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BMRB: 34049


34049
5M1G
Structure of a Spumaretrovirus Gag central domain reveals an ancient retroviral capsid
Authors
Nicastro, G., Ball, N., Taylor, I.A.
Assembly
Gag protein
Entity
1. Gag protein (polymer, Thiol state: not present), 99 monomers, 10939.31 × 2 Da Detail

RTHGTFPMHQ LGNVIKGIVD QEGVATAYTL GMMLSGQNYQ LVSGIIRGYL PGQAVVTALQ QRLDQEIDDQ TRAETFIQHL NAVYEILGLN ARGQSIRLE


Total weight
21878.62 Da
Max. entity weight
10939.31 Da
Source organism
Human spumaretrovirus
Exptl. method
solution NMR
Refine. method
simulated annealing
Data set
assigned_chemical_shifts
Chem. Shift Complete1
Sequence coverage: 98.0 %, Completeness: 73.3 %, Completeness (bb): 66.9 % Detail
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Polymer type: polypeptide(L)

Total1H13C15N
All73.3 % (833 of 1136)87.2 % (512 of 587)67.5 % (295 of 437)23.2 % (26 of 112)
Backbone66.9 % (395 of 590)88.4 % (183 of 207)65.7 % (188 of 286)24.7 % (24 of 97)
Sidechain82.0 % (520 of 634)86.6 % (329 of 380)79.1 % (189 of 239)13.3 % (2 of 15)
Aromatic40.6 % (26 of 64)81.3 % (26 of 32) 0.0 % (0 of 32)
Methyl93.2 % (123 of 132)93.9 % (62 of 66)92.4 % (61 of 66)

1. entity 1

RTHGTFPMHQ LGNVIKGIVD QEGVATAYTL GMMLSGQNYQ LVSGIIRGYL PGQAVVTALQ QRLDQEIDDQ TRAETFIQHL NAVYEILGLN ARGQSIRLE

Show sample condition
Sample

Solvent system 95% H2O/5% D2O, Pressure 1 Pa, Temperature 298 K, pH 7, Details 0.3 nM [U-13C; U-15N] GAG protein, 0.5 mM [U-13C; U-15N; U-2H] GAG protein, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
1GAG protein[U-13C; U-15N; U-2H]0.5 mM
2NaClnatural abundance20 mM
3Trisnatural abundance20 mM

Chem. Shift Complete2
Sequence coverage: 93.9 %, Completeness: 66.5 %, Completeness (bb): 62.9 % Detail
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Polymer type: polypeptide(L)

Total1H13C15N
All66.5 % (1512 of 2272)83.8 % (984 of 1174)46.0 % (402 of 874)56.3 % (126 of 224)
Backbone62.9 % (742 of 1180)87.7 % (363 of 414)47.0 % (269 of 572)56.7 % (110 of 194)
Sidechain69.4 % (880 of 1268)81.7 % (621 of 760)50.8 % (243 of 478)53.3 % (16 of 30)
Aromatic29.7 % (38 of 128)56.3 % (36 of 64) 3.1 % (2 of 64)
Methyl71.6 % (189 of 264)87.9 % (116 of 132)55.3 % (73 of 132)

1. entity 1

RTHGTFPMHQ LGNVIKGIVD QEGVATAYTL GMMLSGQNYQ LVSGIIRGYL PGQAVVTALQ QRLDQEIDDQ TRAETFIQHL NAVYEILGLN ARGQSIRLE

Show sample condition
Sample

Solvent system 95% H2O/5% D2O, Pressure 1 Pa, Temperature 298 K, pH 7, Details 0.3 nM [U-13C; U-15N] GAG protein, 0.5 mM [U-13C; U-15N; U-2H] GAG protein, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
1GAG protein[U-13C; U-15N; U-2H]0.5 mM
2NaClnatural abundance20 mM
3Trisnatural abundance20 mM

Chem. Shift Complete3
Sequence coverage: 57.6 %, Completeness: 54.8 %, Completeness (bb): 52.0 % Detail
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Polymer type: polypeptide(L)

