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BMRB: 19484

2MDF

NMR structure of a two-transmembrane segment TM VI-VII of NHE1

Authors

Lee, B.L., Sykes, B.D., Alves, C., Fliegel, L.

Assembly

tm67

Entity

1. tm67 (polymer, Thiol state: not present), 57 monomers, 6249.294 Da Detail

GSKKKDNLLF GSIISAVDPV AVLAVFEEIH INELLHILVF GESLLNDAVT VVLYKKK

Formula weight

6249.294 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 84.4 %, Completeness (bb): 95.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	84.4 % (293 of 347)	84.4 % (293 of 347)
Backbone	95.7 % (111 of 116)	95.7 % (111 of 116)
Sidechain	78.8 % (182 of 231)	78.8 % (182 of 231)
Aromatic	47.8 % (11 of 23)	47.8 % (11 of 23)
Methyl	100.0 % (49 of 49)	100.0 % (49 of 49)

1. entity

GSKKKDNLLF GSIISAVDPV AVLAVFEEIH INELLHILVF GESLLNDAVT VVLYKKK

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		1.0 ~ 2.0 mM
2	D2O	[U-2H]		5 %
3	DSS	[1,1,2,2,3,3-2H6]		0.25 mM
4	H2O	natural abundance		95 %
5	dodecylphosphocholine	[U-2H]		75.0 ~ 150.0 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-15N]		1.0 ~ 2.0 mM
7	D2O	[U-2H]		100 %
8	DSS	[1,1,2,2,3,3-2H6]		0.25 mM
9	dodecylphosphocholine	[U-2H]		75.0 ~ 150.0 mM

Protein Blocks Logo

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

Release date

2014-06-29

Citation

Structural and functional analysis of the transmembrane segment pair VI and VII of the NHE1 isoform of the Na+/H+ exchanger
Alves, C., Lee, B.L., Sykes, B.D., Fliegel, L.
Biochemistry (2014), 53, 3658-3670, PubMed 24840010 , DOI 10.1021/bi500392y , Abstract

Related entities 1. tm67, : 1 : 9 : 135 entities Detail

Interaction partners 1. tm67, : 13 interactors Detail

More details for 13 interactors identified by 6 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		1.0 ~ 2.0 mM
2	D2O	[U-2H]		5 %
3	DSS	[1,1,2,2,3,3-2H6]		0.25 mM
4	H2O	natural abundance		95 %
5	dodecylphosphocholine	[U-2H]		75.0 ~ 150.0 mM

2 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		1.0 ~ 2.0 mM
2	D2O	[U-2H]		5 %
3	DSS	[1,1,2,2,3,3-2H6]		0.25 mM
4	H2O	natural abundance		95 %
5	dodecylphosphocholine	[U-2H]		75.0 ~ 150.0 mM

3 3D 1H-15N TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		1.0 ~ 2.0 mM
2	D2O	[U-2H]		5 %
3	DSS	[1,1,2,2,3,3-2H6]		0.25 mM
4	H2O	natural abundance		95 %
5	dodecylphosphocholine	[U-2H]		75.0 ~ 150.0 mM

4 2D DQF-COSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		1.0 ~ 2.0 mM
2	D2O	[U-2H]		5 %
3	DSS	[1,1,2,2,3,3-2H6]		0.25 mM
4	H2O	natural abundance		95 %
5	dodecylphosphocholine	[U-2H]		75.0 ~ 150.0 mM

5 2D 1H-1H TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		1.0 ~ 2.0 mM
2	D2O	[U-2H]		5 %
3	DSS	[1,1,2,2,3,3-2H6]		0.25 mM
4	H2O	natural abundance		95 %
5	dodecylphosphocholine	[U-2H]		75.0 ~ 150.0 mM

