BMRBj - BMREntryMaster

Found 1 Document (0.734 seconds)

BMRB: 17378

2L7U

Structure of CEL-PEP-RAGE V domain complex

Authors

Xue, J., Rai, V., Schmidt, A., Frolov, S., Reverdatto, S., Singer, D., Chabierski, S., Xie, J., Burz, D., Shekhtman, A., Hoffman, R.

Assembly

PROTEIN

Entity

1. V domain (polymer, Thiol state: all disulfide bound), 105 monomers, 11554.18 Da Detail

GSAQNITARI GEPLVLKCKG APKKPPQRLE WKLNTGRTEA WKVLSPQGGG PWDSVARVLP NGSLFLPAVG IQDEGIFRCQ AMNRNGKETK SNYRVRVYQI PGKPE

2. CEL-PEP (polymer), 7 monomers, 1088.026 Da Detail

DEFXADE

3. MCL (polymer), 216.234 Da

Total weight

12858.44 Da

Max. entity weight

11554.18 Da

Source organism

Homo sapiens , Bos taurus

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.6 %, Completeness: 76.6 %, Completeness (bb): 88.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.6 % (996 of 1301)	79.9 % (551 of 690)	71.1 % (352 of 495)	80.2 % (93 of 116)
Backbone	88.5 % (572 of 646)	94.6 % (212 of 224)	83.2 % (267 of 321)	92.1 % (93 of 101)
Sidechain	67.5 % (509 of 754)	72.7 % (339 of 466)	62.3 % (170 of 273)	0.0 % (0 of 15)
Aromatic	6.1 % (5 of 82)	12.2 % (5 of 41)	0.0 % (0 of 38)	0.0 % (0 of 3)
Methyl	85.6 % (89 of 104)	94.2 % (49 of 52)	76.9 % (40 of 52)

1. V domain

GSAQNITARI GEPLVLKCKG APKKPPQRLE WKLNTGRTEA WKVLSPQGGG PWDSVARVLP NGSLFLPAVG IQDEGIFRCQ AMNRNGKETK SNYRVRVYQI PGKPE

2. CEL-PEP

DEFXADE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
5	V domain	[U-100% 13C; U-100% 15N]		0.32 mM
6	CEL-PEP	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 25 models in PDB: 2L7U, Strand ID: A, B Detail

Release date

2011-05-17

Citation

Advanced glycation end product recognition by the receptor for AGEs
Xue, J., Rai, V., Singer, D., Chabierski, S., Xie, J., Reverdatto, S., Burz, D.S., Schmidt, A., Hoffmann, R., Shekhtman, A.
Structure (2011), 19, 722-732, PubMed 21565706 , DOI 10.1016/j.str.2011.02.013 , Abstract

Related entities 1. V domain, : 1 : 77 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D HN(CA)CO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
1	V domain	[U-100% 13C; U-100% 15N]		0.1 mM
2	CEL-PEP	natural abundance		0.3 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
5	V domain	[U-100% 13C; U-100% 15N]		0.32 mM
6	CEL-PEP	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
5	V domain	[U-100% 13C; U-100% 15N]		0.32 mM
6	CEL-PEP	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

12 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM potassium phosphate [pH 6.5], 100 mM NaCl, 0.02% (w/v) NaN3

#	Name	Isotope labeling	Type	Concentration
5	V domain	[U-100% 13C; U-100% 15N]		0.32 mM
6	CEL-PEP	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17378_2l7u.nef
Input source #2: Coordindates	2l7u.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:18:CYS:SG	A:79:CYS:SG	oxidized, CA 66.588, CB 42.274 ppm	oxidized, CA 62.728, CB 42.731 ppm	1.858

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)
2:3:PHE:C	2:4:KPI:N	unknown	unknown	n/a
2:4:KPI:C	2:5:ALA:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	4	KPI	(2S)-2-amino-6-[(1-hydroxy-1-oxo-propan-2-ylidene)amino]hexanoic acid	Assigned chemical shifts, Distance restraints, Coordinates

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GSAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSAQNITARIGEPLVLKCKGAPKKPPQRLEWKLNTGRTEAWKVLSPQGGGPWDSVARVLPNGSLFLPAVGIQDEGIFRCQAMNRNGKETKSNYRVRVYQI

-----
PGKPE
|||||
PGKPE

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

-------
DEFXADE
|||||||
DEFXADE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	105	0	0	100.0
B	B	7	0	0	100.0

Content subtype: combined_17378_2l7u.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	997		95.2 (chain: A, length: 105), 85.7 (chain: B, length: 7)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	1363 (1)	noe	93.3 (chain: A, length: 105), 71.4 (chain: B, length: 7)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	3 (1)	disulfide_bond	No information
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	316 (1)	noe	73.3 (chain: A, length: 105), 28.6 (chain: B, length: 7)
4	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	39 (1)	hbond	44.8 (chain: A, length: 105)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	Warning	620 (619)	.	95.2 (chain: A, length: 105), 71.4 (chain: B, length: 7)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 95.2%
  - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 85.7%
- Total number of assignments
  - ¹H chemical shifts: 560
  - ¹³C chemical shifts: 345
  - ¹⁵N chemical shifts: 92
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 93.3%
  - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 71.4%
- Total number of restraints: 1343
- Weight of restraints: 1.0 (1343)
- Potential type of restraints: upper-bound-parabolic (1343)
- Range of distance target values: 2.36, 7.03 (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
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: Warning
  - Experiment type: disulfide_bond
  - Total number of restraints: 3
  - Weight of restraints: 1.0 (3)
  - Potential type of restraints: upper-bound-parabolic (3)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 73.3%
      - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 28.6%
    - Total number of restraints: 306
    - Weight of restraints: 1.0 (306)
    - Potential type of restraints: upper-bound-parabolic (306)
    - Range of distance target values: 2.79, 5.88 (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
    - Saveframe: DYANA/DIANA_distance_constraints_4
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 44.8%
      - Total number of restraints: 39
        Total hydrogen bond restraints: 39
        O...H-x: 5
        O...H-x (too close!): 2
        Long range: 32
        O...H-x: 26
        O...H-x (too close!): 6
      - Weight of restraints: 1.0 (39)
        Total hydrogen bond restraints: 1.0 (39)
        O...H-x: 1.0 (5)
        O...H-x (too close!): 1.0 (2)
        Long range: 1.0 (32)
        O...H-x: 1.0 (26)
        O...H-x (too close!): 1.0 (6)
      - Potential type of restraints: upper-bound-parabolic (39)
        Total hydrogen bond restraints: upper-bound-parabolic (39)
        O...H-x: upper-bound-parabolic (5)
        O...H-x (too close!): upper-bound-parabolic (2)
        Long range: upper-bound-parabolic (32)
        O...H-x: upper-bound-parabolic (26)
        O...H-x (too close!): upper-bound-parabolic (6)
      - Range of distance target values: 1.68, 2.54 (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_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 95.2%
  - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 71.4%
- Total number of restraints: 619
- Total number of restraints per polymer type: 619
- Weight of restraints: 1.0 (619)
- Potential type of restraints: square-well-parabolic (619)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords advanced glycation end products (AGE), carboxyethyl lysine, carboxymethyl lysine, receptor for advanced glycation end products (RAGE), V domain