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BMRB: 19953

2MOV

Receptor for Advanced Glycation End Products (RAGE) Specifically Recognizes Methylglyoxal Derived AGEs.

Authors

Shekhtman, A., Xue, J., Ray, R., Singer, D., Bohme, D., Burz, D.S., Rai, V., Hoffman, R.

Assembly

V domain of RAGE in complex with IOR

Entity

1. V domain (polymer), 105 monomers, 11554.18 Da Detail

GSAQNITARI GEPLVLKCKG APKKPPQRLE WKLNTGRTEA WKVLSPQGGG PWDSVARVLP NGSLFLPAVG IQDEGIFRCQ AMNRNGKETK SNYRVRVYQI PGKPE

2. N~5~-[(2S,4S,5R)-4-hydroxy-5-methylimidazolidin-2-yl]-L-ornithine (non-polymer), 228.248 Da

Total weight

11782.428 Da

Max. entity weight

11554.18 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 78.9 %, Completeness (bb): 91.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.9 % (977 of 1238)	80.2 % (528 of 658)	75.3 % (354 of 470)	86.4 % (95 of 110)
Backbone	91.8 % (560 of 610)	94.8 % (201 of 212)	87.8 % (266 of 303)	97.9 % (93 of 95)
Sidechain	69.6 % (502 of 721)	73.3 % (327 of 446)	66.5 % (173 of 260)	13.3 % (2 of 15)
Aromatic	9.7 % (7 of 72)	16.7 % (6 of 36)	0.0 % (0 of 33)	33.3 % (1 of 3)
Methyl	83.3 % (85 of 102)	90.2 % (46 of 51)	76.5 % (39 of 51)

1. V domain

GSAQNITARI GEPLVLKCKG APKKPPQRLE WKLNTGRTEA WKVLSPQGGG PWDSVARVLP NGSLFLPAVG IQDEGIFRCQ AMNRNGKETK SNYRVRVYQI PGKPE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

Protein Blocks Logo

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

Release date

2014-06-22

Citation

The receptor for advanced glycation end products (RAGE) specifically recognizes methylglyoxal-derived AGEs
Xue, J., Ray, R., Singer, D., Bohme, D.S., Burz, D.S., Rai, V., Hoffman, R., Shekhtman, A.
Biochemistry (2014), 53, 3327-3335, PubMed 24824951 , DOI 10.1021/bi500046t , Abstract

Related entities 1. V domain, : 1 : 1 : 25 : 188 entities Detail

Interaction partners 1. V domain, : 17 interactors Detail

More details for 17 interactors identified by 12 citations

Experiments performed 9 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 V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

3 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 V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

4 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 V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

5 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 V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

6 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 V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

7 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 V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

8 3D HCACO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

9 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 V-domain-IOR complex

#	Name	Isotope labeling	Type	Concentration
1	V_domain	[U-13C; U-15N]		0.1 mM
2	IOR	[U-13C; U-15N]		0.1 mM
3	H2O	natural abundance		90 %
4	D2O	[U-100% 2H]		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19953_2mov.nef
Input source #2: Coordindates	2mov.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	None
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	2.176

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	IOR	N~5~-[(5R)-5-methyl-4-oxo-4,5-dihydro-1H-imidazol-2-yl]-L-ornithine	Assigned chemical shifts

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

Chain assignments

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

Content subtype: combined_19953_2mov.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	964		95.2 (chain: A, length: 105), 100.0 (chain: B, length: 1)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1636 (1)	noe	96.2 (chain: A, length: 105)

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: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 527
  - 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 96.2%
- Total number of restraints: 1604
- Weight of restraints: 1.0 (1604)
- Potential type of restraints: upper-bound-parabolic (1604)
- Range of distance target values: 1.68, 7.5 (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

Keywords PROTEIN/LIGAND