BMRBj - BMREntryMaster

Found 1 Document (0.709 seconds)

BMRB: 18967

2M3L

Solution structure of the C-terminal zinc-binding domain of HPV51 oncoprotein E6

Authors

Mischo, A., Ohlenschlager, O., Gorlach, M.

Assembly

Entity

1. E6 (polymer, Thiol state: all other bound), 76 monomers, 8933.063 Da Detail

GSHMSRSVYG TTLEAITKKS LYDLSIRCHR CQRPLGPEEK QKLVDEKKRF HEIAGRWTGQ CANCWQRTRQ RNETQV

2. ZINC ION (non-polymer, Thiol state: not present), 65.409 Da

Total weight

8998.473 Da

Max. entity weight

8933.063 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS28:SG	2:ZN1:ZN
2	na	sing	1:CYS31:SG	2:ZN1:ZN
3	na	sing	1:CYS61:SG	2:ZN1:ZN
4	na	sing	1:CYS64:SG	2:ZN1:ZN

Source organism

Human papillomavirus

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 95.2 %, Completeness (bb): 95.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.2 % (866 of 910)	94.0 % (455 of 484)	96.5 % (330 of 342)	96.4 % (81 of 84)
Backbone	95.4 % (431 of 452)	93.5 % (145 of 155)	96.4 % (215 of 223)	95.9 % (71 of 74)
Sidechain	95.3 % (504 of 529)	94.2 % (310 of 329)	96.8 % (184 of 190)	100.0 % (10 of 10)
Aromatic	96.8 % (60 of 62)	100.0 % (31 of 31)	93.1 % (27 of 29)	100.0 % (2 of 2)
Methyl	96.8 % (60 of 62)	93.5 % (29 of 31)	100.0 % (31 of 31)

1. E6

GSHMSRSVYG TTLEAITKKS LYDLSIRCHR CQRPLGPEEK QKLVDEKKRF HEIAGRWTGQ CANCWQRTRQ RNETQV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	E6	[U-100% 13C; U-100% 15N]	1.13 mM
2	sodium chloride	natural abundance	90 mM
3	L-arginine	natural abundance	45 mM
4	L-glutamate	natural abundance	45 mM
5	DTT	natural abundance	9 mM
6	sodium azide	natural abundance	0.05 w/v
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.9 mM
10	sodium chloride	natural abundance	90 mM
11	L-arginine	natural abundance	45 mM
12	L-glutamate	natural abundance	45 mM
13	DTT	natural abundance	9 mM
14	sodium azide	natural abundance	0.05 w/v
15	D2O	natural abundance	100 %

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: -0.06 ppm, Outliers: 3 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: -0.06 ppm, Outliers: 3 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: 0.28 ppm, Outliers: 1 Detail

LACS Plot; CO

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: -0.1 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M3L, Strand ID: A Detail

Release date

2013-05-12

Citation

Structural insights into a wildtype domain of the oncoprotein E6 and its interaction with a PDZ domain
Mischo, A., Ohlenschlager, O., Hortschansky, P., Ramachandran, R., Gorlach, M.
PLoS One (2013), 8, e62584-e62584, PubMed 23638119 , DOI 10.1371/journal.pone.0062584 , Abstract

Related entities 1. E6, : 1 : 1 : 55 entities Detail

Interaction partners 1. E6, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	E6	[U-100% 13C; U-100% 15N]	1.13 mM
2	sodium chloride	natural abundance	90 mM
3	L-arginine	natural abundance	45 mM
4	L-glutamate	natural abundance	45 mM
5	DTT	natural abundance	9 mM
6	sodium azide	natural abundance	0.05 w/v
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	E6	[U-100% 13C; U-100% 15N]	1.13 mM
2	sodium chloride	natural abundance	90 mM
3	L-arginine	natural abundance	45 mM
4	L-glutamate	natural abundance	45 mM
5	DTT	natural abundance	9 mM
6	sodium azide	natural abundance	0.05 w/v
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.9 mM
10	sodium chloride	natural abundance	90 mM
11	L-arginine	natural abundance	45 mM
12	L-glutamate	natural abundance	45 mM
13	DTT	natural abundance	9 mM
14	sodium azide	natural abundance	0.05 w/v
15	D2O	natural abundance	100 %

4 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	E6	[U-100% 13C; U-100% 15N]	1.13 mM
2	sodium chloride	natural abundance	90 mM
3	L-arginine	natural abundance	45 mM
4	L-glutamate	natural abundance	45 mM
5	DTT	natural abundance	9 mM
6	sodium azide	natural abundance	0.05 w/v
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 3D HNHA

Instrument

Bruker AvanceIII - 600 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	E6	[U-100% 13C; U-100% 15N]	1.13 mM
2	sodium chloride	natural abundance	90 mM
3	L-arginine	natural abundance	45 mM
4	L-glutamate	natural abundance	45 mM
5	DTT	natural abundance	9 mM
6	sodium azide	natural abundance	0.05 w/v
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

