BMRBj - BMREntryMaster

Found 1 Document (4.75 seconds)

BMRB: 19117

2M68

NMR solution structure ensemble of 3-4D mutant domain 11 IGF2R in complex with IGF2 (domain 11 structure only)

Authors

Strickland, M., Williams, C., Richards, E., Minnall, L., Crump, M.P., Frago, S., Hughes, J., Garner, L., Hoppe, H., Rezgui, D., Zaccheo, O.J., Prince, S.N., Hassan, A.B., Whittaker, S.

Assembly

Domain 11:IGF2 complex

Entity

1. Domain 11:IGF2 complex (polymer, Thiol state: all disulfide bound), 142 monomers, 15416.43 Da Detail

MKSNEHDDCQ VTNPSTGHLF DLSSLSGRAG FTAAYAKGWG VYMSICGENE NCPPGVGACF GQTRISVGKA NKRLRYVDQV LQLVYKDGSP CPSKSGLSYK SVISFVCRPE AGPTNRPMLI SLDKQTCTLF FSWHTPLACE LA

Formula weight

15416.43 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS9:SG	1:CYS46:SG
2	disulfide	sing	1:CYS52:SG	1:CYS59:SG
3	disulfide	sing	1:CYS91:SG	1:CYS127:SG
4	disulfide	sing	1:CYS107:SG	1:CYS139:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.5 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.5 % (1492 of 1596)	94.6 % (782 of 827)	90.9 % (566 of 623)	98.6 % (144 of 146)
Backbone	98.0 % (817 of 834)	98.6 % (284 of 288)	97.1 % (401 of 413)	99.2 % (132 of 133)
Sidechain	90.0 % (802 of 891)	92.4 % (498 of 539)	86.1 % (292 of 339)	92.3 % (12 of 13)
Aromatic	62.5 % (85 of 136)	80.9 % (55 of 68)	42.4 % (28 of 66)	100.0 % (2 of 2)
Methyl	98.5 % (132 of 134)	97.0 % (65 of 67)	100.0 % (67 of 67)

1. Domain 11

MKSNEHDDCQ VTNPSTGHLF DLSSLSGRAG FTAAYAKGWG VYMSICGENE NCPPGVGACF GQTRISVGKA NKRLRYVDQV LQLVYKDGSP CPSKSGLSYK SVISFVCRPE AGPTNRPMLI SLDKQTCTLF FSWHTPLACE LA

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Temperature 310.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
1	Domain_11	natural abundance	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %

Sample #2

Solvent system 93% H2O/7% D2O, Temperature 310.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

LACS Plot; CA

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

Referencing offset: -0.38 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.38 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.18 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M68, Strand ID: A Detail

Heteronucl. T₁

238 T₁ values in 2 lists
Coherence na, Field strength (¹H) 600 MHz, Temperature 298.15 K, pH 4 Detail

Heteronucl. T₂

237 T₂ values in 2 lists
Coherence na, Field strength (¹H) 600 MHz, Temperature 298.15 K, pH 4 Detail

Heteronucl. NOE

238 NOE values in 2 lists
Value type peak height, Field strength (¹H) 600 MHz, Temperature 298.15 K, pH 4 Detail

Heteronucl. T₁/T₂

237 T₁/T₂ values in 2 lists
Field strength (¹H) 600 MHz, Temperature 298.15 K, pH 4 Detail

Release date

2014-10-12

Citation

Directed evolution of structurally selected IGF2R domain 11 binding loop residues generates an IGF2 super-antagonist
Frago, S., Strickland, M., Hughes, J., Williams, C., Garner, L., Hoppe, H., Rezgui, D., Zaccheo, O.J., Prince, S.N., Crump, M.P., Hassan, A.B.
EMBO J.

Related entities 1. Domain 11:IGF2 complex, : 1 : 1 : 122 entities Detail

Interaction partners 1. Domain 11:IGF2 complex, : 39 interactors Detail

More details for 39 interactors identified by 15 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

2 2D 1H-13C HSQC

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

3 3D CBCA(CO)NH

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

4 3D C(CO)NH

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

5 3D HNCO

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

6 3D HNCA

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

7 3D HN(CO)CA

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

8 3D H(CCO)NH

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

9 3D HCCH-TOCSY

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

10 3D 1H-15N NOESY

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

11 3D 1H-15N TOCSY

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

12 3D 1H-13C NOESY aliphatic

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 298.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
4	Domain_11	natural abundance	1 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

13 Heteronuclear NOE ratio

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 310.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
1	Domain_11	natural abundance	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %

