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BMRB: 18816

2M0P

Solution structure of the tenth complement type repeat of human megalin

Authors

Dagil, R., Kragelund, B.

Assembly

CR10

Entity

1. CR10 (polymer, Thiol state: all disulfide bound), 52 monomers, 5864.074 Da Detail

THAPASCLDT QYTCDNHQCI SKNWVCDTDN DCGDGSDEKN CNSTETHHHH HH

2. CALCIUM ION (non-polymer), 40.078 Da

Total weight

5904.1523 Da

Max. entity weight

5864.074 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS7:SG	1:CYS19:SG
2	disulfide	sing	1:CYS14:SG	1:CYS32:SG
3	disulfide	sing	1:CYS26:SG	1:CYS41:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.5 %, Completeness: 79.4 %, Completeness (bb): 82.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.4 % (427 of 538)	79.2 % (217 of 274)	80.0 % (164 of 205)	78.0 % (46 of 59)
Backbone	82.9 % (257 of 310)	83.8 % (88 of 105)	83.1 % (128 of 154)	80.4 % (41 of 51)
Sidechain	77.0 % (214 of 278)	76.3 % (129 of 169)	79.2 % (80 of 101)	62.5 % (5 of 8)
Aromatic	44.2 % (23 of 52)	46.2 % (12 of 26)	40.0 % (10 of 25)	100.0 % (1 of 1)
Methyl	100.0 % (28 of 28)	100.0 % (14 of 14)	100.0 % (14 of 14)

1. CR10

THAPASCLDT QYTCDNHQCI SKNWVCDTDN DCGDGSDEKN CNSTETHHHH HH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
10	calcium chloride	natural abundance	50 mM
11	sodium chloride	natural abundance	100 mM
12	TRIS	natural abundance	50 mM
13	DSS	natural abundance	0.1 mM
14	sodium azide	natural abundance	0.1 %
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	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M0P, Strand ID: A Detail

Release date

2013-01-06

Citation

Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin
Dagil, R., Nykjaer, C., Bonvin, A., Kragelund, A.
J. Biol. Chem. (2013), 288, 4424-4435, PubMed 23275343 , DOI 10.1074/jbc.M112.434159 , Abstract

Related entities 1. CR10, : 1 : 1 : 157 entities Detail

Interaction partners 1. CR10, : 8 interactors Detail

More details for 8 interactors identified by 5 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 2D 1H-1H TOCSY aromatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

4 3D HNCO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 3D HNCA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

6 3D HNCACB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

7 3D C(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

8 3D CBCA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
10	calcium chloride	natural abundance	50 mM
11	sodium chloride	natural abundance	100 mM
12	TRIS	natural abundance	50 mM
13	DSS	natural abundance	0.1 mM
14	sodium azide	natural abundance	0.1 %
15	D2O	natural abundance	100 %

10 3D HN(CO)CA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz Carlsberg Research Center

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
10	calcium chloride	natural abundance	50 mM
11	sodium chloride	natural abundance	100 mM
12	TRIS	natural abundance	50 mM
13	DSS	natural abundance	0.1 mM
14	sodium azide	natural abundance	0.1 %
15	D2O	natural abundance	100 %

12 2D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
10	calcium chloride	natural abundance	50 mM
11	sodium chloride	natural abundance	100 mM
12	TRIS	natural abundance	50 mM
13	DSS	natural abundance	0.1 mM
14	sodium azide	natural abundance	0.1 %
15	D2O	natural abundance	100 %

13 3D H(CCO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

14 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

15 3D 1H-15N TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details pH 6.5

#	Name	Isotope labeling	Concentration
1	CR10	[U-100% 13C; U-100% 15N]	0.6 mM
2	sodium chloride	natural abundance	100 mM
3	calcium chloride	natural abundance	50 mM
4	TRIS	natural abundance	50 mM
5	DSS	natural abundance	0.1 mM
6	sodium azide	natural abundance	0.1 %
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_18816_2m0p.nef
Input source #2: Coordindates	2m0p.cif
Diamagnetism of the molecular assembly	False (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:1109:CYS:SG	A:1121:CYS:SG	oxidized, CA 52.983, CB 36.292 ppm	oxidized, CA 53.116, CB 40.916 ppm	2.029
A:1116:CYS:SG	A:1134:CYS:SG	oxidized, CA 55.624, CB 42.336 ppm	oxidized, CA 58.079, CB 43.039 ppm	2.024
A:1128:CYS:SG	A:1143:CYS:SG	oxidized, CA 56.119, CB 36.015 ppm	oxidized, CA 54.796, CB 39.615 ppm	2.029

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)
1:37:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:27:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:31:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:38:GLU:OE2	2:1:CA:CA	unknown	unknown	n/a
1:29:ASP:O	2:1:CA:CA	unknown	unknown	n/a
1:24:TRP:O	2:1:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CA	CALCIUM ION	None

Sequence alignments

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

----1110------1120------1130------1140------1150----
THAPASCLDTQYTCDNHQCISKNWVCDTDNDCGDGSDEKNCNSTETHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||
THAPASCLDTQYTCDNHQCISKNWVCDTDNDCGDGSDEKNCNSTETHHHHHH
--------10--------20--------30--------40--------50--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	52	0	0	100.0

Content subtype: combined_18816_2m0p.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	9		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	423		88.5 (chain: A, length: 52)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	572 (1)	noe	82.7 (chain: A, length: 52)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	3 (1)	disulfide_bond	11.5 (chain: A, length: 52)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	15 (1)	hbond	42.3 (chain: A, length: 52)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	38 (38)	.	53.8 (chain: A, length: 52)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 88.5%
- Total number of assignments
  - ¹H chemical shifts: 215
  - ¹³C chemical shifts: 164
  - ¹⁵N chemical shifts: 44
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	274	215	78.5
¹³C chemical shifts	205	164	80.0
¹⁵N chemical shifts	59	44	74.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	105	86	81.9
¹³C chemical shifts	104	84	80.8
¹⁵N chemical shifts	51	39	76.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	169	129	76.3
¹³C chemical shifts	101	80	79.2
¹⁵N chemical shifts	8	5	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	14	100.0
¹³C chemical shifts	14	14	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	12	46.2
¹³C chemical shifts	25	10	40.0
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 82.7%
- Total number of restraints: 569
- Weight of restraints: 1.0 (569)
- Potential type of restraints: square-well-parabolic (569)
- Range of distance target values: 1.7, 4.29 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: OK
  - Experiment type: disulfide_bond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 11.5%
  - Total number of restraints: 3
  - Weight of restraints: 1.0 (3)
  - Potential type of restraints: square-well-parabolic (3)
  - Range of distance target values: 2.02, 2.02 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 42.3%
    - Total number of restraints: 15
    - Weight of restraints: 1.0 (15)
    - Potential type of restraints: square-well-parabolic (15)
    - Range of distance target values: 2.21, 2.21 (Å)
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - 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: 52, Sequence coverage: 53.8%
- Total number of restraints: 38
- Total number of restraints per polymer type: 38
- Weight of restraints: 1.0 (38)
- Potential type of restraints: square-well-parabolic (38)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Complement type repeat, ldl receptor family, lrp2, megalin, receptor

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Found 1 Document (0.872 seconds)

BMRB: 18816

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CR10, : 1 : 1 : 157 entities Detail

Interaction partners 1. CR10, : 8 interactors Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 6 contents Detail