BMRBj - BMREntryMaster

Found 1 Document (0.891 seconds)

BMRB: 17967

2LJX

Structure of the monomeric N-terminal domain of HPV16 E6 oncoprotein

Authors

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

Assembly

N-terminal domain of HPV16 E6 oncoprotein

Entity

1. E6 (polymer), 84 monomers, 10133.56 Da Detail

GAMFQDPQER PRKLPQLCTE LQTTIHDIIL ECVYCKQQLL RREVYDFARR DLCIVYRDGN PYAVCDKCLK FYSKISEYRH YSYS

2. ZN (non-polymer), 65.409 Da

Total weight

10198.969 Da

Max. entity weight

10133.56 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS32:SG	2:ZN1:ZN
2	na	sing	1:CYS35:SG	2:ZN1:ZN
3	na	sing	1:CYS65:SG	2:ZN1:ZN
4	na	sing	1:CYS68:SG	2:ZN1:ZN

Source organism

Human papillomavirus type 16

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 81.4 %, Completeness (bb): 82.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.4 % (843 of 1036)	88.3 % (482 of 546)	69.0 % (278 of 403)	95.4 % (83 of 87)
Backbone	82.3 % (408 of 496)	95.8 % (159 of 166)	69.2 % (173 of 250)	95.0 % (76 of 80)
Sidechain	82.8 % (515 of 622)	85.0 % (323 of 380)	78.7 % (185 of 235)	100.0 % (7 of 7)
Aromatic	31.4 % (32 of 102)	56.9 % (29 of 51)	5.9 % (3 of 51)
Methyl	100.0 % (80 of 80)	100.0 % (40 of 40)	100.0 % (40 of 40)

1. E6

GAMFQDPQER PRKLPQLCTE LQTTIHDIIL ECVYCKQQLL RREVYDFARR DLCIVYRDGN PYAVCDKCLK FYSKISEYRH YSYS

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	E6	natural abundance	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	2 mM

Sample #2

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

#	Name	Isotope labeling	Concentration
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #3

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

#	Name	Isotope labeling	Concentration
10	E6	[U-100% 15N]	1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

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: -0.35 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: -0.35 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: 0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LJX, Strand ID: A 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: 17968 released on 2012-04-03
Title Haddock model structure of the N-terminal domain dimer of HPV16 E6

Related entities 1. E6, : 1 : 2 : 4 : 56 entities Detail

Interaction partners 1. E6, : 31 interactors Detail

More details for 31 interactors identified by 23 citations

Experiments performed 13 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
10	E6	[U-100% 15N]	1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

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
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

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
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

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
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

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
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

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
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

7 3D HBHA(CO)NH

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
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

8 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
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

9 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
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

10 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
10	E6	[U-100% 15N]	1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

11 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
7	E6	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

12 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	E6	natural abundance	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	2 mM

13 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 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	E6	natural abundance	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	2 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17967_2ljx.nef
Input source #2: Coordindates	2ljx.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)
1:68:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:65:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:35:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:32:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	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--
GAMFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFARRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYSYS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFARRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYSYS
--------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

Content subtype: combined_17967_2ljx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	E6N	Warning	819		97.6 (chain: A, length: 84)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1429 (1)	noe	96.4 (chain: A, length: 84)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	87 (87)	.	76.2 (chain: A, length: 84)

Assigned chemical shifts

Saveframe: E6N
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 97.6%
- Total number of assignments
  - ¹H chemical shifts: 472
  - ¹³C chemical shifts: 264
  - 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	472	86.4
¹³C chemical shifts	403	264	65.5
¹⁵N chemical shifts	95	83	87.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	166	159	95.8
¹³C chemical shifts	168	82	48.8
¹⁵N chemical shifts	80	76	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	380	313	82.4
¹³C chemical shifts	235	182	77.4
¹⁵N chemical shifts	15	7	46.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	41	100.0
¹³C chemical shifts	41	41	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	27	52.9
¹³C chemical shifts	51	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 96.4%
- Total number of restraints: 1429
- Weight of restraints: 1.0 (1429)
- Potential type of restraints: square-well-parabolic (1429)
- Range of distance target values: 2.13, 3.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- 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: 84, Sequence coverage: 76.2%
- Total number of restraints: 87
- Total number of restraints per polymer type: 87
- Weight of restraints: 1.0 (87)
- Potential type of restraints: square-well-parabolic (87)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords E6, E6N, HPV, HPV16

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Found 1 Document (0.891 seconds)

BMRB: 17967

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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. E6, : 1 : 2 : 4 : 56 entities Detail

Interaction partners 1. E6, : 31 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 4 contents Detail