4JMR: Gag protein

A unique spumavirus gag N-terminal domain with functional properties of orthoretroviral Matrix and Capsid. Determined by X-ray diffraction at 2.9 Å resolution. Released 29 May 2013.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Human foamy virus
Chains: 8
Atoms: 5,931
Mol. weight: 101.3 kDa
Released: 29 May 2013

Explore 4JMR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JMR contains 40 α-helices and 42 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	1
β-strand	12	1	2
α-helix	14-23	10
β-strand	31	1	3
β-strand	35-40	6	1
β-strand	43	1	4
β-strand	46	1	4
β-strand	50-59	10	1
α-helix	64	1
β-strand	65-73	9	1
β-strand	84-88	5	1
α-helix	90-93	4
β-strand	97	1	2
α-helix	105-112	8
α-helix	122-126	5
α-helix	132-135	4
α-helix	140-178	39

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	5
β-strand	12	1	6
α-helix	14-23	10
α-helix	28-30	3
β-strand	31	1	7
β-strand	35-40	6	5
β-strand	50-59	10	5
α-helix	64	1
β-strand	65-73	9	5
β-strand	85-88	4	5
α-helix	90-93	4
β-strand	97	1	6
α-helix	105-112	8
α-helix	122-126	5
α-helix	132-137	6
α-helix	140-176	37

Chain C: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	8
β-strand	12	1	9
α-helix	14-23	10
β-strand	31	1	10
β-strand	35-40	6	8
β-strand	43	1	11
β-strand	46	1	11
β-strand	50-59	10	8
α-helix	64	1
β-strand	65-73	9	8
β-strand	84-88	5	8
α-helix	90-93	4
β-strand	97	1	9
α-helix	102-103	2
α-helix	105-112	8
α-helix	122-126	5
α-helix	129-131	3
α-helix	132-135	4
α-helix	140-171	32

Chain D: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	12
β-strand	12	1	13
α-helix	14-23	10
α-helix	28-30	3
β-strand	31	1	14
β-strand	35-40	6	12
β-strand	43	1	15
β-strand	46	1	15
β-strand	50-59	10	12
α-helix	64	1
β-strand	65-73	9	12
α-helix	74	1
β-strand	84-88	5	12
α-helix	90-93	4
β-strand	97	1	13
α-helix	102-103	2
α-helix	105-112	8
α-helix	122-125	4
α-helix	132-135	4
α-helix	140-172	33

Chain E: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6	1	14
α-helix	7-14	8

Chain F: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	6	1	7
α-helix	7-14	8

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6	1	3
α-helix	7-11	5

Chain H: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6	1	10
α-helix	7-15	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gag protein	A, B, C, D	protein	199	Human foamy virus	P14349
Env protein	E, F, G, H	protein	20	Human foamy virus	Q98830

Sequence of entity 1 (A, B, C, D), FASTA

>4JMR_1 Gag protein (chains A, B, C, D)
MAHHHHHHSAALEVLFQGPGMASGSNVEEYELDVEALVVILRDRNIPRNPLHGEVIGLRL
TEGWWGQIERFQMVRLILQNDDNEPLQRPRYEVIQRAVNPHTMFMISGPLAELQLAFQDL
DLPEGPLRFGPLANGHYVQGDPYSSSYRPVTMAETAQMTRDELEDVLNTQSEIEIQMINL
LELYEVETRALRRQLAERS

Sequence of entity 2 (E, F, G, H), FASTA

>4JMR_2 Env protein (chains E, F, G, H)
MAPPMTLQQWIIWKKMNKAH

Primary 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. et al. PLoS Pathog (2013) 9:e1003376-e1003376. DOI 10.1371/journal.ppat.1003376 · PubMed

Other PDB entries of the same protein (UniProt P14349), best resolution first:

8Q3E 2.17 Å, High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide
4JNH 2.4 Å, A unique spumavirus gag N-terminal domain with functional properties of orthoretroviral…
8Q36 2.6 Å, Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG…
5MLU 2.8 Å, Crystal structure of the PFV GAG CBS bound to a mononucleosome
5M1G Structure of a Spumaretrovirus Gag central domain reveals an ancient retroviral capsid
5M1H Structure of a Spumaretrovirus Gag central domain reveals an ancient retroviral capsid

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