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BMRB: 17874

2LI1

Mono-O-GalNAc glycosylated Mucin sequence based on MUC2 Mucin glycoprotein tandem repeat

Authors

Borgert, A., Heimburg-Molinaro, J., Lasanajak, Y., Ju, T., Liu, M., Thompson, P., Ragupathi, G., Barany, G., Cummings, R., Smith, D., Live, D.

Assembly

MUC2 Mucin Domain Peptide

Entity

1. MUC2 Mucin Domain Peptide (polymer, Thiol state: not present), 9 monomers, 781.948 Da Detail

XPTTTPLKX

2. A2G (non-polymer, Thiol state: not present), 221.208 Da

Total weight

1003.156 Da

Max. entity weight

781.948 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion space simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 77.8 %, Completeness: 96.3 %, Completeness (bb): 94.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (79 of 82)	93.0 % (40 of 43)	100.0 % (34 of 34)	100.0 % (5 of 5)
Backbone	94.7 % (36 of 38)	83.3 % (10 of 12)	100.0 % (21 of 21)	100.0 % (5 of 5)
Sidechain	98.0 % (50 of 51)	96.8 % (30 of 31)	100.0 % (20 of 20)
Methyl	100.0 % (10 of 10)	100.0 % (5 of 5)	100.0 % (5 of 5)

1. MUC2 Mucin Domain Peptide

XPTTTPLKX

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	MUC2_Mucin_Domain_Peptide	natural abundance	2.0 ~ 10.0 mM
2	A2G	natural abundance	2.0 ~ 10.0 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
5	MUC2 Mucin Domain Peptide	natural abundance	2.0 ~ 10.0 mM
6	SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)	natural abundance	2.0 ~ 10.0 mM
7	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 27 models in PDB: 2LI1, Strand ID: A Detail

Release date

2012-03-26

Citation

Deciphering structural elements of mucin glycoprotein recognition
Borgert, A., Heimburg-Molinaro, J., Song, X., Lasanajak, Y., Ju, T., Liu, M., Thompson, P., Ragupathi, G., Barany, G., Smith, D.F., Cummings, R.D., Live, D.
ACS Chem. Biol. (2012), 7, 1031-1039, PubMed 22444368 , DOI 10.1021/cb300076s , Abstract

Experiments performed 7 experiments Detail

1 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
5	MUC2 Mucin Domain Peptide	natural abundance	2.0 ~ 10.0 mM
6	SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)	natural abundance	2.0 ~ 10.0 mM
7	D2O	natural abundance	100 %

2 3D TOCSY-NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	MUC2_Mucin_Domain_Peptide	natural abundance	2.0 ~ 10.0 mM
2	A2G	natural abundance	2.0 ~ 10.0 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

3 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	MUC2_Mucin_Domain_Peptide	natural abundance	2.0 ~ 10.0 mM
2	A2G	natural abundance	2.0 ~ 10.0 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

4 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	MUC2_Mucin_Domain_Peptide	natural abundance	2.0 ~ 10.0 mM
2	A2G	natural abundance	2.0 ~ 10.0 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

5 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	MUC2_Mucin_Domain_Peptide	natural abundance	2.0 ~ 10.0 mM
2	A2G	natural abundance	2.0 ~ 10.0 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

6 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
5	MUC2 Mucin Domain Peptide	natural abundance	2.0 ~ 10.0 mM
6	SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)	natural abundance	2.0 ~ 10.0 mM
7	D2O	natural abundance	100 %

7 2D 1H-13C HMBC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	MUC2_Mucin_Domain_Peptide	natural abundance	2.0 ~ 10.0 mM
2	A2G	natural abundance	2.0 ~ 10.0 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17874_2li1.nef
Input source #2: Coordindates	2li1.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)
1:1:ACE:C	1:2:PRO:N	unknown	unknown	n/a
1:4:THR:OG1	2:1:A2G:C1	unknown	unknown	n/a
1:8:LYS:C	1:9:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	ACE	ACETYL GROUP	Distance restraints, Coordinates
A	9	NH2	AMINO GROUP	Coordinates
B	1	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Assigned chemical shifts, Distance restraints, Torsion angle restraints

Sequence alignments

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

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XPTTTPLKX
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XPTTTPLKX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	9	0	0	100.0

Content subtype: combined_17874_2li1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	96		77.8 (chain: A, length: 9), 100.0 (chain: B, length: 1)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	99 (1)	noe	88.9 (chain: A, length: 9), 100.0 (chain: B, length: 1)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	7 (7)	.	77.8 (chain: A, length: 9), 100.0 (chain: B, length: 1)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 77.8%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 51
  - ¹³C chemical shifts: 40
  - ¹⁵N chemical shifts: 5
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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	47	43	91.5
¹³C chemical shifts	36	34	94.4
¹⁵N chemical shifts	6	5	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	12	92.3
¹³C chemical shifts	14	14	100.0
¹⁵N chemical shifts	6	5	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	31	91.2
¹³C chemical shifts	22	20	90.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	5	83.3
¹³C chemical shifts	6	5	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	8	88.9
¹³C chemical shifts	8	6	75.0
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	6	6	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	1	50.0
¹³C chemical shifts	2	0	0.0
¹⁵N chemical shifts	1	0	0.0

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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 88.9%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 99
- Weight of restraints: 1.0 (99)
- Potential type of restraints: square-well-parabolic (99)
- Range of distance target values: 2.4, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 77.8%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 7
- Total number of restraints per polymer type: 7
- Weight of restraints: 1.0 (7)
- Potential type of restraints: square-well-parabolic (7)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords glycoprotein, glycosylation, MUC2, mucin, Tn antigen

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Found 1 Document (0.582 seconds)

BMRB: 17874

Sample #1

Sample #2

Experiments performed 7 experiments Detail

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NMR combined restraints 4 contents Detail