4WFN: 50S ribosomal protein L2
Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin. Determined by X-ray diffraction at 3.54 Å resolution. Released 23 Dec 2015.
- Method
- X-ray diffraction
- Resolution
- 3.54 Å
- Organisms
- Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422), Deinococcus radiodurans, Deinococcus radiodurans R1
- Chains
- 28
- Atoms
- 84,117
- Mol. weight
- 1348.06 kDa
- Ligands
- ERY, MG
- Released
- 23 Dec 2015
Explore 4WFN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4WFN contains 91 α-helices and 167 β-strands across 26 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: 0 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-12 | 3 | 54 |
| β-strand | 16 | 1 | 55 |
| β-strand | 25-27 | 3 | 54 |
| β-strand | 38-40 | 3 | 55 |
| β-strand | 48-50 | 3 | 55 |
Chain 2: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-14 | 6 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-35 | 11 | |
| α-helix | 43-45 | 3 | |
Chain 3: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16 | 1 | 56 |
| β-strand | 22 | 1 | 56 |
| α-helix | 57-60 | 4 | |
Chain A: 4 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 73 | 1 | 1 |
| β-strand | 76-84 | 9 | 2 |
| β-strand | 91-97 | 7 | 2 |
| β-strand | 102-106 | 5 | 2 |
| β-strand | 108 | 1 | 3 |
| β-strand | 116-118 | 3 | 2 |
| β-strand | 119 | 1 | 1 |
| β-strand | 130-132 | 3 | 4 |
| α-helix | 133-135 | 3 | |
| α-helix | 137 | 1 | |
| β-strand | 141-143 | 3 | 4 |
| β-strand | 145 | 1 | 5 |
| β-strand | 155 | 1 | 5 |
| β-strand | 163-168 | 6 | 4 |
| β-strand | 172-177 | 6 | 4 |
| β-strand | 181-186 | 6 | 4 |
| β-strand | 190-193 | 4 | 4 |
| β-strand | 196 | 1 | 3 |
| α-helix | 211-215 | 5 | |
| α-helix | 263-265 | 3 | |
Chain B: 4 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-16 | 14 | 6 |
| β-strand | 19-27 | 9 | 6 |
| β-strand | 31 | 1 | 7 |
| β-strand | 33-37 | 5 | 8 |
| β-strand | 46-50 | 5 | 8 |
| β-strand | 53 | 1 | 9 |
| α-helix | 61-70 | 10 | |
| β-strand | 75 | 1 | 9 |
| β-strand | 78-82 | 5 | 8 |
| β-strand | 90 | 1 | 7 |
| β-strand | 101-107 | 7 | 6 |
| α-helix | 108-110 | 3 | |
| β-strand | 113-114 | 2 | 10 |
| α-helix | 116-120 | 5 | |
| β-strand | 158-159 | 2 | 10 |
| β-strand | 164-176 | 13 | 6 |
| β-strand | 181-185 | 5 | 6 |
| α-helix | 187-188 | 2 | |
| β-strand | 195-200 | 6 | 6 |
Chain C: 9 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 11 |
| α-helix | 16-18 | 3 | |
| α-helix | 24-38 | 15 | |
| α-helix | 81-82 | 2 | |
| α-helix | 97-109 | 13 | |
| β-strand | 116-118 | 3 | 11 |
| α-helix | 122-124 | 3 | |
| α-helix | 131-140 | 10 | |
| β-strand | 148-150 | 3 | 11 |
| α-helix | 155-158 | 4 | |
| β-strand | 167-169 | 3 | 11 |
| α-helix | 171-173 | 3 | |
| α-helix | 177-182 | 6 | |
| β-strand | 185-189 | 5 | 11 |
Chain D: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-19 | 14 | |
| β-strand | 31-39 | 9 | 12 |
| β-strand | 41 | 1 | 13 |
| β-strand | 44 | 1 | 13 |
| α-helix | 47-60 | 14 | |
| β-strand | 66-68 | 3 | 12 |
| β-strand | 86-91 | 6 | 12 |
| α-helix | 94-101 | 8 | |
| α-helix | 102-107 | 6 | |
| β-strand | 128-130 | 3 | 12 |
| β-strand | 153-158 | 6 | 12 |
| α-helix | 163-172 | 10 | |
Chain E: 3 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-9 | 2 | 14 |
| β-strand | 16-20 | 5 | 15 |
| β-strand | 23-27 | 5 | 15 |
| β-strand | 33 | 1 | 15 |
| β-strand | 42-45 | 4 | 14 |
| β-strand | 50-53 | 4 | 14 |
| α-helix | 60-80 | 21 | |
| β-strand | 83-90 | 8 | 16 |
| β-strand | 95-99 | 5 | 17 |
| β-strand | 102-106 | 5 | 17 |
| β-strand | 113-115 | 3 | 17 |
| β-strand | 122-127 | 6 | 16 |
| β-strand | 130-135 | 6 | 16 |
| α-helix | 138-150 | 13 | |
| α-helix | 153-155 | 3 | |
| β-strand | 161-164 | 4 | 16 |
18 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 50S ribosomal protein L2 | A | protein | 275 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RXJ9 (AlphaFold model) |
| 50S ribosomal protein L3 | B | protein | 211 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RXK2 (AlphaFold model) |
| 50S ribosomal protein L4 | C | protein | 205 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RXK1 (AlphaFold model) |
| 50S ribosomal protein L5 | D | protein | 180 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RXJ0 (AlphaFold model) |
| 50S ribosomal protein L6 | E | protein | 185 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RSL3 |
| 50S ribosomal protein L13 | G | protein | 174 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RXY1 |
| 50S ribosomal protein L14 | H | protein | 134 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RXJ2 |
| 50S ribosomal protein L15 | I | protein | 156 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RSK9 |
| 50S ribosomal protein L16 | J | protein | 141 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RXJ5 |
