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BMRB: 34232

6FGP

NMR solution structure of monomeric CCL5 in complex with a doubly-sulfated N-terminal segment of CCR5

Authors

Anglister, J., Abayev, M.

Assembly

C-C chemokine receptor type 5, C-C motif chemokine 5

Entity

1. C-C chemokine receptor type 5, C-C motif chemokine 5, entity 1 (polymer, Thiol state: not present), 27 monomers, 3355.635 Da Detail

MDYQVSSPIX DINXYTSEPA QKINVKQ

2. C-C chemokine receptor type 5, C-C motif chemokine 5, entity 2 (polymer, Thiol state: all disulfide bound), 68 monomers, 7798.847 Da Detail

SPYSSDTTSC CFAYIARPLP RAHIKEYFYT SGKCSNPAVV FVTRKNRQVC ANPEKKWVRE YINSLSMS

Total weight

11154.482 Da

Max. entity weight

7798.847 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	2:CYS10:SG	2:CYS34:SG
2	disulfide	sing	2:CYS11:SG	2:CYS50:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 36.8 %, Completeness: 16.5 %, Completeness (bb): 10.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	16.5 % (182 of 1102)	23.2 % (134 of 577)	8.4 % (36 of 428)	12.4 % (12 of 97)
Backbone	10.8 % (59 of 544)	10.0 % (18 of 180)	11.2 % (31 of 278)	11.6 % (10 of 86)
Sidechain	20.6 % (134 of 650)	29.2 % (116 of 397)	6.6 % (16 of 242)	18.2 % (2 of 11)
Aromatic	7.8 % (8 of 102)	15.7 % (8 of 51)	0.0 % (0 of 50)	0.0 % (0 of 1)
Methyl	24.4 % (20 of 82)	34.1 % (14 of 41)	14.6 % (6 of 41)

1. entity 1

MDYQVSSPIX DINXYTSEPA QKINVKQ

2. entity 2

SPYSSDTTSC CFAYIARPLP RAHIKEYFYT SGKCSNPAVV FVTRKNRQVC ANPEKKWVRE YINSLSMS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 4.8, Details 120 uM [U-15N] CCL5(P9S)/Nt-CCR5(1-27)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		120 uM
2	entity_2	[U-15N]		120 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 4.8, Details 120 uM [U-13C] CCL5(P9S)/Nt-CCR5(1-27)

#	Name	Isotope labeling	Type	Concentration
3	entity_1	[U-13C]		120 uM
4	entity_2	[U-13C]		120 uM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 4.8, Details 120 uM U-15N;13C CCL5(P9S)/Nt-CCR5(1-27)

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-15N; U-13C]		120 uM
6	entity_2	[U-15N; U-13C]		120 uM

Chem. Shift Complete2

Sequence coverage: 72.6 %, Completeness: 43.9 %, Completeness (bb): 41.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	43.9 % (968 of 2204)	47.1 % (544 of 1154)	40.1 % (343 of 856)	41.8 % (81 of 194)
Backbone	41.0 % (446 of 1088)	41.1 % (148 of 360)	40.5 % (225 of 556)	42.4 % (73 of 172)
Sidechain	45.3 % (589 of 1300)	49.1 % (390 of 794)	39.5 % (191 of 484)	36.4 % (8 of 22)
Aromatic	46.1 % (94 of 204)	50.0 % (51 of 102)	42.0 % (42 of 100)	50.0 % (1 of 2)
Methyl	47.6 % (78 of 164)	52.4 % (43 of 82)	42.7 % (35 of 82)

1. entity 1

MDYQVSSPIX DINXYTSEPA QKINVKQ

2. entity 2

SPYSSDTTSC CFAYIARPLP RAHIKEYFYT SGKCSNPAVV FVTRKNRQVC ANPEKKWVRE YINSLSMS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 4.8, Details 120 uM [U-15N] CCL5(P9S)/Nt-CCR5(1-27)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-15N]		120 uM
2	entity_2	[U-15N]		120 uM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 4.8, Details 120 uM [U-13C] CCL5(P9S)/Nt-CCR5(1-27)

#	Name	Isotope labeling	Type	Concentration
3	entity_1	[U-13C]		120 uM
4	entity_2	[U-13C]		120 uM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 4.8, Details 120 uM U-15N;13C CCL5(P9S)/Nt-CCR5(1-27)

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-15N; U-13C]		120 uM
6	entity_2	[U-15N; U-13C]		120 uM

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: -0.15 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: -0.15 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: -0.02 ppm, Outliers: 1 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: 0.3 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6FGP, Strand ID: A, B Detail

Release date

2019-03-14

Citation

The solution structure of monomeric CCL5 in complex with a doubly-sulfated N-terminal segment of CCR5
Abayev, M., Rodrigues, J., Srivastava, G., Arshava, B., Jaremko, L., Jaremko, M., Naider, F., Levitt, M., Anglister, J.
FEBS J. (2018), 285, 1988-2003, PubMed 29619777 , DOI 10.1111/febs.14460 , Abstract

Related entities 1. C-C chemokine receptor type 5, C-C motif chemokine 5, entity 1, : 1 : 1 : 9 : 44 entities Detail

Related entities 2. C-C chemokine receptor type 5, C-C motif chemokine 5, entity 2, : 1 : 80 entities Detail

Interaction partners 1. C-C chemokine receptor type 5, C-C motif chemokine 5, entity 1, : 15 interactors Detail

More details for 15 interactors identified by 9 citations

Experiments performed 14 experiments Detail

1 3D HNCACB