5DDJ: Foot and mouth disease virus, VP1

Name: PDB 5DDJ: Crystal structure of recombinant foot-and-mouth-disease virus O1M-S2093Y empty capsid
Published: 2015-09-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Crystal structure of recombinant foot-and-mouth-disease virus O1M-S2093Y empty capsid. Determined by X-ray diffraction at 3.5 Å resolution. Released 23 Sept 2015.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Foot-and-mouth disease virus - type O
Chains: 4
Atoms: 5,131
Mol. weight: 80.3 kDa
Released: 23 Sept 2015

Explore 5DDJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DDJ contains 15 α-helices and 40 β-strands across 4 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 1: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	27-30	4
α-helix	34-36	3
β-strand	41-42	2	1
β-strand	49-50	2	2
α-helix	61-64	4
α-helix	66-68	3
β-strand	71-79	9	1
β-strand	82	1	3
β-strand	87	1	4
β-strand	89	1	2
α-helix	95-97	3
β-strand	105	1	4
β-strand	115-117	3	1
β-strand	126-127	2	1
β-strand	167-168	2	2
β-strand	173	1	3
β-strand	176-186	11	1

Chain 2: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	15-19	5	5
β-strand	22-26	5	5
β-strand	52-54	3	6
β-strand	62-69	8	7
β-strand	82-83	2	8
α-helix	90-97	8
β-strand	100-102	3	6
β-strand	105	1	9
β-strand	108-111	4	7
β-strand	120-126	7	8
α-helix	134-139	6
β-strand	145-147	3	8
β-strand	155	1	7
β-strand	170	1	6
β-strand	177-185	9	8
β-strand	197-203	7	7
β-strand	205	1	9
β-strand	209-211	3	6

Chain 3: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	44-50	7
β-strand	53-54	2	10
α-helix	65-67	3
α-helix	95-97	3
β-strand	98-102	5	11
β-strand	105-108	4	10
β-strand	119	1	12
β-strand	120-126	7	13
α-helix	136-139	4
β-strand	145-148	4	13
β-strand	156-159	4	10
α-helix	160	1
β-strand	169	1	11
β-strand	183-187	5	13
β-strand	191	1	12
β-strand	202-205	4	10
β-strand	210-214	5	11

Chain 4: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	28-30	3
α-helix	33-34	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Foot and mouth disease virus, VP1	1	protein	211	Foot-and-mouth disease virus - type O	Q6PMW3
Foot and mouth disease virus, VP2	2	protein	218	Foot-and-mouth disease virus - type O	Q6PMW3
Foot and mouth disease virus, VP3	3	protein	220	Foot-and-mouth disease virus - type O	Q6PMW3
Genome polyprotein	4	protein	85	Foot-and-mouth disease virus - type O	Q6PMW3

Sequence of entity 1 (1), FASTA

>5DDJ_1 Foot and mouth disease virus, VP1 (chains 1)
TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHT
LVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPEAALDNTTNPTAYHKAPLTRLALPYT
APHRVLATVYNGNSKYGDGTVANVRGDLQVLAQKAARALPTSFNYGAIKATRVTELLYRM
KRAETYCPRPLLAIHPDQARHKQKIVAPVKQ

Sequence of entity 2 (2), FASTA

>5DDJ_2 Foot and mouth disease virus, VP2 (chains 2)
DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATAEDFVSGPNTSGLETRVAQAER
FFKTHLFDWVTSDPFGRCHLLELPTDHKGVYGYLTDSYAYMRNGWDVEVTAVGNQFNGGC
LLVAMVPELCSIQKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLV
VMVVAPLTVNSEGAPQIKVYANIAPTNVHVAGEFPSKE

Sequence of entity 3 (3), FASTA

>5DDJ_3 Foot and mouth disease virus, VP3 (chains 3)
GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLHFEGD
VPYVTTKTDSDRVLAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKAR
YMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYAYTASDTAETTNV
QGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ

Sequence of entity 4 (4), FASTA

>5DDJ_4 Genome polyprotein (chains 4)
GAGQSSPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDNATSGGSNEGSTDTTSTHTT
NTQNNDWFSKLASSAFSGLFGALLA

Primary citation

Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design. Kotecha, A., Seago, J., Scott, K. et al. Nat Struct Mol Biol (2015) 22:788-794. DOI 10.1038/nsmb.3096 · PubMed

Other PDB entries of the same protein (UniProt Q6PMW3), best resolution first:

5NEJ 3.1 Å, CryoEM Structure of Foot and Mouth Disease Virus O1 Manisa
5AC9 3.2 Å, Structure-based energetics of protein interfaces guide Foot-and-Mouth disease virus…
5NET 8.6 Å, Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease…
5NEU 12.3 Å, Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease…

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