1QGC: Protein

Structure of the complex of a FAB fragment of a neutralizing antibody with foot and mouth disease virus. Determined by electron microscopy at 30.0 Å resolution. Released 26 Jan 2000.

Method: Electron microscopy
Resolution: 30.0 Å
Organisms: Foot-and-mouth disease virus - type C, Mus musculus
Chains: 6
Atoms: 8,279
Mol. weight: 120.91 kDa
Released: 26 Jan 2000

Explore 1QGC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1QGC contains 36 α-helices and 80 β-strands across 6 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	15-18	4
α-helix	27-30	4
α-helix	32-35	4
β-strand	39-42	4	1
β-strand	48-50	3	1
α-helix	53-55	3
α-helix	61-66	6
β-strand	69-89	21	1
α-helix	95-99	5
β-strand	105-106	2	1
β-strand	112-117	6	1
β-strand	126-127	2	1
β-strand	167-188	22	1

Chain 2: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	16-19	4	2
β-strand	22-25	4	2
β-strand	33-34	2	3
α-helix	46-48	3
β-strand	53-54	2	3
β-strand	62-69	8	3
β-strand	78-82	5	4
α-helix	89-97	9
β-strand	98-112	15	3
β-strand	118-127	10	4
α-helix	135-137	3
β-strand	145-148	4	4
β-strand	155-160	6	3
β-strand	169	1	3
α-helix	171-173	3
β-strand	177-188	12	4
β-strand	197-213	17	3
α-helix	214-215	2

Chain 3: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
α-helix	44-50	7
α-helix	52	1
β-strand	53-54	2	5
α-helix	55	1
β-strand	65	1	6
β-strand	73-78	6	7
α-helix	90-95	6
β-strand	98-102	5	8
β-strand	105-111	7	5
β-strand	118-126	9	7
α-helix	136-139	4
β-strand	143-148	6	7
β-strand	156-159	4	5
β-strand	168-169	2	8
β-strand	183-192	10	7
β-strand	198	1	6
β-strand	199-205	7	5
β-strand	210-214	5	8

Chain 4: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-13	4	10
β-strand	19-25	7	9
β-strand	30-31	2	11
β-strand	34-35	2	11
β-strand	37-42	6	10
β-strand	49-52	4	10
α-helix	57	1
β-strand	58	1	10
α-helix	59	1
β-strand	66-71	6	9
β-strand	74-79	6	9
α-helix	84-86	3
β-strand	88-94	7	10
β-strand	102	1	10
β-strand	106-110	5	10
β-strand	115	1	12
α-helix	116-117	2
β-strand	118-122	5	13
α-helix	126-130	5
β-strand	133-143	11	13
β-strand	144	1	12
β-strand	148-154	7	14
β-strand	157-159	3	14
β-strand	163-168	6	13
α-helix	169-171	3
β-strand	177-186	10	13
α-helix	187-191	5
β-strand	195-202	8	14
β-strand	209-214	6	14
α-helix	215-217	3

Chain 5: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	145-147	3

Chain A: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	10-12	3	16
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	34-40	7	17
β-strand	44-51	8	17
β-strand	58-59	2	17
α-helix	62-64	3
β-strand	68-73	6	15
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	93-98	6	17
β-strand	110	1	17
β-strand	114-115	2	17
β-strand	116-118	3	16
β-strand	124	1	18
α-helix	125-126	2
β-strand	127-131	5	19
α-helix	132-134	3
α-helix	135-137	3
β-strand	142-150	9	19
β-strand	153	1	18
β-strand	158-161	4	20
α-helix	162-164	3
β-strand	170-172	3	19
β-strand	176-178	3	21
β-strand	181-183	3	21
β-strand	184-191	8	19
β-strand	192-193	2	22
α-helix	194-197	4
β-strand	201-206	6	20
α-helix	207-209	3
β-strand	211-216	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (virus capsid protein VP1)	1	protein	207	Foot-and-mouth disease virus - type C	P03311
Protein (virus capsid protein VP2)	2	protein	218	Foot-and-mouth disease virus - type C	P15072 (AlphaFold model)
Protein (virus capsid protein VP3)	3	protein	219	Foot-and-mouth disease virus - type C	P15072 (AlphaFold model)
Protein (immunoglobulin light chain)	4	protein	218	Mus musculus	P01837 (AlphaFold model)
Protein (immunoglobulin heavy chain)	A	protein	220	Mus musculus
Protein (gh-loop from virus capsid protein VP1)	5	protein	24	Foot-and-mouth disease virus - type C	P03311

Sequence of entity 1 (1), FASTA

>1QGC_1 PROTEIN (VIRUS CAPSID PROTEIN VP1) (chains 1)
TTTTGESADPVTTTVENYGGETQVQRRHHTDVAFVLDRFVKVTVSDNQHTLDVMQAHKDN
IVGALLRAATYYFSDLEIAVTHTGKLTWVPNGAPVSALNNTTNPTAYHKGPVTRLALPYT
APHRVLATAYTGTTTYTASARGDLAHLTTTHARHLPTSFNFGAVKAETITELLVRMKRAE
LYCPRPILPIQPTGDRHKQPLVAPAKQ

Sequence of entity 2 (2), FASTA

>1QGC_2 PROTEIN (VIRUS CAPSID PROTEIN VP2) (chains 2)
DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTFGYATAEDSTSGPNTSALETRVHQAER
FFKMALFDWVPSQNFGHMHKVVLPHEPKGVYGGLVKSYAYMRNGWDVEVTAVGNQFNGGC
LLVALVPEMGDISDREKYQLTLYPHQFINPRTNMTAHITVPYVGVNRYDQYKQHRPWTLV
VMVVAPLTTNTAGAQQIKVYANIAPTNVHVAGELPSKE

Sequence of entity 3 (3), FASTA

>1QGC_3 PROTEIN (VIRUS CAPSID PROTEIN VP3) (chains 3)
GIFPVACSDGYGNMVTTDPKTADPAYGKVYNPPRTALPGRFTNYLDVAEACPTFLMFENV
PYVSTRTDGQRLLAKFDVSLAAKHMSNTYLAGLAQYYTQYTGTINLHFMFTGPTDAKARY
MVAYVPPGMDAPDNPEEAAHCIHAEWDTGLNSKFTFSIPYISAADYTYTASHEAETTCVQ
GWVCVYQITHGKADADALVVSASAGKDFELRLPVDARQQ

Sequence of entity 4 (4), FASTA

>1QGC_4 PROTEIN (IMMUNOGLOBULIN LIGHT CHAIN) (chains 4)
DIVLTQSPASLAVSLGQRATISCRASESVDSSGHSFMHWYQQKPGQPPKLLIYRASNLES
GIPDRFSGSGSRTDFTLTIDPVEADDVATYYCQQSNEVPLTFGAGTKLDLKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (A), FASTA

>1QGC_5 PROTEIN (IMMUNOGLOBULIN HEAVY CHAIN) (chains A)
EVMLVESGGGLVKPGGSLKLSCTASGFIFNRCAMSWVRQTPEKRLEWVATISSGGTYTYY
PDSVKGRFTISRDNAKNTLYLQMSSLRSADTAMYYCVRREDGGDEGFAYWGQGTVVTVSA
AKTTPPSVYPLAPGSAAAAASMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 6 (5), FASTA

>1QGC_6 PROTEIN (GH-LOOP FROM VIRUS CAPSID PROTEIN VP1) (chains 5)
TTAYTASARGDLAHLTTTAARTLP

Primary citation

Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: positioning of a highly mobile antigenic loop. Hewat, E.A., Verdaguer, N., Fita, I. et al. EMBO J (1997) 16:1492-1500. DOI 10.1093/emboj/16.7.1492 · PubMed

Other PDB entries of the same protein (UniProt P03311), best resolution first:

8C1N 1.7 Å, FMDV 3D polymerase in complex with 3B1 protein solved in P212121 space group
4WYW 1.8 Å, Mutant K20E of 3D polymerase from Foot-and-Mouth Disease Virus
6KWL 1.8 Å, Crystal structure of pSLA-1*0401(R156A) complex with FMDV-derived epitope MTAHITVPY
8C2P 1.85 Å, FMDV 3D polymerase in complex with 3B3
4WYL 2.0 Å, Mutant K18E of 3D polymerase from Foot-and-Moth Disease Virus
6GVY 2.2 Å, Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus…
6S2L 2.3 Å, FMDV 3D polymerase crystallized in presence of (F)uridylylated VPg peptide
6GVV 2.35 Å, Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus
5N8X 2.4 Å, Trigonal structure of mutant V173I of 3D polymerase from Foot-and-Mouth Disease Virus
6KWK 2.5 Å, Crystal structure of pSLA-1*0401 complex with FMDV-derived epitope MTAHITVPY
9I3H 2.5 Å, CP of RHDV mutant - N15
4WZM 2.52 Å, Mutant K18E of RNA dependent RNA polymerase from Foot-and-Mouth Disease Virus complexed…

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