14 Heteronuclear NOE ratio

Instrument

Varian VNMRS - 900 MHz Fitted with a cryogenically cooled probehead. HWB-NMR/Welcome Trust.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 310.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
1	Domain_11	natural abundance	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %

15 T1 experiments

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 310.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
1	Domain_11	natural abundance	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %

16 T1 experiments

Instrument

Varian VNMRS - 900 MHz Fitted with a cryogenically cooled probehead. HWB-NMR/Welcome Trust.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 310.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
1	Domain_11	natural abundance	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %

17 T2 experiments

Instrument

Varian VNMRS - 600 MHz Fitted with a cryogenically cooled probehead. Bristol University.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 310.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
1	Domain_11	natural abundance	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %

18 T2 experiments

Instrument

Varian VNMRS - 900 MHz Fitted with a cryogenically cooled probehead. HWB-NMR/Welcome Trust.

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Temperature 310.15 K, pH 4, Details STRUCTURAL STUDIES: Lyophilised IGF2 was added to solution state domain 11 at pH 4 in a 1:1 ratio.

#	Name	Isotope labeling	Concentration
1	Domain_11	natural abundance	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19117_2m68.nef
Input source #2: Coordindates	2m68.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:1516:CYS:SG	A:1553:CYS:SG	oxidized, CA 58.543, CB 41.645 ppm	oxidized, CA 57.157, CB 41.785 ppm	2.011
A:1559:CYS:SG	A:1566:CYS:SG	unknown, CA 51.191 ppm	oxidized, CA 56.911, CB 43.947 ppm	2.028
A:1598:CYS:SG	A:1634:CYS:SG	unknown, CA 52.629 ppm	oxidized, CA 58.071, CB 41.759 ppm	2.033
A:1614:CYS:SG	A:1646:CYS:SG	oxidized, CA 57.662, CB 39.415 ppm	oxidized, CA 54.822, CB 43.25 ppm	2.032

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

--1510---1520------1530------1540------1550------1560------1570------1580------1590------1600------1
MKSNEHDDCQVTNPSTGHLFDLSSLSGRAGFTAAYAKGWGVYMSICGENENCPPGVGACFGQTRISVGKANKRLRYVDQVLQLVYKDGSPCPSKSGLSYK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKSNEHDDCQVTNPSTGHLFDLSSLSGRAGFTAAYAKGWGVYMSICGENENCPPGVGACFGQTRISVGKANKRLRYVDQVLQLVYKDGSPCPSKSGLSYK
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

610------1620------1630------1640---------
SVISFVCRPEAGPTNRPMLISLDKQTCTLFFSWHTPLACELA
||||||||||||||||||||||||||||||||||||||||||
SVISFVCRPEAGPTNRPMLISLDKQTCTLFFSWHTPLACELA
-------110-------120-------130-------140--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	142	0	0	100.0

Content subtype: combined_19117_2m68.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1500		99.3 (chain: A, length: 142)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3202 (1)	noe	99.3 (chain: A, length: 142)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	52 (1)	hbond	21.8 (chain: A, length: 142)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 99.3%
- Total number of assignments
  - ¹H chemical shifts: 792
  - ¹³C chemical shifts: 558
  - ¹⁵N chemical shifts: 150
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1573	SER	HG	5.664
1592	TYR	HH	9.901
1642	THR	HG1	6.535

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	827	789	95.4
¹³C chemical shifts	623	558	89.6
¹⁵N chemical shifts	152	150	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	288	286	99.3
¹³C chemical shifts	284	271	95.4
¹⁵N chemical shifts	133	132	99.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	539	503	93.3
¹³C chemical shifts	339	287	84.7
¹⁵N chemical shifts	19	18	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	70	100.0
¹³C chemical shifts	70	70	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	55	80.9
¹³C chemical shifts	66	24	36.4
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 99.3%
- Total number of restraints: 3202
- Weight of restraints: 1.0 (3202)
- Potential type of restraints: square-well-parabolic (3202)
- Range of distance target values: 1.43, 5.75 (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: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 21.8%
  - Total number of restraints: 52
  - Weight of restraints: 1.0 (52)
  - Potential type of restraints: square-well-parabolic (52)
  - Range of distance target values: 2.0, 3.15 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords 3-4D, Complex, Domain 11, IGF2, IGF2R, Mutant, NMR, Solution

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (4.75 seconds)

BMRB: 19117

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Domain 11:IGF2 complex, : 1 : 1 : 122 entities Detail

Interaction partners 1. Domain 11:IGF2 complex, : 39 interactors Detail

Experiments performed 18 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail