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BMRB: 30171

5T82

HIV-1 reverse transcriptase thumb subdomain

Authors

Gronenborn, A.M., Sharaf, N.G., Byeon, I.L.

Assembly

Reverse transcriptase

Entity

1. Reverse transcriptase (polymer, Thiol state: not present), 90 monomers, 10442.85 Da Detail

DKWTVQPIVL PEKDSWTVND IQKLVGKLNW ASQIYPGIKV RQLSKLLRGT KALTEVIPLT EEAELELAEN REILKEPVHG VYLEHHHHHH

Formula weight

10442.85 Da

Source organism

Human immunodeficiency virus 1

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.2 %, Completeness: 76.3 %, Completeness (bb): 75.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.3 % (840 of 1101)	81.0 % (465 of 574)	66.7 % (288 of 432)	91.6 % (87 of 95)
Backbone	75.5 % (400 of 530)	86.0 % (154 of 179)	63.5 % (169 of 266)	90.6 % (77 of 85)
Sidechain	78.8 % (518 of 657)	78.7 % (311 of 395)	78.2 % (197 of 252)	100.0 % (10 of 10)
Aromatic	37.5 % (30 of 80)	60.0 % (24 of 40)	8.1 % (3 of 37)	100.0 % (3 of 3)
Methyl	88.5 % (108 of 122)	88.5 % (54 of 61)	88.5 % (54 of 61)

1. entity 1

DKWTVQPIVL PEKDSWTVND IQKLVGKLNW ASQIYPGIKV RQLSKLLRGT KALTEVIPLT EEAELELAEN REILKEPVHG VYLEHHHHHH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details [U-13C],[U-15N]-labeled RT thumb subdomain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1 mM
2	Sodium Phosphate	natural abundance		25 mM
3	NaCl	natural abundance		100 mM

LACS Plot; CA

Referencing offset: -0.07 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.07 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 5T82, Strand ID: A Detail

Release date

2016-11-10

Citation

NMR structure of the HIV-1 reverse transcriptase thumb subdomain
Sharaf, N.G., Brereton, A.E., Byeon, I.L., Karplus, P.A., Gronenborn, A.M.
J. Biomol. NMR (2016), 66, 273-280, PubMed 27858311 , DOI 10.1007/s10858-016-0077-2 , Abstract

Related entities 1. Reverse transcriptase, : 1 : 169 entities Detail

Interaction partners 1. Reverse transcriptase, : 3 interactors Detail

More details for 3 interactors identified by 3 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance600 - 600 MHz 5 mm triple resonance, Z-axis gradient cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details [U-13C],[U-15N]-labeled RT thumb subdomain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1 mM
2	Sodium Phosphate	natural abundance		25 mM
3	NaCl	natural abundance		100 mM

2 3D HN(CO)CACB

Instrument

Bruker Avance700 - 700 MHz 5 mm triple resonance, Z-axis gradient cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details [U-13C],[U-15N]-labeled RT thumb subdomain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1 mM
2	Sodium Phosphate	natural abundance		25 mM
3	NaCl	natural abundance		100 mM

3 3D HNCACB

Instrument

Bruker Avance700 - 700 MHz 5 mm triple resonance, Z-axis gradient cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details [U-13C],[U-15N]-labeled RT thumb subdomain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1 mM
2	Sodium Phosphate	natural abundance		25 mM
3	NaCl	natural abundance		100 mM

4 3D HCCH-TOCSY

Instrument

Bruker Avance700 - 700 MHz 5 mm triple resonance, Z-axis gradient cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details [U-13C],[U-15N]-labeled RT thumb subdomain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1 mM
2	Sodium Phosphate	natural abundance		25 mM
3	NaCl	natural abundance		100 mM

5 3D H(CCO)NH

Instrument

Bruker Avance700 - 700 MHz 5 mm triple resonance, Z-axis gradient cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details [U-13C],[U-15N]-labeled RT thumb subdomain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1 mM
2	Sodium Phosphate	natural abundance		25 mM
3	NaCl	natural abundance		100 mM

6 3D C(CO)NH

Instrument

Bruker Avance700 - 700 MHz 5 mm triple resonance, Z-axis gradient cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details [U-13C],[U-15N]-labeled RT thumb subdomain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1 mM
2	Sodium Phosphate	natural abundance		25 mM
3	NaCl	natural abundance		100 mM

7 3D SIMULTANEOUS 13C- and 15N- EDITED NOESY

Instrument

Bruker Avance700 - 700 MHz 5 mm triple resonance, Z-axis gradient cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details [U-13C],[U-15N]-labeled RT thumb subdomain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		1 mM
2	Sodium Phosphate	natural abundance		25 mM
3	NaCl	natural abundance		100 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30171_5t82.nef
Input source #2: Coordindates	5t82.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

---240-----250-------260-------270-------280-------290-------300-------310-------320------
DKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYLEHHHHHH
--------10--------20--------30--------40--------50--------60--------70--------80--------90

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	90	0	0	100.0

Content subtype: combined_30171_5t82.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	829		91.1 (chain: A, length: 90)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	2621 (1)	noe	92.2 (chain: A, length: 90)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	46 (1)	hbond	35.6 (chain: A, length: 90)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	46 (1)	hbond	35.6 (chain: A, length: 90)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	116 (116)	.	76.7 (chain: A, length: 90)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 91.1%
- Total number of assignments
  - ¹H chemical shifts: 467
  - ¹³C chemical shifts: 276
  - ¹⁵N chemical shifts: 86
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 92.2%
- Total number of restraints: 2621
- Weight of restraints: 1.0 (2621)
- Potential type of restraints: square-well-parabolic (2621)
- Range of distance target values: 2.15, 4.9 (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
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 35.6%
  - Total number of restraints: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: square-well-parabolic (46)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 35.6%
    - Total number of restraints: 46
    - Weight of restraints: 1.0 (46)
    - Potential type of restraints: square-well-parabolic (46)
    - Range of distance target values: 2.05, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 76.7%
- Total number of restraints: 116
- Total number of restraints per polymer type: 116
- Weight of restraints: 1.0 (116)
- Potential type of restraints: square-well-parabolic (116)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords HYDROLASE, thumb subdomain