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-15N]		1.0 ~ 2.0 mM
2	D2O	[U-2H]		5 %
3	DSS	[1,1,2,2,3,3-2H6]		0.25 mM
4	H2O	natural abundance		95 %
5	dodecylphosphocholine	[U-2H]		75.0 ~ 150.0 mM

7 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-15N]		1.0 ~ 2.0 mM
7	D2O	[U-2H]		100 %
8	DSS	[1,1,2,2,3,3-2H6]		0.25 mM
9	dodecylphosphocholine	[U-2H]		75.0 ~ 150.0 mM

NMR combined restraints 11 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19484_2mdf.nef
Input source #2: Coordindates	2mdf.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

-------230-------240-------250-------260-------270-------
GSKKKDNLLFGSIISAVDPVAVLAVFEEIHINELLHILVFGESLLNDAVTVVLYKKK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSKKKDNLLFGSIISAVDPVAVLAVFEEIHINELLHILVFGESLLNDAVTVVLYKKK
--------10--------20--------30--------40--------50-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	57	0	0	100.0

Content subtype: combined_19484_2mdf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	295		98.2 (chain: A, length: 57)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	929 (1)	noe	96.5 (chain: A, length: 57)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	326 (1)	noe	66.7 (chain: A, length: 57)
3	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1138 (1)	noe	93.0 (chain: A, length: 57)
4	Distance restraints	CNS/XPLOR_distance_constraints_8	Warning	2 (1)	noe	7.0 (chain: A, length: 57)
5	Distance restraints	CNS/XPLOR_distance_constraints_7	Warning	422 (1)	noe	80.7 (chain: A, length: 57)
6	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	314 (1)	noe	96.5 (chain: A, length: 57)
7	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	465 (1)	noe	98.2 (chain: A, length: 57)
8	Distance restraints	CNS/XPLOR_distance_constraints_9	Warning	183 (1)	noe	70.2 (chain: A, length: 57)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_10	OK	70 (70)	.	71.9 (chain: A, length: 57)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 98.2%
- Total number of assignments
  - ¹H chemical shifts: 295
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 96.5%
- Total number of restraints: 929
- Weight of restraints: 1.0 (929)
- Potential type of restraints: square-well-parabolic (929)
- Range of distance target values: 2.3, 3.65 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 66.7%
  - Total number of restraints: 326
  - Weight of restraints: 1.0 (326)
  - Potential type of restraints: square-well-parabolic (326)
  - Range of distance target values: 2.75, 4.92 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_2
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 93.0%
    - Total number of restraints: 1138
    - Weight of restraints: 1.0 (1138)
    - Potential type of restraints: square-well-parabolic (1138)
    - Range of distance target values: 2.15, 3.79 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_8
      - Status: Warning
      - Experiment type: noe
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 7.0%
      - Total number of restraints: 2
        Medium range restraints, 1 < | i - j | < 5 : 1
        Backbone-side chain: 1
        Long range restraints, | i - j | >= 5 : 1
      - Weight of restraints: 1.0 (2)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (1)
        Backbone-side chain: 1.0 (1)
        Long range restraints, | i - j | >= 5 : 1.0 (1)
      - Potential type of restraints: square-well-parabolic (2)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (1)
        Backbone-side chain: square-well-parabolic (1)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (1)
      - Range of distance target values: 4.4, 4.4 (Å)
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
      - Saveframe: CNS/XPLOR_distance_constraints_7
        Status: Warning
        Experiment type: noe
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 80.7%
        -------230-------240-------250-------260-------270------- GSKKKDNLLFGSIISAVDPVAVLAVFEEIHINELLHILVFGESLLNDAVTVVLYKKK        ||||||| |||||||||||||| ||||||| || |||||||||||||||| .......LLFGSII.AVDPVAVLAVFEEI.INELLHI.VF.ESLLNDAVTVVLYKKK