6 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	E6	[U-100% 13C; U-100% 15N]	1.13 mM
2	sodium chloride	natural abundance	90 mM
3	L-arginine	natural abundance	45 mM
4	L-glutamate	natural abundance	45 mM
5	DTT	natural abundance	9 mM
6	sodium azide	natural abundance	0.05 w/v
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

7 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 600 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.9 mM
10	sodium chloride	natural abundance	90 mM
11	L-arginine	natural abundance	45 mM
12	L-glutamate	natural abundance	45 mM
13	DTT	natural abundance	9 mM
14	sodium azide	natural abundance	0.05 w/v
15	D2O	natural abundance	100 %

8 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 600 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.9 mM
10	sodium chloride	natural abundance	90 mM
11	L-arginine	natural abundance	45 mM
12	L-glutamate	natural abundance	45 mM
13	DTT	natural abundance	9 mM
14	sodium azide	natural abundance	0.05 w/v
15	D2O	natural abundance	100 %

9 3D HCCH-COSY

Instrument

Bruker AvanceIII - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
9	E6	[U-100% 13C; U-100% 15N]	0.9 mM
10	sodium chloride	natural abundance	90 mM
11	L-arginine	natural abundance	45 mM
12	L-glutamate	natural abundance	45 mM
13	DTT	natural abundance	9 mM
14	sodium azide	natural abundance	0.05 w/v
15	D2O	natural abundance	100 %

10 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	E6	[U-100% 13C; U-100% 15N]	1.13 mM
2	sodium chloride	natural abundance	90 mM
3	L-arginine	natural abundance	45 mM
4	L-glutamate	natural abundance	45 mM
5	DTT	natural abundance	9 mM
6	sodium azide	natural abundance	0.05 w/v
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18967_2m3l.nef
Input source #2: Coordindates	2m3l.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)
1:61:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:64:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:31:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:28: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

---80--------90-------100-------110-------120-------130-------140-------150-
GSHMSRSVYGTTLEAITKKSLYDLSIRCHRCQRPLGPEEKQKLVDEKKRFHEIAGRWTGQCANCWQRTRQRNETQV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMSRSVYGTTLEAITKKSLYDLSIRCHRCQRPLGPEEKQKLVDEKKRFHEIAGRWTGQCANCWQRTRQRNETQV
--------10--------20--------30--------40--------50--------60--------70------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0

Content subtype: combined_18967_2m3l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	882		97.4 (chain: A, length: 76)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	6 (1)	undefined	5.3 (chain: A, length: 76)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	2308 (1)	noe	97.4 (chain: A, length: 76)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	30 (1)	hbond	27.6 (chain: A, length: 76)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	Warning	248 (244)	.	96.1 (chain: A, length: 76)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 465
  - ¹³C chemical shifts: 337
  - ¹⁵N chemical shifts: 80
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
132	TRP	CE2	139.43
138	ASN	CG	176.394
140	TRP	CE2	138.343

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	484	465	96.1
¹³C chemical shifts	342	334	97.7
¹⁵N chemical shifts	93	80	86.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	148	95.5
¹³C chemical shifts	152	148	97.4
¹⁵N chemical shifts	74	70	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	329	317	96.4
¹³C chemical shifts	190	186	97.9
¹⁵N chemical shifts	19	10	52.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	31	96.9
¹³C chemical shifts	32	31	96.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	31	100.0
¹³C chemical shifts	29	27	93.1
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 5.3%
- Total number of restraints: 6
- Weight of restraints: 1.0 (6)
- Potential type of restraints: upper-bound-parabolic (6)
- Range of distance target values: 3.8, 3.8 (Å)
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 97.4%
  - Total number of restraints: 2255
  - Weight of restraints: 1.0 (2255)
  - Potential type of restraints: upper-bound-parabolic (2255)
  - Range of distance target values: 2.0, 10.67 (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
  - Saveframe: DYANA/DIANA_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 27.6%
    - Total number of restraints: 30
    - Weight of restraints: 1.0 (30)
    - Potential type of restraints: upper-bound-parabolic (30)
    - Range of distance target values: 1.8, 2.7 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_5
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 96.1%
- Total number of restraints: 244
- Total number of restraints per polymer type: 244
- Weight of restraints: 1.0 (244)
- Potential type of restraints: square-well-parabolic (244)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords E6, HPV, NMR, Oncogene Proteins, Oncoprotein E6, Papillomavirus E6 Proteins, Viral, Zinc Fingers

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.709 seconds)

BMRB: 18967

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. E6, : 1 : 1 : 55 entities Detail

Interaction partners 1. E6, : 1 interactors Detail

Experiments performed 10 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail