1C04: Ribosomal protein L2

Identification of known protein and RNA structures in a 5 a map of the large ribosomal subunit from haloarcula marismortui. Determined by X-ray diffraction at 5.0 Å resolution. Released 31 Aug 1999.

Method: X-ray diffraction
Resolution: 5.0 Å
Organism: Haloarcula marismortui
Chains: 6
Atoms: 5,570
Mol. weight: 82.72 kDa
Released: 31 Aug 1999

Explore 1C04 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1C04 contains 12 α-helices and 39 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 A: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	61-63	3
β-strand	64	1	1
β-strand	75-83	9	1
β-strand	88-95	8	1
β-strand	100-104	5	1
β-strand	114-115	2	1
β-strand	117	1	2
β-strand	128-130	3	2
α-helix	131-133	3
β-strand	139-141	3	2
β-strand	143-144	2	3
β-strand	151-153	3	3
β-strand	161-162	2	2
β-strand	163-167	5	4
β-strand	170-174	5	4
β-strand	180-184	5	4
β-strand	188-191	4	2

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	5
β-strand	15-19	5	6
β-strand	22-27	6	6
β-strand	30-35	6	6
β-strand	41-45	5	5
β-strand	48-52	5	5
α-helix	58-79	22
β-strand	83-89	7	7
β-strand	94-98	5	8
β-strand	101-105	5	8
β-strand	112-114	3	8
β-strand	120-126	7	7
β-strand	129-134	6	7
α-helix	137-148	12
α-helix	152-154	3
β-strand	160-163	4	7

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-18	9
α-helix	36-40	5
α-helix	41-47	7
α-helix	48-50	3
α-helix	56-70	15

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	9
β-strand	7-10	4	10
β-strand	16-24	9	10
β-strand	33	1	9
β-strand	38-46	9	10
β-strand	57-64	8	10
β-strand	69-70	2	11
β-strand	76-77	2	11
β-strand	83-86	4	10
β-strand	102	1	12
α-helix	105-108	4
α-helix	112-117	6
β-strand	121	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
23S rRNA fragment	E	RNA	58	Haloarcula marismortui
23S rRNA fragment	F	RNA	29	Haloarcula marismortui
Ribosomal protein L2	A	protein	137	Haloarcula marismortui	P04257 (AlphaFold model)
Ribosomal protein L6	B	protein	177	Haloarcula marismortui	P02391 (AlphaFold model)
Ribosomal protein L11	C	protein	67	Haloarcula marismortui	P56210 (AlphaFold model)
Ribosomal protein L14	D	protein	122	Haloarcula marismortui	P04450 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>1C04_1 23S RRNA FRAGMENT (chains E)
GCCAGGAUGUAGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGU

Sequence of entity 2 (F), FASTA

>1C04_2 23S RRNA FRAGMENT (chains F)
GGGUGCUCAGUACGAGAGGAACCGCACCC

Sequence of entity 3 (A), FASTA

>1C04_3 RIBOSOMAL PROTEIN L2 (chains A)
QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEIMSGP
DADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGE
VRMILGKCRATVGEVGN

Sequence of entity 4 (B), FASTA

>1C04_4 RIBOSOMAL PROTEIN L6 (chains B)
SRVGKKPIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKHH
RALHGTTRSLLANMVEGVSKGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEGL
EIEVPSQTKIIVKGADKQRVGELAANIRAVRPPEPYKGKGIRYEGELVRLKEGKTGK

Sequence of entity 5 (C), FASTA

>1C04_5 RIBOSOMAL PROTEIN L11 (chains C)
KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEG
TARSMGI

Sequence of entity 6 (D), FASTA

>1C04_6 RIBOSOMAL PROTEIN L14 (chains D)
MIQQESRLKVADNSGAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVKKGQVVKA
VVVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELRDKDFMKIISLAPE
VI

Primary citation

Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit. Ban, N., Nissen, P., Hansen, J. et al. Nature (1999) 400:841-847. DOI 10.1038/23641 · PubMed

Other PDB entries of the same protein (UniProt P04257 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RL2 2.3 Å, Ribosomal protein L2 RNA-binding domain from bacillus stearothermophilus
4V42 5.5 Å, Crystal structure of the ribosome at 5.5 A resolution.
487D 7.5 Å, Seven ribosomal proteins fitted to a CRYO-electron microscopic map of the large 50S…
1ML5 14.0 Å, Structure of the E. coli ribosomal termination complex with release factor 2

Browse structure collections

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