        Total number of restraints: 422
        Intra-residue restraints, i = j : 46
        Sequential restraints, | i - j | = 1 : 107
        Backbone-backbone: 2
        Backbone-side chain: 22
        Side chain-side chain: 83
        Medium range restraints, 1 < | i - j | < 5 : 228
        Backbone-backbone: 3
        Backbone-side chain: 41
        Side chain-side chain: 184
        Long range restraints, | i - j | >= 5 : 41
        Weight of restraints: 1.0 (422)
        Intra-residue restraints, i = j : 1.0 (46)
        Sequential restraints, | i - j | = 1 : 1.0 (107)
        Backbone-backbone: 1.0 (2)
        Backbone-side chain: 1.0 (22)
        Side chain-side chain: 1.0 (83)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (228)
        Backbone-backbone: 1.0 (3)
        Backbone-side chain: 1.0 (41)
        Side chain-side chain: 1.0 (184)
        Long range restraints, | i - j | >= 5 : 1.0 (41)
        Potential type of restraints: square-well-parabolic (422)
        Intra-residue restraints, i = j : square-well-parabolic (46)
        Sequential restraints, | i - j | = 1 : square-well-parabolic (107)
        Backbone-backbone: square-well-parabolic (2)
        Backbone-side chain: square-well-parabolic (22)
        Side chain-side chain: square-well-parabolic (83)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (228)
        Backbone-backbone: square-well-parabolic (3)
        Backbone-side chain: square-well-parabolic (41)
        Side chain-side chain: square-well-parabolic (184)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (41)
        Range of distance target values: 2.56, 5.91 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Saveframe: CNS/XPLOR_distance_constraints_4
        Status: Warning
        Experiment type: noe
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 96.5%
        -------230-------240-------250-------260-------270------- GSKKKDNLLFGSIISAVDPVAVLAVFEEIHINELLHILVFGESLLNDAVTVVLYKKK   ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..KKKDNLLFGSIISAVDPVAVLAVFEEIHINELLHILVFGESLLNDAVTVVLYKKK
        Total number of restraints: 314
        Intra-residue restraints, i = j : 66
        Sequential restraints, | i - j | = 1 : 77
        Backbone-backbone: 21
        Backbone-side chain: 54
        Side chain-side chain: 2
        Medium range restraints, 1 < | i - j | < 5 : 142
        Backbone-backbone: 31
        Backbone-side chain: 99
        Side chain-side chain: 12
        Long range restraints, | i - j | >= 5 : 29
        Weight of restraints: 1.0 (314)
        Intra-residue restraints, i = j : 1.0 (66)
        Sequential restraints, | i - j | = 1 : 1.0 (77)
        Backbone-backbone: 1.0 (21)
        Backbone-side chain: 1.0 (54)
        Side chain-side chain: 1.0 (2)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (142)
        Backbone-backbone: 1.0 (31)
        Backbone-side chain: 1.0 (99)
        Side chain-side chain: 1.0 (12)
        Long range restraints, | i - j | >= 5 : 1.0 (29)
        Potential type of restraints: square-well-parabolic (314)
        Intra-residue restraints, i = j : square-well-parabolic (66)
        Sequential restraints, | i - j | = 1 : square-well-parabolic (77)
        Backbone-backbone: square-well-parabolic (21)
        Backbone-side chain: square-well-parabolic (54)
        Side chain-side chain: square-well-parabolic (2)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (142)
        Backbone-backbone: square-well-parabolic (31)
        Backbone-side chain: square-well-parabolic (99)
        Side chain-side chain: square-well-parabolic (12)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (29)
        Range of distance target values: 2.17, 4.4 (Å)
        Histogram of distance target values
        Histogram of discrepancy in distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Saveframe: CNS/XPLOR_distance_constraints_5
        Status: Warning
        Experiment type: noe
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 98.2%
