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BMRB: 18613

2LW8

NMR solution structure of Eph receptor

Authors

Qin, H., Song, J.

Assembly

Eph receptor

Entity

1. Eph receptor (polymer, Thiol state: all disulfide bound), 183 monomers, 20967.54 Da Detail

GSNEVTLLDS RSVQGELGWI ASPLEGGWEE VSIMDEKNTP IRTYQVCNVM EPSQNNWLRT DWITREGAQR VYIEIKFTLR DCNSLPGVMG TCKETFNLYY YESDNDKERF IRENQFVKID TIAADESFTQ VDIGDRIMKL NTEIRDVGPL SKKGFYLAFQ DVGACIALVS VRVFYKKAPL TVR

Formula weight

20967.54 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS82:SG	1:CYS92:SG
2	disulfide	sing	1:CYS47:SG	1:CYS165:SG

Source organism

Exptl. method

Refine. method

distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.0 %, Completeness: 69.6 %, Completeness (bb): 78.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	69.6 % (1507 of 2164)	73.3 % (825 of 1125)	61.5 % (517 of 841)	83.3 % (165 of 198)
Backbone	78.5 % (853 of 1086)	90.9 % (338 of 372)	65.9 % (354 of 537)	91.0 % (161 of 177)
Sidechain	64.7 % (808 of 1249)	64.8 % (488 of 753)	66.5 % (316 of 475)	19.0 % (4 of 21)
Aromatic	10.9 % (20 of 184)	9.8 % (9 of 92)	12.5 % (11 of 88)	0.0 % (0 of 4)
Methyl	80.9 % (165 of 204)	83.3 % (85 of 102)	78.4 % (80 of 102)

1. entity

GSNEVTLLDS RSVQGELGWI ASPLEGGWEE VSIMDEKNTP IRTYQVCNVM EPSQNNWLRT DWITREGAQR VYIEIKFTLR DCNSLPGVMG TCKETFNLYY YESDNDKERF IRENQFVKID TIAADESFTQ VDIGDRIMKL NTEIRDVGPL SKKGFYLAFQ DVGACIALVS VRVFYKKAPL TVR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

Protein Blocks Logo

Calculated from 10 models in PDB: 2LW8, Strand ID: A Detail

Release date

2013-06-10

Citation 1

Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations
Qin, H., Lim, L., Song, J.
BMC Biophys. (2012), 5, 2-2, PubMed 22277260 , DOI 10.1186/2046-1682-5-2 , Abstract

Show more 1 citaion

Citation 2

NMR solution structure of Eph receptor
Qin, H., Fan, J., Song, J.
Not known

Hide non-primary 1 citaion

Related entities 1. Eph receptor, : 1 : 6 : 154 entities Detail

Interaction partners 1. Eph receptor, : 8 interactors Detail

More details for 8 interactors identified by 3 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

4 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

6 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-99% 15N]		0.5 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium azide	natural abundance		0.00002 mM
4	D2O	natural abundance		10 % v/v
5	H2O	natural abundance		100 % v/v
6	DTT	natural abundance		0 w/v

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18613_2lw8.nef
Input source #2: Coordindates	2lw8.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:47:CYS:SG	A:165:CYS:SG	oxidized, CA 58.459, CB 46.341 ppm	oxidized, CA 56.009, CB 45.052 ppm	1.976
A:82:CYS:SG	A:92:CYS:SG	oxidized, CA 58.459, CB 39.766 ppm	oxidized, CA 57.556, CB 40.861 ppm	2.087

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

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

-------110-------120-------130-------140-------150-------160-------170-------180---
YESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKAPLTVR
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
YESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKAPLTVR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	183	0	0	100.0

Content subtype: combined_18613_2lw8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1396		92.9 (chain: A, length: 183)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1538 (1)	noe	86.3 (chain: A, length: 183)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	237 (237)	.	90.7 (chain: A, length: 183)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 183, Sequence coverage: 92.9%
- Total number of assignments
  - ¹H chemical shifts: 784
  - ¹³C chemical shifts: 449
  - ¹⁵N chemical shifts: 163
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: 183, Sequence coverage: 86.3%
- Total number of restraints: 1537
- Weight of restraints: 1.0 (1537)
- Potential type of restraints: upper-bound-parabolic (1537)
- Range of distance target values: 3.0, 7.0 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 183, Sequence coverage: 90.7%
- Total number of restraints: 237
- Total number of restraints per polymer type: 237
- Weight of restraints: 1.0 (237)
- Potential type of restraints: square-well-parabolic (237)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Eph receptor, NMR, ephrin