Total1H13C15N
All54.8 % (1868 of 3408)67.7 % (1193 of 1761)39.6 % (519 of 1311)46.4 % (156 of 336)
Backbone52.0 % (921 of 1770)70.4 % (437 of 621)40.1 % (344 of 858)48.1 % (140 of 291)
Sidechain57.0 % (1085 of 1902)66.3 % (756 of 1140)43.7 % (313 of 717)35.6 % (16 of 45)
Aromatic43.2 % (83 of 192)65.6 % (63 of 96)20.8 % (20 of 96)
Methyl60.9 % (241 of 396)75.3 % (149 of 198)46.5 % (92 of 198)

1. entity 1

RTHGTFPMHQ LGNVIKGIVD QEGVATAYTL GMMLSGQNYQ LVSGIIRGYL PGQAVVTALQ QRLDQEIDDQ TRAETFIQHL NAVYEILGLN ARGQSIRLE

Show sample condition
Sample

Solvent system 95% H2O/5% D2O, Pressure 1 Pa, Temperature 298 K, pH 7, Details 0.3 nM [U-13C; U-15N] GAG protein, 0.5 mM [U-13C; U-15N; U-2H] GAG protein, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
1GAG protein[U-13C; U-15N; U-2H]0.5 mM
2NaClnatural abundance20 mM
3Trisnatural abundance20 mM

Chem. Shift Complete4
Sequence coverage: 98.0 %, Completeness: 59.7 %, Completeness (bb): 55.8 % Detail
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Polymer type: polypeptide(L)

Total1H13C15N
All59.7 % (2714 of 4544)71.2 % (1671 of 2348)48.3 % (845 of 1748)44.2 % (198 of 448)
Backbone55.8 % (1316 of 2360)70.4 % (583 of 828)48.5 % (555 of 1144)45.9 % (178 of 388)
Sidechain63.8 % (1619 of 2536)71.6 % (1088 of 1520)53.5 % (511 of 956)33.3 % (20 of 60)
Aromatic47.3 % (121 of 256)73.4 % (94 of 128)21.1 % (27 of 128)
Methyl68.8 % (363 of 528)79.9 % (211 of 264)57.6 % (152 of 264)

1. entity 1

RTHGTFPMHQ LGNVIKGIVD QEGVATAYTL GMMLSGQNYQ LVSGIIRGYL PGQAVVTALQ QRLDQEIDDQ TRAETFIQHL NAVYEILGLN ARGQSIRLE

Show sample condition
Sample

Solvent system 95% H2O/5% D2O, Pressure 1 Pa, Temperature 298 K, pH 7, Details 0.3 nM [U-13C; U-15N] GAG protein, 0.5 mM [U-13C; U-15N; U-2H] GAG protein, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
1GAG protein[U-13C; U-15N; U-2H]0.5 mM
2NaClnatural abundance20 mM
3Trisnatural abundance20 mM

LACS Plot; CA
Referencing offset: -0.38 ppm, Outliers: 1 Detail
LACS Plot; CB
Referencing offset: -0.38 ppm, Outliers: 1 Detail
LACS Plot; HA
Referencing offset: 0.04 ppm, Outliers: 2 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 5M1G, Strand ID: A, B Detail

Release date
2019-03-18
Citation
A unique spumavirus Gag N-terminal domain with functional properties of orthoretroviral matrix and capsid
Goldstone, D.C., Flower, T.G., Ball, N.J., Sanz-Ramos, M., Yap, M.W., Ogrodowicz, R.W., Stanke, N., Reh, J., Lindemann, D., Stoye, J.P., Taylor, I.A.
PLoS Pathog. (2013), 9, e1003376-e1003376, PubMed 23675305 , DOI 10.1371/journal.ppat.1003376 ,
Related entities 1. Gag protein, : 1 : 1 : 5 entities Detail
More details for 7 related entities
Experiments performed 2 experiments Detail
nullKeywords FOAMY VIRUS, GAG, VIRAL PROTEIN