        -------230-------240-------250-------260-------270------- GSKKKDNLLFGSIISAVDPVAVLAVFEEIHINELLHILVFGESLLNDAVTVVLYKKK |||||||||||||||||||||||||||||||||||||||||||||||||||||||| .SKKKDNLLFGSIISAVDPVAVLAVFEEIHINELLHILVFGESLLNDAVTVVLYKKK
        Total number of restraints: 465
        Intra-residue restraints, i = j : 168
        Sequential restraints, | i - j | = 1 : 176
        Backbone-backbone: 69
        Backbone-side chain: 107
        Medium range restraints, 1 < | i - j | < 5 : 121
        Backbone-backbone: 58
        Backbone-side chain: 55
        Side chain-side chain: 8
        Weight of restraints: 1.0 (465)
        Intra-residue restraints, i = j : 1.0 (168)
        Sequential restraints, | i - j | = 1 : 1.0 (176)
        Backbone-backbone: 1.0 (69)
        Backbone-side chain: 1.0 (107)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (121)
        Backbone-backbone: 1.0 (58)
        Backbone-side chain: 1.0 (55)
        Side chain-side chain: 1.0 (8)
        Potential type of restraints: square-well-parabolic (465)
        Intra-residue restraints, i = j : square-well-parabolic (168)
        Sequential restraints, | i - j | = 1 : square-well-parabolic (176)
        Backbone-backbone: square-well-parabolic (69)
        Backbone-side chain: square-well-parabolic (107)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (121)
        Backbone-backbone: square-well-parabolic (58)
        Backbone-side chain: square-well-parabolic (55)
        Side chain-side chain: square-well-parabolic (8)
        Range of distance target values: 2.07, 4.54 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Saveframe: CNS/XPLOR_distance_constraints_9
        Status: Warning
        Experiment type: noe
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 70.2%
        -------230-------240-------250-------260-------270------- GSKKKDNLLFGSIISAVDPVAVLAVFEEIHINELLHILVFGESLLNDAVTVVLYKKK   | |  ||| |||  ||||||||||||| ||||| | || | |||  |||||||   ..K.K..LLF.SII..VDPVAVLAVFEEI.INELL.I.VF.E.LLN..VTVVLYK -------230-------240-------250-------260-------270-----
        Total number of restraints: 183
        Intra-residue restraints, i = j : 83
        Sequential restraints, | i - j | = 1 : 29
        Backbone-side chain: 10
        Side chain-side chain: 19
        Medium range restraints, 1 < | i - j | < 5 : 69
        Backbone-backbone: 1
        Backbone-side chain: 29
        Side chain-side chain: 39
        Long range restraints, | i - j | >= 5 : 2
        Weight of restraints: 1.0 (183)
        Intra-residue restraints, i = j : 1.0 (83)
        Sequential restraints, | i - j | = 1 : 1.0 (29)
        Backbone-side chain: 1.0 (10)
        Side chain-side chain: 1.0 (19)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (69)
        Backbone-backbone: 1.0 (1)
        Backbone-side chain: 1.0 (29)
        Side chain-side chain: 1.0 (39)
        Long range restraints, | i - j | >= 5 : 1.0 (2)
        Potential type of restraints: square-well-parabolic (183)
        Intra-residue restraints, i = j : square-well-parabolic (83)
        Sequential restraints, | i - j | = 1 : square-well-parabolic (29)
        Backbone-side chain: square-well-parabolic (10)
        Side chain-side chain: square-well-parabolic (19)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (69)
        Backbone-backbone: square-well-parabolic (1)
        Backbone-side chain: square-well-parabolic (29)
        Side chain-side chain: square-well-parabolic (39)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (2)
        Range of distance target values: 2.89, 4.84 (Å)
        Histogram of distance target values
        Histogram of discrepancy in distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_10
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 71.9%
- Total number of restraints: 70
- Total number of restraints per polymer type: 70
- Weight of restraints: 1.0 (70)
- Potential type of restraints: square-well-parabolic (70)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Na+/H+ exchanger, NHE1, NMR, transmembrane