)
Methyl	23.1 % (50 of 216)	23.1 % (25 of 108)	23.1 % (25 of 108)

1. SPRY

GTELTDARRY WVDVTLATNN ISHAVIAEDK RQVSSRNPQI MYQAPGTLFT FPSLTNFNYC TGVLGSQSIT SGKHYWEVDV SKKSAWILGV CAGFQSDAMY NIEQNENYQP KYGYWVIGLQ EGVKYSVFQD GSSHTPFAPF IVPLSVIICP DRVGVFVDYE ACTVSFFNIT NHGFLIYKFS QCSFSKPVFP YLNPRKCTVP MTLCSPSS

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SPRY	[U-98% 15N]		250 mM
2	H2O	natural abundance		93 %
3	D2O	natural abundance		7 %

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
4	SPRY	[U-99% 13C; U-99% 15N]		250 mM
5	H2O	natural abundance		93 %
6	D2O	natural abundance		7 %

Sample #3

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	SPRY	[U-13C; U-15N; U-2H]		250 mM
8	H2O	natural abundance		93 %
9	D2O	natural abundance		7 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2LM3, Strand ID: A Detail

Release date

2012-08-05

Citation

Structure of the rhesus monkey TRIM5α PRYSPRY domain, the HIV capsid recognition module
Biris, N., Yang, Y., Taylor, A.B., Tomashevski, A., Guo, M., Hart, P., Diaz-Griffero, F., Ivanov, D.N.
Proc. Natl. Acad. Sci. U. S. A. (2012), 109, 13278-13283, PubMed 22847415 , DOI 10.1073/pnas.1203536109 , Abstract

Related entities 1. rhesus SPRY domain, : 1 : 2 : 195 entities Detail

Interaction partners 1. rhesus SPRY domain, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SPRY	[U-98% 15N]		250 mM
2	H2O	natural abundance		93 %
3	D2O	natural abundance		7 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
4	SPRY	[U-99% 13C; U-99% 15N]		250 mM
5	H2O	natural abundance		93 %
6	D2O	natural abundance		7 %

3 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	SPRY	[U-13C; U-15N; U-2H]		250 mM
8	H2O	natural abundance		93 %
9	D2O	natural abundance		7 %

4 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	SPRY	[U-13C; U-15N; U-2H]		250 mM
8	H2O	natural abundance		93 %
9	D2O	natural abundance		7 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	SPRY	[U-13C; U-15N; U-2H]		250 mM
8	H2O	natural abundance		93 %
9	D2O	natural abundance		7 %

6 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	SPRY	[U-13C; U-15N; U-2H]		250 mM
8	H2O	natural abundance		93 %
9	D2O	natural abundance		7 %

7 3D HN(COCA)CB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	SPRY	[U-13C; U-15N; U-2H]		250 mM
8	H2O	natural abundance		93 %
9	D2O	natural abundance		7 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	SPRY	[U-98% 15N]		250 mM
2	H2O	natural abundance		93 %
3	D2O	natural abundance		7 %

9 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	SPRY	[U-13C; U-15N; U-2H]		250 mM
8	H2O	natural abundance		93 %
9	D2O	natural abundance		7 %

10 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
7	SPRY	[U-13C; U-15N; U-2H]		250 mM
8	H2O	natural abundance		93 %
9	D2O	natural abundance		7 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
4	SPRY	[U-99% 13C; U-99% 15N]		250 mM
5	H2O	natural abundance		93 %
6	D2O	natural abundance		7 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18097_2lm3.nef
Input source #2: Coordindates	2lm3.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

290-----300-------310-------320-------330-------340-------350-------360-------370-------380-------39
GTELTDARRYWVDVTLATNNISHAVIAEDKRQVSSRNPQIMYQAPGTLFTFPSLTNFNYCTGVLGSQSITSGKHYWEVDVSKKSAWILGVCAGFQSDAMY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GTELTDARRYWVDVTLATNNISHAVIAEDKRQVSSRNPQIMYQAPGTLFTFPSLTNFNYCTGVLGSQSITSGKHYWEVDVSKKSAWILGVCAGFQSDAMY
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------400-------410-------420-------430-------440-------450-------460-------470-------480-------49
NIEQNENYQPKYGYWVIGLQEGVKYSVFQDGSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITNHGFLIYKFSQCSFSKPVFPYLNPRKCTVP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NIEQNENYQPKYGYWVIGLQEGVKYSVFQDGSSHTPFAPFIVPLSVIICPDRVGVFVDYEACTVSFFNITNHGFLIYKFSQCSFSKPVFPYLNPRKCTVP
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

0-------
MTLCSPSS
||||||||
MTLCSPSS
--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	208	0	0	100.0

Content subtype: combined_18097_2lm3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	788		70.2 (chain: A, length: 208)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	440 (1)	noe	10.1 (chain: A, length: 208)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 70.2%
- Total number of assignments
  - ¹H chemical shifts: 319
  - ¹³C chemical shifts: 326
  - ¹⁵N chemical shifts: 143
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 10.1%
- Total number of restraints: 428
- Weight of restraints: 1.0 (428)
- Potential type of restraints: square-well-parabolic (428)
- Range of distance target values: 2.25, 4.4 (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

Keywords HIV, SPRY, trim5a, Tripartite motif, innate immunity