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Found 1 Document (1.007 seconds)

BMRB: 17968

2LJY

Haddock model structure of the N-terminal domain dimer of HPV16 E6

Authors

Zanier, K., ould M'hamed ould Sidi, A., Boulade-Ladame, C., Rybin, V., Chappelle, A., Atkinson, A., Kieffer, B., Trave, G.

Assembly

HPV16 E6

Entity

1. HPV16 E6 (polymer), 82 monomers, 9874.298 × 2 Da Detail

GAMFQDPQER PRKLPQLCTE LQTTIHDIIL ECVYCKQQLL RREVYDFAFR DLCIVYRDGN PYAVCDKCLK FYSKISEYRH YS

2. ZN (non-polymer, Thiol state: not present), 65.409 × 2 Da

Total weight

19879.414 Da

Max. entity weight

9874.298 Da

Source organism

Human papillomavirus type 16

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.7 %, Completeness (bb): 83.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.7 % (819 of 1015)	86.9 % (464 of 534)	68.4 % (271 of 396)	98.8 % (84 of 85)
Backbone	83.5 % (404 of 484)	97.5 % (158 of 162)	69.3 % (169 of 244)	98.7 % (77 of 78)
Sidechain	81.0 % (495 of 611)	82.3 % (306 of 372)	78.4 % (182 of 232)	100.0 % (7 of 7)
Aromatic	31.7 % (33 of 104)	57.7 % (30 of 52)	5.8 % (3 of 52)
Methyl	100.0 % (80 of 80)	100.0 % (40 of 40)	100.0 % (40 of 40)

1. HPV16 E6

GAMFQDPQER PRKLPQLCTE LQTTIHDIIL ECVYCKQQLL RREVYDFAFR DLCIVYRDGN PYAVCDKCLK FYSKISEYRH YS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details unlabelled sample

#	Name	Isotope labeling	Concentration
1	HPV16_E6	natural abundance	0.3 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaCl	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N labelled sample

#	Name	Isotope labeling	Concentration
5	E6	[U-100% 15N]	0.3 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	NaCl	natural abundance	50 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N, 13C labelled sample

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.3 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	NaCl	natural abundance	50 mM

LACS Plot; CA

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

Referencing offset: -0.39 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.39 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LJY, Strand ID: A, B Detail

Release date

2012-04-03

Citation

Solution structure analysis of the HPV16 E6 oncoprotein reveals a self-association mechanism required for E6-mediated degradation of p53
Zanier, K., Boulade-Ladame, A., Rybin, C., Chappelle, V., Atkinson, A., Kieffer, A., Trave, B.
Structure (2012), 20, 604-617, PubMed 22483108 , DOI 10.1016/j.str.2012.02.001 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 17967 released on 2012-04-03
Title Structure of the monomeric N-terminal domain of HPV16 E6 oncoprotein

Related entities 1. HPV16 E6, : 1 : 4 : 52 entities Detail

Interaction partners 1. HPV16 E6, : 31 interactors Detail

More details for 31 interactors identified by 23 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N labelled sample

#	Name	Isotope labeling	Concentration
5	E6	[U-100% 15N]	0.3 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	NaCl	natural abundance	50 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N, 13C labelled sample

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.3 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	NaCl	natural abundance	50 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N, 13C labelled sample

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.3 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	NaCl	natural abundance	50 mM

4 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N, 13C labelled sample

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.3 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	NaCl	natural abundance	50 mM

5 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N, 13C labelled sample

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.3 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	NaCl	natural abundance	50 mM

6 3D HN(CO)CA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N, 13C labelled sample

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.3 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	NaCl	natural abundance	50 mM

7 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N, 13C labelled sample

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.3 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	NaCl	natural abundance	50 mM

8 3D HCCH-COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N, 13C labelled sample

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.3 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	NaCl	natural abundance	50 mM

9 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N labelled sample

#	Name	Isotope labeling	Concentration
5	E6	[U-100% 15N]	0.3 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %
8	NaCl	natural abundance	50 mM

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details 15N, 13C labelled sample

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.3 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %
12	NaCl	natural abundance	50 mM

11 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details unlabelled sample

#	Name	Isotope labeling	Concentration
1	HPV16_E6	natural abundance	0.3 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaCl	natural abundance	50 mM

12 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296 K, pH 6.8, Details unlabelled sample

#	Name	Isotope labeling	Concentration
1	HPV16_E6	natural abundance	0.3 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaCl	natural abundance	50 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17968_2ljy.nef
Input source #2: Coordindates	2ljy.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:32:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:68:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:65:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
1:68:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
2:32:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
2:65:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
2:35:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:35:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	ZN	ZINC ION	None
C	2	ZN	ZINC ION	None

Sequence alignments

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

-0--------10--------20--------30--------40--------50--------60--------70--------80--
GAMFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYSYS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYSYS
--------10--------20--------30--------40--------50--------60--------70--------80----

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

-0--------10--------20--------30--------40--------50--------60--------70--------80--
GAMFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYSYS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYSYS
--------10--------20--------30--------40--------50--------60--------70--------80----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	84	0	0	100.0
B	B	84	0	0	100.0

Content subtype: combined_17968_2ljy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	E6Ndimer	Warning	811		95.2 (chain: A, length: 84)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	22 (1)	noe	7.1 (chain: A, length: 84), 7.1 (chain: B, length: 84)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	146 (146)	.	67.9 (chain: A, length: 84), 67.9 (chain: B, length: 84)

Assigned chemical shifts

Saveframe: E6Ndimer
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 95.2%
- Total number of assignments
  - ¹H chemical shifts: 469
  - ¹³C chemical shifts: 259
  - ¹⁵N chemical shifts: 83
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	546	469	85.9
¹³C chemical shifts	406	259	63.8
¹⁵N chemical shifts	94	83	88.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	166	157	94.6
¹³C chemical shifts	168	80	47.6
¹⁵N chemical shifts	80	76	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	380	312	82.1
¹³C chemical shifts	238	179	75.2
¹⁵N chemical shifts	14	7	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	40	97.6
¹³C chemical shifts	41	40	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	30	53.6
¹³C chemical shifts	56	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 7.1%
  - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 7.1%
- Total number of restraints: 22
- Weight of restraints: 1.0 (22)
- Potential type of restraints: square-well-parabolic (22)
- Range of distance target values: 3.9, 3.9 (Å)
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 67.9%
  - Entity_assembly_ID: B, Chain length: 84, Sequence coverage: 67.9%
- Total number of restraints: 146
- Total number of restraints per polymer type: 146
- Weight of restraints: 1.0 (146)
- Potential type of restraints: square-well-parabolic (146)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords E6, E6N, E6N dimer, HPV, HPV16

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Found 1 Document (1.007 seconds)

BMRB: 17968

Sample #1

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Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. HPV16 E6, : 1 : 4 : 52 entities Detail

Interaction partners 1. HPV16 E6, : 31 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail