1CD3: Procapsid of bacteriophage PHIX174

Name: PDB 1CD3: Procapsid of bacteriophage PHIX174
Published: 1999-04-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Procapsid of bacteriophage PHIX174. Determined by X-ray diffraction at 3.5 Å resolution. Released 14 Apr 1999.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Enterobacteria phage phiX174
Chains: 7
Atoms: 9,851
Mol. weight: 149.15 kDa
Released: 14 Apr 1999

Explore 1CD3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1CD3 contains 69 α-helices and 50 β-strands across 7 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: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	34-38	5
α-helix	45-47	3
α-helix	48-66	19
α-helix	72-74	3
α-helix	75-85	11
α-helix	88-98	11
α-helix	104-108	5
α-helix	114-116	3
α-helix	117-130	14
α-helix	136-145	10

Chain 2: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	12-23	12
α-helix	33-38	6
α-helix	42-44	3
α-helix	45-47	3
α-helix	48-64	17
α-helix	75-85	11
α-helix	88-98	11
β-strand	106-107	2	1
β-strand	112-113	2	1
α-helix	114-116	3
α-helix	117-127	11
α-helix	131-134	4

Chain 3: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	9-23	15
α-helix	31-38	8
α-helix	42-44	3
α-helix	48-60	13
α-helix	62-65	4
α-helix	68-70	3
α-helix	72-74	3
α-helix	75-85	11
α-helix	88-98	11
β-strand	102	1	2
α-helix	105-108	4
β-strand	114	1	2
α-helix	117-127	11

Chain 4: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	11-20	10
α-helix	24-26	3
α-helix	31-38	8
α-helix	42-44	3
α-helix	45-47	3
α-helix	48-64	17
α-helix	71-74	4
α-helix	75-85	11
α-helix	88-99	12
α-helix	109-111	3
α-helix	117-128	12
α-helix	136-149	14

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	62-79	18
α-helix	85-93	9
α-helix	112-116	5

Chain F: 20 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	10-13	4	3
β-strand	16-22	7	3
β-strand	28-35	8	4
β-strand	40-51	12	3
α-helix	52-53	2
β-strand	54	1	5
β-strand	62-72	11	4
α-helix	73-75	3
α-helix	80-87	8
α-helix	88-90	3
β-strand	96-98	3	6
α-helix	107-109	3
β-strand	118-120	3	6
α-helix	121-130	10
α-helix	131-135	5
α-helix	148-150	3
α-helix	153-157	5
β-strand	163	1	7
α-helix	164	1
β-strand	186	1	8
β-strand	189	1	8
α-helix	192-210	19
α-helix	215-221	7
β-strand	235-238	4	4
β-strand	241-244	4	4
β-strand	247-250	4	9
β-strand	253	1	10
β-strand	256	1	10
β-strand	260-263	4	9
β-strand	266-276	11	3
β-strand	281-290	10	4
β-strand	295	1	11
β-strand	298	1	12
α-helix	301-304	4
α-helix	310-314	5
α-helix	317-321	5
β-strand	326	1	13
β-strand	329	1	14
α-helix	330-332	3
β-strand	334	1	12
β-strand	342	1	14
β-strand	345	1	13
α-helix	349-352	4
α-helix	360-363	4
β-strand	371	1	11
β-strand	384	1	7
α-helix	388-391	4
β-strand	394	1	5
β-strand	398	1	15
β-strand	400	1	15
β-strand	402-414	13	3

Chain G: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	15-17	3	16
β-strand	22-23	2	16
β-strand	30	1	17
β-strand	31	1	18
β-strand	39-49	11	16
β-strand	52-61	10	18
β-strand	70-81	12	16
β-strand	88-96	9	18
β-strand	102	1	17
β-strand	109-110	2	18
β-strand	115-117	3	16
β-strand	120-130	11	16
β-strand	139-150	12	18
β-strand	153-164	12	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (scaffolding protein gpd)	1, 2, 3, 4	protein	152	Enterobacteria phage phiX174	P69486
Protein (capsid protein gpf)	F	protein	426	Enterobacteria phage phiX174	P03641
Protein (spike protein gpg)	G	protein	175	Enterobacteria phage phiX174	P03643
Protein (scaffolding protein gpb)	B	protein	120	Enterobacteria phage phiX174	P03633

Sequence of entity 1 (1, 2, 3, 4), FASTA

>1CD3_1 PROTEIN (SCAFFOLDING PROTEIN GPD) (chains 1, 2, 3, 4)
MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVY
GTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAEL
FAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM

Sequence of entity 2 (F), FASTA

>1CD3_2 PROTEIN (CAPSID PROTEIN GPF) (chains F)
SNIQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEMDAVGALRLSPLRRGLAI
DSTVDIFTFYVPHRHVYGEQWIKFMKDGVNATPLPTVNTTGYIDHAAFLGTINPDTNKIP
KHLFQGYLNIYNNYFKAPWMPDRTEANPNELNQDDARFGFRCCHLKNIWTAPLPPETELS
RQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYRDVISSFGGKTSYDADNRPLLVMRS
NLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQ
YLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSP
AYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTR
DSIMTS

Sequence of entity 3 (G), FASTA

>1CD3_3 PROTEIN (SPIKE PROTEIN GPG) (chains G)
MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCI
QMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGY
YTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK

Sequence of entity 4 (B), FASTA

>1CD3_4 PROTEIN (SCAFFOLDING PROTEIN GPB) (chains B)
MEQLTKNQAVATSQEAVQNQNEPQLRDENAHNDKSVHGVLNPTYQAGLRRDAVQPDIEAE
RKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQPAEFYRFHDAEVNTFGYF

Primary citation

The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174. Dokland, T., Bernal, R.A., Burch, A. et al. J Mol Biol (1999) 288:595-608. DOI 10.1006/jmbi.1999.2699 · PubMed

Other PDB entries of the same protein (UniProt P69486), best resolution first:

1TX9 3.31 Å, gpd prior to capsid assembly
1AL0 3.5 Å, Procapsid of bacteriophage PHIX174
1M0F 16.0 Å, Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy

Browse structure collections

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