| 50S ribosomal protein L17 | K | protein | 116 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RSJ5 |
| 50S ribosomal protein L18 | L | protein | 114 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RSL2 |
| 50S ribosomal protein L19 | M | protein | 165 | Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) | Q9RWB4 |
16 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>4WFN_1 50S ribosomal protein L2 (chains A)
MAVKKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKR
LYRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAG
PEAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSG
ELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRT
GAGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTRRK
Sequence of entity 2 (B), FASTA
>4WFN_2 50S ribosomal protein L3 (chains B)
MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVN
KPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRW
NFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGEN
LILVKGAIPGANGGLVVLRSAAKASAAKGGK
Sequence of entity 3 (C), FASTA
>4WFN_3 50S ribosomal protein L4 (chains C)
MAQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYG
QKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAV
DGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDI
LRHDRLVIDAAALEIVEEEAGEEQQ
Sequence of entity 4 (D), FASTA
>4WFN_4 50S ribosomal protein L5 (chains D)
MQQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALI
TLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPN
AFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRKQ
Sequence of entity 5 (E), FASTA
>4WFN_5 50S ribosomal protein L6 (chains E)
MSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQK
HRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAG
VTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATG
GKGKK
Sequence of entity 6 (G), FASTA
>4WFN_6 50S ribosomal protein L13 (chains G)
MAFPDTDVSPPRGGPSSPAKSPLLRSFKVKTYIPKNDEQNWVVVDASGVPLGRLATLIAS
RIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALS
KHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPLEVK
Sequence of entity 7 (H), FASTA
>4WFN_7 50S ribosomal protein L14 (chains H)
MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAP
RGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRD
RRFMKIVSLAPEVL
Sequence of entity 8 (I), FASTA
>4WFN_8 50S ribosomal protein L15 (chains I)
MKLHDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTV
HVDAASAAAIKAVEAAGGRVVLPEVQTQQDDAQKAE
Sequence of entity 9 (J), FASTA
>4WFN_9 50S ribosomal protein L16 (chains J)
MLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRR
GGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRL
AGHKLPIQTKMVKREVYDEAQ
Sequence of entity 10 (K), FASTA
>4WFN_10 50S ribosomal protein L17 (chains K)
MRHGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDL
HSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIELV
Sequence of entity 11 (L), FASTA
>4WFN_11 50S ribosomal protein L18 (chains L)
MATATTIRRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAALK
SGNKTDTAAAVGKALAAAAAEKGIKQVVFDRGSYKYHGRVKALADAAREGGLDF
Sequence of entity 12 (M), FASTA
>4WFN_12 50S ribosomal protein L19 (chains M)
QTHIKINRGELLRGIEQDHTRQLPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSG
SRKSFTVRKISFGEGVERVFPFASPLVNQVTIVERGKVRRAKLYYLRELRGKAARIKSDR
SRVMKDAARAQQDKANASASQAAAAQADVTVISAAPEVAPETQGE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ERY | Erythromycin a | C37 H67 N O13 | 1 |
| MG | Magnesium ion | Mg | 70 |
Primary citation
The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel. Wekselman, I., Zimmerman, E., Davidovich, C. et al. Structure (2017) 25:1233-1241.e3. DOI 10.1016/j.str.2017.06.004 · PubMed
Other PDB entries of the same protein (UniProt Q9RXJ9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5DM6 2.9 Å, Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans
- 2ZJR 2.91 Å, Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans
- 5DM7 3.0 Å, Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex…
- 1NKW 3.1 Å, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans
- 4IO9 3.2 Å, Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus…
- 4IOA 3.2 Å, Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus…
- 7A0S 3.22 Å, 50S Deinococcus radiodurans ribosome bounded with mycinamicin I
- 3PIO 3.25 Å, Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in…
- 1NWY 3.3 Å, Complex of the large ribosomal subunit from deinococcus radiodurans with azithromycin
- 2ZJQ 3.3 Å, Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans…
- 3CF5 3.3 Å, Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus…
- 7A0R 3.3 Å, 50S Deinococcus radiodurans ribosome bounded with mycinamicin I
Browse structure collections
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