1RB8: Capsid protein

The phiX174 DNA binding protein J in two different capsid environments. Determined by X-ray diffraction at 3.5 Å resolution. Released 13 Apr 2004.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Enterobacteria phage alpha3, Enterobacteria phage phiX174
Chains: 4
Atoms: 5,112
Mol. weight: 76.03 kDa
Ligands: DC
Released: 13 Apr 2004

Explore 1RB8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RB8 contains 27 α-helices and 42 β-strands across 3 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 F: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	1
β-strand	17-23	7	1
β-strand	27	1	2
β-strand	29-36	8	3
β-strand	41-52	12	1
β-strand	55	1	4
β-strand	61	1	5
α-helix	62	1
β-strand	63-73	11	3
α-helix	74-78	5
α-helix	80-88	9
α-helix	89-91	3
α-helix	95-96	2
β-strand	97-99	3	6
α-helix	108-110	3
α-helix	113-115	3
β-strand	119-121	3	6
α-helix	122-131	10
α-helix	132-136	5
α-helix	142-144	3
α-helix	154-159	6
β-strand	162	1	2
β-strand	164	1	7
α-helix	165-167	3
β-strand	174	1	8
α-helix	193-212	20
α-helix	216-223	8
β-strand	236-245	10	3
β-strand	247-251	5	9
α-helix	252	1
β-strand	261-265	5	9
β-strand	266-277	12	1
β-strand	282-291	10	3
β-strand	299	1	10
α-helix	302-305	4
α-helix	311-314	4
α-helix	318-321	4
β-strand	327-330	4	8
α-helix	331-333	3
β-strand	335	1	10
β-strand	343-346	4	8
α-helix	347	1
α-helix	350-352	3
α-helix	361-365	5
α-helix	384-388	5
β-strand	389	1	7
α-helix	393-396	4
β-strand	399	1	4
β-strand	403	1	11
β-strand	405	1	11
β-strand	407-419	13	1
α-helix	424-428	5

Chain G: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	17-24	8	12
β-strand	32-34	3	13
β-strand	35	1	14
β-strand	41	1	14
β-strand	45-54	10	12
β-strand	62-69	8	14
β-strand	78-89	12	12
β-strand	96-104	9	14
β-strand	111-113	3	13
α-helix	114-116	3
β-strand	118-120	3	14
β-strand	126-127	2	12
β-strand	131-141	11	12
β-strand	150-159	10	14
β-strand	165-175	11	12

Chain J: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	17	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein	F	protein	431	Enterobacteria phage alpha3	P08767
Major spike protein	G	protein	187	Enterobacteria phage alpha3	P31281
Small core protein	J	protein	37	Enterobacteria phage phiX174	P69592
DNA (5'-d(pcpapapa)-3')	X	DNA	4

Sequence of entity 1 (F), FASTA

>1RB8_1 Capsid protein (chains F)
MSNVQTSAEREIVDLSHLAFDCGMLGRLKTVSWTPVIAGDSFELDAVGALRLSPLRRGLA
IDSKVDFFTFYIPHRHVYGDQWIQFMRDGVNAQPLPSVTCNRYPDHAGYVGTIVPANNRI
PKFLHQSYLNIYNNYFRAPWMPERTEANPSNLNEDDARYGFRCCHLKNIWSAPLPPETKL
AEEMGIESNSIDIMGLQAAYAQLHTEQERTYFMQRYRDVISSFGGSTSYDADNRPLLVMH
TDFWASGYDVDGTDQSSLGQFSGRVQQTFKHSVPRFFVPEHGVMMTLALIRFPPISPLEH
HYLAGKSQLTYTDLAGDPALIGNLPPREISYRDLFRDGRSGIKIKVAESIWYRTHPDYVN
FKYHDLHGFPFLDDAPGTSTGDNLQEAILVRHQDYDACFQSQQLLQWNKQARYNVSVYRH
MPTVRDSIMTS

Sequence of entity 2 (G), FASTA

>1RB8_2 Major spike protein (chains G)
MYQNFVTKHDTAIQTSRFSVTGNVIPAAPTGNIPVINGGSITAERAVVNLYANMNVSTSS
DGSFIVAMKVDTSPTDPNCVISAGVNLSFAGTSYPIVGIVRFESASEQPTSIAGSEVEHY
PIEMSVGSGGVCSARDCATVDIHPRTSGNNVFVGVICSSAKWTSGRVIGTIATTQVIHEY
QVLQPLK

Sequence of entity 3 (J), FASTA

>1RB8_3 Small core protein (chains J)
SKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF

Sequence of entity 4 (X), FASTA

>1RB8_4 DNA (5'-D(P*CP*AP*AP*A)-3') (chains X)
CAAA

Ligands and cofactors

ID	Name	Formula	Copies
DC	2'-deoxycytidine-5'-monophosphate	C9 H14 N3 O7 P	6

Primary citation

The phiX174 Protein J Mediates DNA Packaging and Viral Attachment to Host Cells. Bernal, R.A., Hafenstein, S., Esmeralda, R. et al. J Mol Biol (2004) 337:1109-1122. DOI 10.1016/j.jmb.2004.02.033 · PubMed

Other PDB entries of the same protein (UniProt P08767), best resolution first:

1M06 3.5 Å, Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography
1M0F 16.0 Å, Structural Studies of Bacteriophage alpha3 Assembly, Cryo-electron microscopy

Browse structure collections

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